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Huang P, Peslak SA, Shehu V, Keller CA, Giardine B, Shi J, Hardison RC, Blobel GA, Khandros E. let-7 miRNAs repress HIC2 to regulate BCL11A transcription and hemoglobin switching. Blood 2024; 143:1980-1991. [PMID: 38364109 DOI: 10.1182/blood.2023023399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
ABSTRACT The switch from fetal hemoglobin (γ-globin, HBG) to adult hemoglobin (β-globin, HBB) gene transcription in erythroid cells serves as a paradigm for a complex and clinically relevant developmental gene regulatory program. We previously identified HIC2 as a regulator of the switch by inhibiting the transcription of BCL11A, a key repressor of HBG production. HIC2 is highly expressed in fetal cells, but the mechanism of its regulation is unclear. Here we report that HIC2 developmental expression is controlled by microRNAs (miRNAs), as loss of global miRNA biogenesis through DICER1 depletion leads to upregulation of HIC2 and HBG messenger RNA. We identified the adult-expressed let-7 miRNA family as a direct posttranscriptional regulator of HIC2. Ectopic expression of let-7 in fetal cells lowered HIC2 levels, whereas inhibition of let-7 in adult erythroblasts increased HIC2 production, culminating in decommissioning of a BCL11A erythroid enhancer and reduced BCL11A transcription. HIC2 depletion in let-7-inhibited cells restored BCL11A-mediated repression of HBG. Together, these data establish that fetal hemoglobin silencing in adult erythroid cells is under the control of a miRNA-mediated inhibitory pathway (let-7 ⊣ HIC2 ⊣ BCL11A ⊣ HBG).
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Affiliation(s)
- Peng Huang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Scott A Peslak
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Vanessa Shehu
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA
- Genomics Research Incubator, Pennsylvania State University, University Park, PA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA
| | - Gerd A Blobel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eugene Khandros
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
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2
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Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria ME, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv 2024:2023.04.02.535219. [PMID: 37066352 PMCID: PMC10103973 DOI: 10.1101/2023.04.02.535219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
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Affiliation(s)
- Guanjue Xiang
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215
| | - Xi He
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kathryn J. Isaac
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Dylan J. Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Camden Jansen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Alexander Q. Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Qian Qi
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yanghua He
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Stacie M. Anderson
- Flow Cytometry Core, National Human Genome Research Institute, Bethesda, MD 20892
| | - Jing Luan
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marit W. Vermunt
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL 60611
| | - Michael E.G. Sauria
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jim R. Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Douglas R. Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yong Cheng
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Gerd A. Blobel
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David M. Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
| | - Qunhua Li
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
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3
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles revealed in condensin-depleted mitotic chromosomes. bioRxiv 2023:2023.11.09.566494. [PMID: 38014261 PMCID: PMC10680603 DOI: 10.1101/2023.11.09.566494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co- depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1Π and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensin-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.
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4
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Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. Author Correction: HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 2023; 55:1608. [PMID: 37524792 DOI: 10.1038/s41588-023-01488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Henry W Bell
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Qin K, Lan X, Huang P, Saari MS, Khandros E, Keller CA, Giardine B, Abdulmalik O, Shi J, Hardison RC, Blobel GA. Molecular basis of polycomb group protein-mediated fetal hemoglobin repression. Blood 2023; 141:2756-2770. [PMID: 36893455 PMCID: PMC10273169 DOI: 10.1182/blood.2022019578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
The switch from fetal hemoglobin (HbF) to adult hemoglobin (HbA) is a paradigm for developmental gene expression control with relevance to sickle cell disease and β-thalassemia. Polycomb repressive complex (PRC) proteins regulate this switch, and an inhibitor of PRC2 has entered a clinical trial for HbF activation. Yet, how PRC complexes function in this process, their target genes, and relevant subunit composition are unknown. Here, we identified the PRC1 subunit BMI1 as a novel HbF repressor. We uncovered the RNA binding proteins LIN28B, IGF2BP1, and IGF2BP3 genes as direct BMI1 targets, and demonstrate that they account for the entirety of BMI1's effect on HbF regulation. BMI1 functions as part of the canonical PRC1 (cPRC1) subcomplex as revealed by the physical and functional dissection of BMI1 protein partners. Lastly, we demonstrate that BMI1/cPRC1 acts in concert with PRC2 to repress HbF through the same target genes. Our study illuminates how PRC silences HbF, highlighting an epigenetic mechanism involved in hemoglobin switching.
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Affiliation(s)
- Kunhua Qin
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Xianjiang Lan
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Huang
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Megan S. Saari
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eugene Khandros
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Osheiza Abdulmalik
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Gerd A. Blobel
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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6
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Xiang G, Giardine B, An L, Sun C, Keller CA, Heuston EF, Anderson SM, Kirby M, Bodine D, Zhang Y, Hardison RC. Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation. BMC Bioinformatics 2023; 24:102. [PMID: 36941541 PMCID: PMC10026520 DOI: 10.1186/s12859-023-05223-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation. RESULTS To reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation. This package first introduces a binarized indexing strategy for clustering the cCREs. It then provides a series of easily interpretable figures for visualizing the signal and epigenetic state patterns of the cCREs clusters during the cell differentiation. It can also use different hierarchies of cell types to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from a consortium project for ValIdated Systematic IntegratiON (VISION) of epigenomic data in hematopoiesis. CONCLUSION The package Snapshot can identify all distinct clusters of genomic locations with unique epigenetic signal patterns during cell differentiation. It outperforms other methods in terms of interpreting and reproducing the identified cCREs clusters. The package of Snapshot is available at GitHub: https://github.com/guanjue/Snapshot .
