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Fan K, Pfister E, Weng Z. Toward a comprehensive catalog of regulatory elements. Hum Genet 2023; 142:1091-1111. [PMID: 36935423 DOI: 10.1007/s00439-023-02519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 03/21/2023]
Abstract
Regulatory elements are the genomic regions that interact with transcription factors to control cell-type-specific gene expression in different cellular environments. A precise and complete catalog of functional elements encoded by the human genome is key to understanding mammalian gene regulation. Here, we review the current state of regulatory element annotation. We first provide an overview of assays for characterizing functional elements, including genome, epigenome, transcriptome, three-dimensional chromatin interaction, and functional validation assays. We then discuss computational methods for defining regulatory elements, including peak-calling and other statistical modeling methods. Finally, we introduce several high-quality lists of regulatory element annotations and suggest potential future directions.
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Affiliation(s)
- Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Edith Pfister
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA.
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Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D. Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. Sci Rep 2023; 13:11693. [PMID: 37474564 PMCID: PMC10359366 DOI: 10.1038/s41598-023-38865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023] Open
Abstract
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a significant role in the condensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto, and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines. We have compared ourselves to the baseline ExPecto model, which obtained a 0.82 Spearman's rank correlation coefficient (SCC) score, and 0.85, which is reported by newer Enformer were able to obtain the average correlation score of 0.83. However, in some cases (e.g. RNAPOL2 on GM12878), our improvement reached 0.04, and in some cases (e.g. RNAPOL2 on H1), we reached an SCC of 0.86.
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Affiliation(s)
- Mateusz Chiliński
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | | | - Abhishek Agarwal
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Zhejiang, Hangzhou, China
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662, Warsaw, Poland.
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.
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Thomas S, Xu TH, Carpenter B, Pierce S, Dickson B, Liu M, Liang G, Jones P. DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding. Nucleic Acids Res 2023; 51:5997-6005. [PMID: 37094063 PMCID: PMC10325916 DOI: 10.1093/nar/gkad293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/23/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
CpG methylation generally occurs on both DNA strands and is essential for mammalian development and differentiation. Until recently, hemimethylation, in which only one strand is methylated, was considered to be simply a transitory state generated during DNA synthesis. The discovery that a subset of CCCTC-binding factor (CTCF) binding sites is heritably hemimethylated suggests that hemimethylation might have an unknown biological function. Here we show that the binding of CTCF is profoundly altered by which DNA strand is methylated and by the specific CTCF binding motif. CpG methylation on the motif strand can inhibit CTCF binding by up to 7-fold, whereas methylation on the opposite strand can stimulate binding by up to 4-fold. Thus, hemimethylation can alter binding by up to 28-fold in a strand-specific manner. The mechanism for sensing methylation on the opposite strand requires two critical residues, V454 and S364, within CTCF zinc fingers 7 and 4. Similar to methylation, CpG hydroxymethylation on the motif strand can inhibit CTCF binding by up to 4-fold. However, hydroxymethylation on the opposite strand removes the stimulatory effect. Strand-specific methylation states may therefore provide a mechanism to explain the transient and dynamic nature of CTCF-mediated chromatin interactions.
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Affiliation(s)
- Stacey L Thomas
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ting-Hai Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Steven E Pierce
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bradley M Dickson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Minmin Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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Zeng S, Chen L, Liu X, Tang H, Wu H, Liu C. Single-cell multi-omics analysis reveals dysfunctional Wnt signaling of spermatogonia in non-obstructive azoospermia. Front Endocrinol (Lausanne) 2023; 14:1138386. [PMID: 37334314 PMCID: PMC10273265 DOI: 10.3389/fendo.2023.1138386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Background Non-obstructive azoospermia (NOA) is the most severe type that leads to 1% of male infertility. Wnt signaling governs normal sperm maturation. However, the role of Wnt signaling in spermatogonia in NOA has incompletely been uncovered, and upstream molecules regulating Wnt signaling remain unclear. Methods Bulk RNA sequencing (RNA-seq) of NOA was used to identify the hub gene module in NOA utilizing weighted gene co-expression network analyses (WGCNAs). Single-cell RNA sequencing (scRNA-seq) of NOA was employed to explore dysfunctional signaling pathways in the specific cell type with gene sets of signaling pathways. Single-cell regulatory network inference and clustering (pySCENIC) for Python analysis was applied to speculate putative transcription factors in spermatogonia. Moreover, single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) determined the regulated genes of these transcription factors. Finally, spatial transcriptomic data were used to analyze cell type and Wnt signaling spatial distribution. Results The Wnt signaling pathway was demonstrated to be enriched in the hub gene module of NOA by bulk RNA-seq. Then, scRNA-seq data revealed the downregulated activity and dysfunction of Wnt signaling of spermatogonia in NOA samples. Conjoint analyses of the pySCENIC algorithm and scATAC-seq data indicated that three transcription factors (CTCF, AR, and ARNTL) were related to the activities of Wnt signaling in NOA. Eventually, spatial expression localization of Wnt signaling was identified to be in accordance with the distribution patterns of spermatogonia, Sertoli cells, and Leydig cells. Conclusion In conclusion, we identified that downregulated Wnt signaling of spermatogonia in NOA and three transcription factors (CTCF, AR, and ARNTL) may be involved in this dysfunctional Wnt signaling. These findings provide new mechanisms for NOA and new therapeutic targets for NOA patients.
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Affiliation(s)
- Shengjie Zeng
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liuxun Chen
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xvdong Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haibin Tang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hao Wu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chuan Liu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Plant E