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Affiliation(s)
- Guanjue Xiang
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Lin An
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Chen Sun
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | | | - David Bodine
- NHGRI Hematopoiesis Section, GMBB, Bethesda, MD, USA
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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7
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Vermunt MW, Luan J, Zhang Z, Thrasher AJ, Huang A, Saari MS, Khandros E, Beagrie RA, Zhang S, Vemulamada P, Brilleman M, Lee K, Yano JA, Giardine BM, Keller CA, Hardison RC, Blobel GA. Gene silencing dynamics are modulated by transiently active regulatory elements. Mol Cell 2023; 83:715-730.e6. [PMID: 36868189 PMCID: PMC10719944 DOI: 10.1016/j.molcel.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/05/2022] [Accepted: 02/03/2023] [Indexed: 03/05/2023]
Abstract
Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via the FOG1/NuRD deacetylase complex, as revealed by the study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - A Josephine Thrasher
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert A Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pranay Vemulamada
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matilda Brilleman
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kiwon Lee
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer A Yano
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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8
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Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. CTCF blocks antisense transcription initiation at divergent promoters. Nat Struct Mol Biol 2022; 29:1136-1144. [PMID: 36369346 DOI: 10.1101/2021.10.30.465508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Camille M Syrett
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Clarion Healthcare, LLC, Boston, MA, USA
| | - Allison Coté
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Shape Therapeutics Inc, Seattle, WA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jennifer M Luppino
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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9
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Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. CTCF blocks antisense transcription initiation at divergent promoters. Nat Struct Mol Biol 2022; 29:1136-1144. [PMID: 36369346 PMCID: PMC10015438 DOI: 10.1038/s41594-022-00855-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/29/2022] [Indexed: 11/13/2022]
Abstract
Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Camille M Syrett
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Clarion Healthcare, LLC, Boston, MA, USA
| | - Allison Coté
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Shape Therapeutics Inc, Seattle, WA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jennifer M Luppino
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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10
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Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 2022; 611:387-398. [PMID: 36289338 PMCID: PMC10060167 DOI: 10.1038/s41586-022-05365-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
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Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Fan Song
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mikoto Kobayashi
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Baozhen Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ziyu Zhao
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bei Jia
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Lena Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Josiah Hiu-Yuen Wong
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yihao Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Sinisa Dovat
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yue Yang
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tomoko Yamada
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Aaron D Viny
- Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Hong Zheng
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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11
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Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet 2022; 54:1417-1426. [PMID: 35941187 PMCID: PMC9940634 DOI: 10.1038/s41588-022-01152-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 07/05/2022] [Indexed: 02/02/2023]
Abstract
The fetal-to-adult switch in hemoglobin production is a model of developmental gene control with relevance to the treatment of hemoglobinopathies. The expression of transcription factor BCL11A, which represses fetal β-type globin (HBG) genes in adult erythroid cells, is predominantly controlled at the transcriptional level but the underlying mechanism is unclear. We identify HIC2 as a repressor of BCL11A transcription. HIC2 and BCL11A are reciprocally expressed during development. Forced expression of HIC2 in adult erythroid cells inhibits BCL11A transcription and induces HBG expression. HIC2 binds to erythroid BCL11A enhancers to reduce chromatin accessibility and binding of transcription factor GATA1, diminishing enhancer activity and enhancer-promoter contacts. DNA-binding and crystallography studies reveal direct steric hindrance as one mechanism by which HIC2 inhibits GATA1 binding at a critical BCL11A enhancer. Conversely, loss of HIC2 in fetal erythroblasts increases enhancer accessibility, GATA1 binding and BCL11A transcription. HIC2 emerges as an evolutionarily conserved regulator of hemoglobin switching via developmental control of BCL11A.
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Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Scott A. Peslak
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene Khandros
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kunhua Qin
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Henry W. Bell
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Xianjiang Lan
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - John R. Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stella T. Chou
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Correspondence and requests for materials should be addressed to Peng Huang or Gerd A. Blobel. ;
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12
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Xu J, Song F, Zhang B, Lyu H, Kobayashi M, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wang Q, Jin Q, Jin Q, Fu Y, Hardison RC, Dovat S, Platanias LC, Yang Y, Yamada T, Viny AD, Levine RL, Claxton DF, Broach JR, Zheng H, Yue F. Abstract 2953: Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute myeloid leukemia (AML) represents a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors, and kinases that can cause epigenetic reshaping. It is unclear to what extent AML mutations drive chromatin 3D structure alteration and contribute to myeloid transformation. We first performed Hi-C and whole-genome sequencing in 25 AML patient samples and seven healthy donor samples, and identified recurrent alterations of A/B compartments, TADs, and chromatin loops that are unique to different subtypes. To investigate how altered chromatin organization contributes to transcriptional misregulation, we performed RNA-Seq, ATAC-Seq and CUT&ag for CTCF, H3K27ac, and H3K27me3 in the same AML samples. We identified extensive and recurrent AML-specific promoter-enhancer and promoter-repressor loops. We performed both CRISPR deletion and interference experiments and validated two repressor loops that downregulated cancer related genes IKZF2 and RTTN. Furthermore, by using our recently developed algorithm, we identified structural variation-induced enhancer-hijacking and repressor-hijacking events in AML samples. We further demonstrated the role of hijacked enhancers in AML cell growth by CRISPR screening, and the role of hijacked repressors by CRISPR de-repression. We performed whole-genome bisulfite sequencing in 20 AML and normal samples, and showed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Finally, by treating the AML cells with the DNA hypomethylating agent and performing triple knockdown of DNMT1/3A/3B, we demonstrated the impact of altered DNA methylation on gene expression and 3D genome organization. Overall this study provides an invaluable resource for leukemia studies and also highlighted the role of repressor-loops and hijacked cis-elements in gene regulation and human diseases.
Citation Format: Jie Xu, Fan Song, Baozhen Zhang, Huijue Lyu, Mikoto Kobayashi, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Ross C. Hardison, Sinisa Dovat, Leonidas C. Platanias, Yue Yang, Tomoko Yamada, Aaron D. Viny, Ross L. Levine, David F. Claxton, James R. Broach, Hong Zheng, Feng Yue. Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2953.
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Affiliation(s)
- Jie Xu
- 1Northwestern University, Chicago, IL
| | - Fan Song
- 1Northwestern University, Chicago, IL
| | | | | | | | - Ziyu Zhao
- 1Northwestern University, Chicago, IL
| | - Ye Hou
- 1Northwestern University, Chicago, IL
| | | | - Yu Luan
- 1Northwestern University, Chicago, IL
| | - Bei Jia
- 2Penn State University, Hershey, PA
| | | | | | - Qi Jin
- 1Northwestern University, Chicago, IL
| | | | - Yihao Fu
- 1Northwestern University, Chicago, IL
| | | | | | | | - Yue Yang
- 1Northwestern University, Chicago, IL
| | | | | | | | | | | | | | - Feng Yue
- 1Northwestern University, Chicago, IL
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13
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Qin K, Huang P, Feng R, Keller CA, Peslak SA, Khandros E, Saari MS, Lan X, Mayuranathan T, Doerfler PA, Abdulmalik O, Giardine B, Chou ST, Shi J, Hardison RC, Weiss MJ, Blobel GA. Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells. Nat Genet 2022; 54:906. [PMID: 35650318 DOI: 10.1038/s41588-022-01112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Qin K, Huang P, Feng R, Keller CA, Peslak SA, Khandros E, Saari MS, Lan X, Mayuranathan T, Doerfler PA, Abdulmalik O, Giardine B, Chou ST, Shi J, Hardison RC, Weiss MJ, Blobel GA. Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells. Nat Genet 2022; 54:874-884. [PMID: 35618846 PMCID: PMC9203980 DOI: 10.1038/s41588-022-01076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
The mechanisms by which the fetal-type β-globin-like genes HBG1 and HBG2 are silenced in adult erythroid precursor cells remain a fundamental question in human biology and have therapeutic relevance to sickle cell disease (SCD) and β-thalassemia. Here, we identify via a CRISPR-Cas9 genetic screen two members of the NFI transcription factor family – NFIA and NFIX – as HBG1/2 repressors. NFIA and NFIX are expressed at elevated levels in adult erythroid cells compared to fetal cells, and function cooperatively to repress HBG1/2 in cultured cells and in human-to-mouse xenotransplants. Genomic profiling, genome editing, and DNA binding assays demonstrate that the potent concerted activity of NFIA and NFIX is explained in part by their ability to stimulate the expression of BCL11A, a known silencer of the HBG1/2 genes, and in part by directly repressing the HBG1/2 genes. Thus, NFI factors emerge as versatile regulators of the fetal-to-adult switch in β-globin production.
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Affiliation(s)
- Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Cheon H, Xing JC, Moosic KB, Ung J, Chan VW, Chung DS, Toro MF, Elghawy O, Wang JS, Hamele CE, Hardison RC, Olson TL, Tan SF, Feith DJ, Ratan A, Loughran TP. Genomic landscape of TCRαβ and TCRγδ T-large granular lymphocyte leukemia. Blood 2022; 139:3058-3072. [PMID: 35015834 PMCID: PMC9121841 DOI: 10.1182/blood.2021013164] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/18/2021] [Indexed: 11/20/2022] Open
Abstract
Large granular lymphocyte (LGL) leukemia comprises a group of rare lymphoproliferative disorders whose molecular landscape is incompletely defined. We leveraged paired whole-exome and transcriptome sequencing in the largest LGL leukemia cohort to date, which included 105 patients (93 T-cell receptor αβ [TCRαβ] T-LGL and 12 TCRγδ T-LGL). Seventy-six mutations were observed in 3 or more patients in the cohort, and out of those, STAT3, KMT2D, PIK3R1, TTN, EYS, and SULF1 mutations were shared between both subtypes. We identified ARHGAP25, ABCC9, PCDHA11, SULF1, SLC6A15, DDX59, DNMT3A, FAS, KDM6A, KMT2D, PIK3R1, STAT3, STAT5B, TET2, and TNFAIP3 as recurrently mutated putative drivers using an unbiased driver analysis approach leveraging our whole-exome cohort. Hotspot mutations in STAT3, PIK3R1, and FAS were detected, whereas truncating mutations in epigenetic modifying enzymes such as KMT2D and TET2 were observed. Moreover, STAT3 mutations co-occurred with mutations in chromatin and epigenetic modifying genes, especially KMT2D and SETD1B (P < .01 and P < .05, respectively). STAT3 was mutated in 50.5% of the patients. Most common Y640F STAT3 mutation was associated with lower absolute neutrophil count values, and N647I mutation was associated with lower hemoglobin values. Somatic activating mutations (Q160P, D170Y, L287F) in the STAT3 coiled-coil domain were characterized. STAT3-mutant patients exhibited increased mutational burden and enrichment of a mutational signature associated with increased spontaneous deamination of 5-methylcytosine. Finally, gene expression analysis revealed enrichment of interferon-γ signaling and decreased phosphatidylinositol 3-kinase-Akt signaling for STAT3-mutant patients. These findings highlight the clinical and molecular heterogeneity of this rare disorder.
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Affiliation(s)
- HeeJin Cheon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Jeffrey C Xing
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Katharine B Moosic
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Vivian W Chan
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - David S Chung
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Mariella F Toro
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Omar Elghawy
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - John S Wang
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Cait E Hamele
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA
| | - Thomas L Olson
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - David J Feith
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA; and
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville VA
| | - Thomas P Loughran
- Department of Medicine, University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
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16
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Hardison RC, Xiang G, Jansen C, Keller CA, Giardine BM, Cockburn A, He X, Sauria ME, Weaver K, Li Q, Zhang Y. Systematic Integration of Epigenomic Landscapes in Human and Mouse Blood Cells to Predict Activity and Targets of Regulatory Elements. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ross C. Hardison
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | | | - Camden Jansen
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | - Cheryl A. Keller
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | - Belinda M. Giardine
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | - April Cockburn
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | - Xi He
- Bioinformatics and GenomicsThe Pennsylvania State UniversityUniversity ParkPA
| | | | | | - Qunhua Li
- StatisticsThe Pennsylvania State UniversityUniversity ParkPA
| | - Yu Zhang
- StatisticsThe Pennsylvania State UniversityUniversity ParkPA
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17
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Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2022; 605:E3. [PMID: 35474001 PMCID: PMC9095460 DOI: 10.1038/s41586-021-04226-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Jill E Moore
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Michael J Purcaro
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Henry E Pratt
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | | | - Noam Shoresh
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Trupti Kawli
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Carrie A Davis
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David U Gorkin
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Yin Shen
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.,Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Yupeng He
- Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiao-Ou Zhang
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Shaimae I Elhajjajy
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Jack Huey
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Xiaofeng Wang
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | | | | | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Jialing Zhang
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Alec Victorsen
- Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | | | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric Lécuyer
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Job Dekker
- HHMI and Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Rinn
- University of Colorado Boulder, Boulder, CO, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Joseph R Ecker
- Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Manolis Kellis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Anshul Kundaje
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Roderic Guigó
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | | | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Comparative Biochemistry Program, University of California, Berkeley, CA, USA.
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. .,Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA.
| | - Bradley E Bernstein
- Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Thomas R Gingeras
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA. .,Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
| | - Zhiping Weng
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA. .,Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Bioinformatics Program, Boston University, Boston, MA, USA.
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18
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Cochran K, Srivastava D, Shrikumar A, Balsubramani A, Hardison RC, Kundaje A, Mahony S. Domain adaptive neural networks improve cross-species prediction of transcription factor binding. Genome Res 2022; 32:512-523. [PMID: 35042722 PMCID: PMC8896468 DOI: 10.1101/gr.275394.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
The intrinsic DNA sequence preferences and cell type–specific cooperative partners of transcription factors (TFs) are typically highly conserved. Hence, despite the rapid evolutionary turnover of individual TF binding sites, predictive sequence models of cell type–specific genomic occupancy of a TF in one species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomic background and evaluate their performance within and across species. Cross-species predictive performance is consistently worse than within-species performance, which we show is caused in part by species-specific repeats. To account for this domain shift, we use an augmented network architecture to automatically discourage learning of training species–specific sequence features. This domain adaptation approach corrects for prediction errors on species-specific repeats and improves overall cross-species model performance. Our results show that cross-species TF binding prediction is feasible when models account for domain shifts driven by species-specific repeats.
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19
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Patrinos GP, Chui DHK, Hardison RC, Steinberg MH. Strategies to improve pharmacogenomic-guided treatment options for patients with β-hemoglobinopathies. Expert Rev Hematol 2021; 14:883-885. [PMID: 34490838 PMCID: PMC9306350 DOI: 10.1080/17474086.2021.1977117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Drug efficacy and toxicity are closely related to the unique genetic profile of individuals, or pharmacogenomics. Despite the fact that cardiology, psychiatry and oncology are among the clinical specialties in which pharmacogenomics has become a clinical reality, the utility of pharmacogenomics has yet to be demonstrated for several other medical specialties. Over the last 15 years, genomic variants in a number of loci have been shown to be significantly associated with the fetal hemoglobin (HbF) response to hydroxyurea, the only approved drug for HbF induction for sickle cell disease. Here, we provide an update and discuss future challenges to the application of pharmacogenomics to improve therapies for β-hemoglobinopathies in relation to the current pharmacological treatment modalities for those disorders.
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Affiliation(s)
- George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece
- United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, UAE
- United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
| | - David H. K. Chui
- Boston University School of Medicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
| | - Ross C. Hardison
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, PA, USA
| | - Martin H. Steinberg
- Boston University School of Medicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
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20
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Olson TL, Cheon H, Xing JC, Olson KC, Paila U, Hamele CE, Neelamraju Y, Shemo BC, Schmachtenberg M, Sundararaman SK, Toro MF, Keller CA, Farber EA, Onengut-Gumuscu S, Garrett-Bakelman FE, Hardison RC, Feith DJ, Ratan A, Loughran TP. Frequent somatic TET2 mutations in chronic NK-LGL leukemia with distinct patterns of cytopenias. Blood 2021; 138:662-673. [PMID: 33786584 PMCID: PMC8394905 DOI: 10.1182/blood.2020005831] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 03/30/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic natural killer large granular lymphocyte (NK-LGL) leukemia, also referred to as chronic lymphoproliferative disorder of NK cells, is a rare disorder defined by prolonged expansion of clonal NK cells. Similar prevalence of STAT3 mutations in chronic T-LGL and NK-LGL leukemia is suggestive of common pathogenesis. We undertook whole-genome sequencing to identify mutations unique to NK-LGL leukemia. The results were analyzed to develop a resequencing panel that was applied to 58 patients. Phosphatidylinositol 3-kinase pathway gene mutations (PIK3CD/PIK3AP1) and TNFAIP3 mutations were seen in 5% and 10% of patients, respectively. TET2 was exceptional in that mutations were present in 16 (28%) of 58 patient samples, with evidence that TET2 mutations can be dominant and exclusive to the NK compartment. Reduced-representation bisulfite sequencing revealed that methylation patterns were significantly altered in TET2 mutant samples. The promoter of TET2 and that of PTPRD, a negative regulator of STAT3, were found to be methylated in additional cohort samples, largely confined to the TET2 mutant group. Mutations in STAT3 were observed in 19 (33%) of 58 patient samples, 7 of which had concurrent TET2 mutations. Thrombocytopenia and resistance to immunosuppressive agents were uniquely observed in those patients with only TET2 mutation (Games-Howell post hoc test, P = .0074; Fisher's exact test, P = .00466). Patients with STAT3 mutation, inclusive of those with TET2 comutation, had lower hematocrit, hemoglobin, and absolute neutrophil count compared with STAT3 wild-type patients (Welch's t test, P ≤ .015). We present the discovery of TET2 mutations in chronic NK-LGL leukemia and evidence that it identifies a unique molecular subtype.
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Affiliation(s)
- Thomas L Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - HeeJin Cheon
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Jeffrey C Xing
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Kristine C Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Umadevi Paila
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | - Cait E Hamele
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Bryna C Shemo
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Matt Schmachtenberg
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Shriram K Sundararaman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Mariella F Toro
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - Emily A Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | | | - Francine E Garrett-Bakelman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - David J Feith
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Thomas P Loughran
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
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21
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Cheng L, Li Y, Qi Q, Xu P, Feng R, Palmer L, Chen J, Wu R, Yee T, Zhang J, Yao Y, Sharma A, Hardison RC, Weiss MJ, Cheng Y. Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression. Nat Genet 2021; 53:869-880. [PMID: 33958780 PMCID: PMC8628368 DOI: 10.1038/s41588-021-00861-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023]
Abstract
Pinpointing functional noncoding DNA sequences and defining their contributions to health-related traits is a major challenge for modern genetics. We developed a high-throughput framework to map noncoding DNA functions with single-nucleotide resolution in four loci that control erythroid fetal hemoglobin (HbF) expression, a genetically determined trait that modifies sickle cell disease (SCD) phenotypes. Specifically, we used the adenine base editor ABEmax to introduce 10,156 separate A•T to G•C conversions in 307 predicted regulatory elements and quantified the effects on erythroid HbF expression. We identified numerous regulatory elements, defined their epigenomic structures and linked them to low-frequency variants associated with HbF expression in an SCD cohort. Targeting a newly discovered γ-globin gene repressor element in SCD donor CD34+ hematopoietic progenitors raised HbF levels in the erythroid progeny, inhibiting hypoxia-induced sickling. Our findings reveal previously unappreciated genetic complexities of HbF regulation and provide potentially therapeutic insights into SCD.
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Affiliation(s)
- Li Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Qi
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peng Xu
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lance Palmer
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Chen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ruiqiong Wu
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tiffany Yee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Zhang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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22
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Keller CA, Wixom AQ, Heuston EF, Giardine B, Hsiung CCS, Long MR, Miller A, Anderson SM, Cockburn A, Blobel GA, Bodine DM, Hardison RC. Effects of sheared chromatin length on ChIP-seq quality and sensitivity. G3 (Bethesda) 2021; 11:6206780. [PMID: 33788948 PMCID: PMC8495733 DOI: 10.1093/g3journal/jkab101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023]
Abstract
Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.
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Affiliation(s)
- Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexander Q Wixom
- Mayo Clinic, Department of Gastroenterology and Hepatology , Rochester, MN 55905, USA
| | - Elisabeth F Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chris C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, CA 94305, USA.,Department of Urology, University of California, CA 94158, USA
| | - Maria R Long
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stacie M Anderson
- NHGRI Flow Cytometry Core, National Institutes of Health, Bethesda, MD 20882, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David M Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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23
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Xiang G, Giardine BM, Mahony S, Zhang Y, Hardison RC. S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Bioinformatics 2021; 37:3011-3013. [PMID: 33681991 PMCID: PMC8479670 DOI: 10.1093/bioinformatics/btab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY Epigenetic modifications reflect key aspects of transcriptional regulation, and many epigenomic datasets have been generated under different biological contexts to provide insights into regulatory processes. However, the technical noise in epigenomic datasets and the many dimensions (features) examined make it challenging to effectively extract biologically meaningful inferences from these datasets. We developed a package that reduces noise while normalizing the epigenomic data by a novel normalization method, followed by integrative dimensional reduction by learning and assigning epigenetic states. This package, called S3V2-IDEAS, can be used to identify epigenetic states for multiple features, or identify discretized signal intensity levels and a master peak list across different cell types for a single feature. We illustrate the outputs and performance of S3V2-IDEAS using 137 epigenomics datasets from the VISION project that provides ValIdated Systematic IntegratiON of epigenomic data in hematopoiesis. AVAILABILITY AND IMPLEMENTATION S3V2-IDEAS pipeline is freely available as open source software released under an MIT license at: https://github.com/guanjue/S3V2_IDEAS_ESMP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guanjue Xiang
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- To whom correspondence should be addressed. or
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- To whom correspondence should be addressed. or
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24
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Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep 2021; 34:108783. [PMID: 33626344 PMCID: PMC7999233 DOI: 10.1016/j.celrep.2021.108783] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner independent of bound CTCF. Moreover, CTCF at different binding sites (CBSs) displays highly variable resistance to degradation. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and chromatin loop anchors, as well as co-occupancy with cohesin, are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, which has ramifications regarding architectural CTCF functions. Our study highlights the heterogeneity of CBSs, uncovers properties specific to architecturally important CBSs, and provides insights into the basic processes of genome organization and transcription regulation.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanjue Xiang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA.
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25
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Giardine BM, Joly P, Pissard S, Wajcman H, K Chui DH, Hardison RC, Patrinos GP. Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res 2021; 49:D1192-D1196. [PMID: 33125055 PMCID: PMC7778921 DOI: 10.1093/nar/gkaa959] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is a widely-used locus-specific database (LSDB) launched 20 years ago by a multi-center academic effort to provide timely information on the numerous genomic variants leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Here, we report several advances for the database. We made clinically relevant updates of HbVar, implemented as additional querying options in the HbVar query page, allowing the user to explore the clinical phenotype of compound heterozygous patients. We also made significant improvements to the HbVar front page, making comparative data querying, analysis and output more user-friendly. We continued to expand and enrich the regular data content, involving 1820 variants, 230 of which are new entries. We also increased the querying potential and expanded the usefulness of HbVar database in the clinical setting. These several additions, expansions and updates should improve the utility of HbVar both for the globin research community and in a clinical setting.
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Affiliation(s)
- Belinda M Giardine
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA
| | - Philippe Joly
- Biochimie des pathologies érythrocytaires, Laboratoire de Biochimie et Biologie Moléculaire Grand-Est, Groupement hospitalier Est, Hospices Civils de Lyon, Bron, France.,Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge'', Université Claude Bernard Lyon 1, COMUE Lyon, France
| | - Serge Pissard
- Assistance Publique Hopitaux de Paris), Department of Genetics GHU (Groupe Hospitalier Universitaire Henri Mondor) H. Mondor and Institut Mondor de Recherche biomedicale - INSERM U955 eq2, Creteil France
| | | | - David H K Chui
- Boston University School of Medicine, Department of Medicine, Pathology and Laboratory Medicine, Boston, MA, USA
| | - Ross C Hardison
- The Pennsylvania State University, Center for Computational Biology and Bioinformatics, University Park, PA, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece.,Erasmus University Medical Center Rotterdam, Faculty of Medicine and Health Sciences, Department of Pathology, Bioinformatics Unit, Rotterdam, the Netherlands.,United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, UAE.,United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
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26
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Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Mol Cell 2020; 81:239-254.e8. [PMID: 33301730 DOI: 10.1016/j.molcel.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels.. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies.
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Affiliation(s)
- Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Yemin Lan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicholas Aboreden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeremy D Grevet
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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27
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Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature 2020; 588:337-343. [PMID: 33239788 DOI: 10.1038/s41586-020-2962-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/17/2020] [Indexed: 01/08/2023]
Abstract
The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Hyung Joo Lee
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Khai Chung Ang
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Xiaoyun Xing
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Iyyanki Sriranga
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | - Tarik Salameh
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Mayank N K Choudhary
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jacek Topczewski
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Keith C Cheng
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
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28
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Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Alteration of genome folding via contact domain boundary insertion. Nat Genet 2020; 52:1076-1087. [PMID: 32868908 PMCID: PMC7541666 DOI: 10.1038/s41588-020-0680-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Abstract
Animal chromosomes are partitioned into contact domains. Pathogenic domain disruptions can result from chromosomal rearrangements or perturbation of architectural factors. However, such broad-scale alterations are insufficient to define the minimal requirements for domain formation. Moreover, to what extent domains can be engineered is just beginning to be explored. In an attempt to create contact domains, we inserted a 2-kb DNA sequence underlying a tissue-invariant domain boundary-containing a CTCF-binding site (CBS) and a transcription start site (TSS)-into 16 ectopic loci across 11 chromosomes, and characterized its architectural impact. Depending on local constraints, this fragment variably formed new domains, partitioned existing ones, altered compartmentalization and initiated contacts reflecting chromatin loop extrusion. Deletions of the CBS or the TSS individually or in combination within inserts revealed its distinct contributions to genome folding. Altogether, short DNA insertions can suffice to shape the spatial genome in a manner influenced by chromatin context.
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Affiliation(s)
- Di Zhang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Peng Huang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Haoyue Zhang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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29
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Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020; 583:699-710. [PMID: 32728249 PMCID: PMC7410828 DOI: 10.1038/s41586-020-2493-4] [Citation(s) in RCA: 879] [Impact Index Per Article: 219.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 05/27/2020] [Indexed: 12/13/2022]
Abstract
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
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Affiliation(s)
- Jill E Moore
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Michael J Purcaro
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Henry E Pratt
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | | | - Noam Shoresh
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Trupti Kawli
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Carrie A Davis
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David U Gorkin
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Yin Shen
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Yupeng He
- Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiao-Ou Zhang
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Shaimae I Elhajjajy
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Jack Huey
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Xiaofeng Wang
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | | | | | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Jialing Zhang
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Alec Victorsen
- Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | | | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric Lécuyer
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Job Dekker
- HHMI and Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Rinn
- University of Colorado Boulder, Boulder, CO, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Joseph R Ecker
- Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Manolis Kellis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Anshul Kundaje
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Roderic Guigó
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | | | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA.
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
- Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA.
| | - Bradley E Bernstein
- Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Thomas R Gingeras
- Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
| | - Zhiping Weng
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China.
- Bioinformatics Program, Boston University, Boston, MA, USA.
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30
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He P, Williams BA, Trout D, Marinov GK, Amrhein H, Berghella L, Goh ST, Plajzer-Frick I, Afzal V, Pennacchio LA, Dickel DE, Visel A, Ren B, Hardison RC, Zhang Y, Wold BJ. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature 2020; 583:760-767. [PMID: 32728245 PMCID: PMC7410830 DOI: 10.1038/s41586-020-2536-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.
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Affiliation(s)
- Peng He
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Henry Amrhein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Libera Berghella
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Say-Tar Goh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Yu Zhang
- Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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31
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Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Perspectives on ENCODE. Nature 2020; 583:693-698. [PMID: 32728248 PMCID: PMC7410827 DOI: 10.1038/s41586-020-2449-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/05/2020] [Indexed: 12/25/2022]
Abstract
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.
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Affiliation(s)
- Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
- Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA.
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jill E Moore
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
| | - Zhiping Weng
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China
- Bioinformatics Program, Boston University, Boston, MA, USA
| | | | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Elise A Feingold
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Pazin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Pagan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel A Gilchrist
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin C Hitz
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Bradley E Bernstein
- Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric M Mendenhall
- Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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32
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Xiang G, Keller CA, Giardine B, An L, Li Q, Zhang Y, Hardison RC. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Nucleic Acids Res 2020; 48:e43. [PMID: 32086521 PMCID: PMC7192629 DOI: 10.1093/nar/gkaa105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Quantitative comparison of epigenomic data across multiple cell types or experimental conditions is a promising way to understand the biological functions of epigenetic modifications. However, differences in sequencing depth and signal-to-noise ratios in the data from different experiments can hinder our ability to identify real biological variation from raw epigenomic data. Proper normalization is required prior to data analysis to gain meaningful insights. Most existing methods for data normalization standardize signals by rescaling either background regions or peak regions, assuming that the same scale factor is applicable to both background and peak regions. While such methods adjust for differences in sequencing depths, they do not address differences in the signal-to-noise ratios across different experiments. We developed a new data normalization method, called S3norm, that normalizes the sequencing depths and signal-to-noise ratios across different data sets simultaneously by a monotonic nonlinear transformation. We show empirically that the epigenomic data normalized by our method, compared to existing methods, can better capture real biological variation, such as impact on gene expression regulation.
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Affiliation(s)
- Guanjue Xiang
- The Bioinformatics and Genomics program, Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl A Keller
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Belinda Giardine
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Lin An
- The Bioinformatics and Genomics program, Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qunhua Li
- Dept. of Statistics, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Yu Zhang
- Dept. of Statistics, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
| | - Ross C Hardison
- Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, USA
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33
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Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res 2020; 30:472-484. [PMID: 32132109 PMCID: PMC7111515 DOI: 10.1101/gr.255760.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/21/2020] [Indexed: 01/29/2023]
Abstract
Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for validated systematic integration of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By using IDEAS as our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of more than 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.
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Affiliation(s)
- Guanjue Xiang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elisabeth Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Lin An
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alexander Q Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael E G Sauria
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Kathryn Weaver
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Jens Lichtenberg
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Qunhua Li
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James Taylor
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Gerd A Blobel
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Jim Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Yu Zhang
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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34
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Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, Hughes J, Higgs DR, Göttgens B. Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells. IUBMB Life 2020; 72:27-38. [PMID: 31769130 PMCID: PMC6972633 DOI: 10.1002/iub.2195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/17/2019] [Indexed: 01/15/2023]
Abstract
Members of the GATA family of transcription factors play key roles in the differentiation of specific cell lineages by regulating the expression of target genes. Three GATA factors play distinct roles in hematopoietic differentiation. In order to better understand how these GATA factors function to regulate genes throughout the genome, we are studying the epigenomic and transcriptional landscapes of hematopoietic cells in a model-driven, integrative fashion. We have formed the collaborative multi-lab VISION project to conduct ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis. The epigenomic data included nuclease accessibility in chromatin, CTCF occupancy, and histone H3 modifications for 20 cell types covering hematopoietic stem cells, multilineage progenitor cells, and mature cells across the blood cell lineages of mouse. The analysis used the Integrative and Discriminative Epigenome Annotation System (IDEAS), which learns all common combinations of features (epigenetic states) simultaneously in two dimensions-along chromosomes and across cell types. The result is a segmentation that effectively paints the regulatory landscape in readily interpretable views, revealing constitutively active or silent loci as well as the loci specifically induced or repressed in each stage and lineage. Nuclease accessible DNA segments in active chromatin states were designated candidate cis-regulatory elements in each cell type, providing one of the most comprehensive registries of candidate hematopoietic regulatory elements to date. Applications of VISION resources are illustrated for the regulation of genes encoding GATA1, GATA2, GATA3, and Ikaros. VISION resources are freely available from our website http://usevision.org.
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Affiliation(s)
- Ross C. Hardison
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Yu Zhang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Cheryl A. Keller
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Guanjue Xiang
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Lin An
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Belinda M. Giardine
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - David Bodine
- Genetics and Molecular Biology Branch, Hematopoiesis SectionNational Institutes of Health, NHGRIBethesdaMD
| | - Shaun Mahony
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Qunhua Li
- Departments of Biochemistry and Molecular Biology and of StatisticsThe Pennsylvania State University, University ParkPA
| | - Feng Yue
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State University College of MedicineHershey, PA
| | - Mitchell J. Weiss
- Hematology DepartmentSt. Jude Children's Research HospitalMemphis, TN
| | | | - James Taylor
- Departments of Biology and of Computer ScienceJohns Hopkins UniversityBaltimore, MD
| | - Jim Hughes
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Douglas R. Higgs
- Laboratory of Gene RegulationWeatherall Institute of Molecular Medicine, Oxford UniversityOxfordUK
| | - Berthold Göttgens
- Department of Hematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
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35
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An L, Yang T, Yang J, Nuebler J, Xiang G, Hardison RC, Li Q, Zhang Y. OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. Genome Biol 2019; 20:282. [PMID: 31847870 PMCID: PMC6918570 DOI: 10.1186/s13059-019-1893-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 11/20/2019] [Indexed: 01/04/2023] Open
Abstract
The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.
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Affiliation(s)
- Lin An
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA USA
- Camp4 Therapeutics, Cambridge, MA USA
| | - Tao Yang
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA USA
| | - Jiahao Yang
- Department of Mathematics, Tsinghua University, Beijing, China
| | - Johannes Nuebler
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Guanjue Xiang
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA USA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA USA
| | - Qunhua Li
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA USA
- Department of Statistics, Pennsylvania State University, University Park, PA USA
| | - Yu Zhang
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, PA USA
- Department of Statistics, Pennsylvania State University, University Park, PA USA
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36
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Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA. Chromatin structure dynamics during the mitosis-to-G1 phase transition. Nature 2019; 576:158-162. [PMID: 31776509 PMCID: PMC6895436 DOI: 10.1038/s41586-019-1778-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
Features of higher-order chromatin organization-such as A/B compartments, topologically associating domains and chromatin loops-are temporarily disrupted during mitosis1,2. Because these structures are thought to influence gene regulation, it is important to understand how they are re-established after mitosis. Here we examine the dynamics of chromosome reorganization by Hi-C after mitosis in highly purified, synchronous mouse erythroid cell populations. We observed rapid establishment of A/B compartments, followed by their gradual intensification and expansion. Contact domains form from the 'bottom up'-smaller subTADs are formed initially, followed by convergence into multi-domain TAD structures. CTCF is partially retained on mitotic chromosomes and immediately resumes full binding in ana/telophase. By contrast, cohesin is completely evicted from mitotic chromosomes and regains focal binding at a slower rate. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contact patterns-anchored by CTCF-grow in length, which is consistent with a loop-extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, with rates exceeding those of CTCF/cohesin-anchored contacts. Notably, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering chromatin loops. We also describe the relationship between transcription reactivation and architectural features. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin reconfiguration.
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Affiliation(s)
- Haoyue Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel J Emerson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Katelyn R Titus
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongxin Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | | | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A. Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Mol Cell 2019; 73:519-532.e4. [PMID: 30554946 PMCID: PMC6368450 DOI: 10.1016/j.molcel.2018.11.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/06/2018] [Accepted: 11/01/2018] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation occurs via changes to rates of different biochemical steps of transcription, but it remains unclear which rates are subject to change upon biological perturbation. Biochemical studies have suggested that stimuli predominantly affect the rates of RNA polymerase II (Pol II) recruitment and polymerase release from promoter-proximal pausing. Single-cell studies revealed that transcription occurs in discontinuous bursts, suggesting that features of such bursts like frequency and intensity could also be regulated. We combined Pol II chromatin immunoprecipitation sequencing (ChIP-seq) and single-cell transcriptional measurements to show that an independently regulated burst initiation step is required before polymerase recruitment can occur. Using a number of global and targeted transcriptional regulatory perturbations, we showed that biological perturbations regulated both burst initiation and polymerase pause release rates but seemed not to regulate polymerase recruitment rate. Our results suggest that transcriptional regulation primarily acts by changing the rates of burst initiation and polymerase pause release.
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Affiliation(s)
- Caroline R Bartman
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole Hamagami
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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38
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Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 2018; 50:1388-1398. [PMID: 30202056 PMCID: PMC6301019 DOI: 10.1038/s41588-018-0195-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
Abstract
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin structural domains. Our results indicate that noncoding SVs may be underappreciated mutational drivers in cancer genomes.
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Affiliation(s)
- Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Victoria T Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Darrin V Bann
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Royden Clark
- Penn State College of Medicine, Informatics and Technology, Hershey, PA, USA
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Lin An
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Christopher Pool
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | | | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rajinder Kaul
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | | | - Kristen Lee
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Morgan Diegel
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Dubravka Pezic
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | | | - James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | | | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
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Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, Liebhaber SA, Hardison RC, Shi J, Blobel GA. Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Science 2018; 361:285-290. [PMID: 30026227 PMCID: PMC6257981 DOI: 10.1126/science.aao0932] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 04/15/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022]
Abstract
Increasing fetal hemoglobin (HbF) levels in adult red blood cells provides clinical benefit to patients with sickle cell disease and some forms of β-thalassemia. To identify potentially druggable HbF regulators in adult human erythroid cells, we employed a protein kinase domain-focused CRISPR-Cas9-based genetic screen with a newly optimized single-guide RNA scaffold. The screen uncovered the heme-regulated inhibitor HRI (also known as EIF2AK1), an erythroid-specific kinase that controls protein translation, as an HbF repressor. HRI depletion markedly increased HbF production in a specific manner and reduced sickling in cultured erythroid cells. Diminished expression of the HbF repressor BCL11A accounted in large part for the effects of HRI depletion. Taken together, these results suggest HRI as a potential therapeutic target for hemoglobinopathies.
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Affiliation(s)
- Jeremy D Grevet
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole Hamagami
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher R Edwards
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Xinjun Ji
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saurabh K Bhardwaj
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carolyne J Face
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David F Posocco
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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40
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Liao C, Hardison RC, Kennett MJ, Carlson BA, Paulson RF, Prabhu KS. Selenoproteins regulate stress erythroid progenitors and spleen microenvironment during stress erythropoiesis. Blood 2018; 131:2568-2580. [PMID: 29615406 PMCID: PMC5992864 DOI: 10.1182/blood-2017-08-800607] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 03/15/2018] [Indexed: 12/30/2022] Open
Abstract
Micronutrient selenium (Se) plays a key role in redox regulation through its incorporation into selenoproteins as the 21st amino acid selenocysteine (Sec). Because Se deficiency appears to be a cofactor in the anemia associated with chronic inflammatory diseases, we reasoned that selenoproteins may contribute to erythropoietic recovery from anemia, referred to as stress erythropoiesis. Here, we report that loss of selenoproteins through Se deficiency or by mutation of the Sec tRNA (tRNA[Sec]) gene (Trsp) severely impairs stress erythropoiesis at 2 stages. Early stress erythroid progenitors failed to expand and properly differentiate into burst-forming unit-erythroid cells , whereas late-stage erythroid progenitors exhibited a maturation defect that affected the transition of proerythroblasts to basophilic erythroblasts. These defects were, in part, a result of the loss of selenoprotein W (SelenoW), whose expression was reduced at both transcript and protein levels in Se-deficient erythroblasts. Mutation of SelenoW in the bone marrow cells significantly decreased the expansion of stress burst-forming unit-erythroid cell colonies, which recapitulated the phenotypes induced by Se deficiency or mutation of Trsp Similarly, mutation of SelenoW in murine erythroblast (G1E) cell line led to defects in terminal differentiation. In addition to the erythroid defects, the spleens of Se-deficient mice contained fewer red pulp macrophages and exhibited impaired development of erythroblastic island macrophages, which make up the niche supporting erythroblast development. Taken together, these data reveal a critical role of selenoproteins in the expansion and development of stress erythroid progenitors, as well as the erythroid niche during acute anemia recovery.
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Affiliation(s)
- Chang Liao
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA; and
| | | | - Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Robert F Paulson
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
| | - K Sandeep Prabhu
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
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41
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Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM, Hardison RC, Bodine DM. Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Epigenetics Chromatin 2018; 11:22. [PMID: 29807547 PMCID: PMC5971425 DOI: 10.1186/s13072-018-0195-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Enhancers and promoters are cis-acting regulatory elements associated with lineage-specific gene expression. Previous studies showed that different categories of active regulatory elements are in regions of open chromatin, and each category is associated with a specific subset of post-translationally marked histones. These regulatory elements are systematically activated and repressed to promote commitment of hematopoietic stem cells along separate differentiation paths, including the closely related erythrocyte (ERY) and megakaryocyte (MK) lineages. However, the order in which these decisions are made remains unclear. RESULTS To characterize the order of cell fate decisions during hematopoiesis, we collected primary cells from mouse bone marrow and isolated 10 hematopoietic populations to generate transcriptomes and genome-wide maps of chromatin accessibility and histone H3 acetylated at lysine 27 binding (H3K27ac). Principle component analysis of transcriptional and open chromatin profiles demonstrated that cells of the megakaryocyte lineage group closely with multipotent progenitor populations, whereas erythroid cells form a separate group distinct from other populations. Using H3K27ac and open chromatin profiles, we showed that 89% of immature MK (iMK)-specific active regulatory regions are present in the most primitive hematopoietic cells, 46% of which contain active enhancer marks. These candidate active enhancers are enriched for transcription factor binding site motifs for megakaryopoiesis-essential proteins, including ERG and ETS1. In comparison, only 64% of ERY-specific active regulatory regions are present in the most primitive hematopoietic cells, 20% of which containing active enhancer marks. These regions were not enriched for any transcription factor consensus sequences. Incorporation of genome-wide DNA methylation identified significant levels of de novo methylation in iMK, but not ERY. CONCLUSIONS Our results demonstrate that megakaryopoietic profiles are established early in hematopoiesis and are present in the majority of the hematopoietic progenitor population. However, megakaryopoiesis does not constitute a "default" differentiation pathway, as extensive de novo DNA methylation accompanies megakaryopoietic commitment. In contrast, erythropoietic profiles are not established until a later stage of hematopoiesis, and require more dramatic changes to the transcriptional and epigenetic programs. These data provide important insights into lineage commitment and can contribute to ongoing studies related to diseases associated with differentiation defects.
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42
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Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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43
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Zhang Y, Hardison RC. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Nucleic Acids Res 2017; 45:9823-9836. [PMID: 28973456 PMCID: PMC5622376 DOI: 10.1093/nar/gkx659] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
The Roadmap Epigenomics Consortium has published whole-genome functional annotation maps in 127 human cell types by integrating data from studies of multiple epigenetic marks. These maps have been widely used for studying gene regulation in cell type-specific contexts and predicting the functional impact of DNA mutations on disease. Here, we present a new map of functional elements produced by applying a method called IDEAS on the same data. The method has several unique advantages and outperforms existing methods, including that used by the Roadmap Epigenomics Consortium. Using five categories of independent experimental datasets, we compared the IDEAS and Roadmap Epigenomics maps. While the overall concordance between the two maps is high, the maps differ substantially in the prediction details and in their consistency of annotation of a given genomic position across cell types. The annotation from IDEAS is uniformly more accurate than the Roadmap Epigenomics annotation and the improvement is substantial based on several criteria. We further introduce a pipeline that improves the reproducibility of functional annotation maps. Thus, we provide a high-quality map of candidate functional regions across 127 human cell types and compare the quality of different annotation methods in order to facilitate biomedical research in epigenomics.
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Affiliation(s)
- Yu Zhang
- Department of Statistics, the Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, PA 16802, USA
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44
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Oudelaar AM, Hanssen LL, Hardison RC, Kassouf MT, Hughes JR, Higgs DR. Between form and function: the complexity of genome folding. Hum Mol Genet 2017; 26:R208-R215. [PMID: 28977451 PMCID: PMC5886466 DOI: 10.1093/hmg/ddx306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/24/2023] Open
Abstract
It has been known for over a century that chromatin is not randomly distributed within the nucleus. However, the question of how DNA is folded and the influence of such folding on nuclear processes remain topics of intensive current research. A longstanding, unanswered question is whether nuclear organization is simply a reflection of nuclear processes such as transcription and replication, or whether chromatin is folded by independent mechanisms and this per se encodes function? Evidence is emerging that both may be true. Here, using the α-globin gene cluster as an illustrative model, we provide an overview of the most recent insights into the layers of genome organization across different scales and how this relates to gene activity.
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Affiliation(s)
- A. Marieke Oudelaar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Lars L.P. Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
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45
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Huang P, Keller CA, Giardine B, Grevet JD, Davies JOJ, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA. Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Genes Dev 2017; 31:1704-1713. [PMID: 28916711 PMCID: PMC5647940 DOI: 10.1101/gad.303461.117] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/21/2017] [Indexed: 01/04/2023]
Abstract
In this study, Huang et al. compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. Their results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements. Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detected distinct folding patterns at the developmentally controlled β-globin locus. Specifically, new fetal stage-specific contacts were uncovered between a region separating the fetal (γ) and adult (δ and β) globin genes (encompassing the HBBP1 and BGLT3 noncoding genes) and two distal chromosomal sites (HS5 and 3′HS1) that flank the locus. In contrast, in adult cells, the HBBP1–BGLT3 region contacts the embryonic ε-globin gene, physically separating the fetal globin genes from the enhancer (locus control region [LCR]). Deletion of the HBBP1 region in adult cells alters contact landscapes in ways more closely resembling those of fetal cells, including increased LCR–γ-globin contacts. These changes are accompanied by strong increases in γ-globin transcription. Notably, the effects of HBBP1 removal on chromatin architecture and gene expression closely mimic those of deleting the fetal globin repressor BCL11A, implicating BCL11A in the function of the HBBP1 region. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.
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Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeremy D Grevet
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James O J Davies
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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46
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Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Res 2017; 27:1939-1949. [PMID: 28855260 PMCID: PMC5668950 DOI: 10.1101/gr.220640.117] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 08/07/2017] [Indexed: 01/07/2023]
Abstract
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach.
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Affiliation(s)
- Tao Yang
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Feipeng Zhang
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Galip Gürkan Yardımcı
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Fan Song
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.,Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98105, USA
| | - Feng Yue
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Qunhua Li
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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47
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Hsiung CCS, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA. A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Genes Dev 2017; 30:1423-39. [PMID: 27340175 PMCID: PMC4926865 DOI: 10.1101/gad.280859.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/23/2016] [Indexed: 01/07/2023]
Abstract
Hsiung et al. tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. During the earliest rounds of transcription at the mitosis–G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. During mitosis, RNA polymerase II (Pol II) and many transcription factors dissociate from chromatin, and transcription ceases globally. Transcription is known to restart in bulk by telophase, but whether de novo transcription at the mitosis–G1 transition is in any way distinct from later in interphase remains unknown. We tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. Unexpectedly, during the earliest rounds of transcription at the mitosis–G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. Enhancer–promoter chromatin contacts are depleted during mitosis and restored rapidly upon G1 entry but do not spike. Of the chromatin-associated features examined, histone H3 Lys27 acetylation levels at individual loci in mitosis best predict the mitosis–G1 transcriptional spike. Single-molecule RNA imaging supports that the mitosis–G1 transcriptional spike can constitute the maximum transcriptional activity per DNA copy throughout the cell division cycle. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. Our results raise the possibility that passage through the mitosis–G1 transition might predispose cells to diverge in gene expression states.
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Affiliation(s)
- Chris C-S Hsiung
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Caroline R Bartman
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Paul Ginart
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA, Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Aaron J Stonestrom
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carolyne Face
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kristen S Jahn
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Perry Evans
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Laavanya Sankaranarayanan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Arjun Raj
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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48
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Abstract
A new study helps resolve a controversy about determinants of gene expression variability and might facilitate the effective translation of research results across species.
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Affiliation(s)
- Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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49
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Zhang Y, An L, Yue F, Hardison RC. Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Res 2016; 44:6721-31. [PMID: 27095202 PMCID: PMC5772166 DOI: 10.1093/nar/gkw278] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/06/2016] [Indexed: 12/16/2022] Open
Abstract
Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an integrative and discriminative epigenome annotation system, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
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Affiliation(s)
- Yu Zhang
- Dept. of Statistics, Penn State University, 325 Thomas Building, University Park, PA 16803, USA
| | - Lin An
- Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, Penn State University, 101 Huck Life Sciences Building, University Park, PA 16802, USA
| | - Feng Yue
- Dept. of Biochemistry and Molecular Biology, Penn State School of Medicine, 500 University Drive, MC H171, Hershey, PA 17033, USA
| | - Ross C Hardison
- Dept. of Biochemistry and Molecular Biology, Penn State University, 304 Wartik Laboratory, University Park, PA 16802, USA
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50
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Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JOJ, Hughes JR, Hardison RC, Blobel GA, Weiss MJ. Unlinking an lncRNA from Its Associated cis Element. Mol Cell 2016; 62:104-10. [PMID: 27041223 DOI: 10.1016/j.molcel.2016.02.029] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/01/2016] [Accepted: 02/24/2016] [Indexed: 01/24/2023]
Abstract
Long non-coding (lnc) RNAs can regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (lncRNA downstream of Cdkn1b), a 434-nt polyadenylated lncRNA originating 4 kb 3' to the Cdkn1b gene. Deletion of the 25-kb Lockd locus reduced Cdkn1b transcription by approximately 70% in an erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by >90% with no effect on Cdkn1b transcription. The Lockd promoter contains a DNase-hypersensitive site, binds numerous transcription factors, and physically associates with the Cdkn1b promoter in chromosomal conformation capture studies. Therefore, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, whereas the lncRNA itself is dispensable, which may be the case for other lncRNAs.
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Affiliation(s)
- Vikram R Paralkar
- Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Cristian C Taborda
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Rishi Prasad
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jing Luan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James O J Davies
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Jim R Hughes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16801, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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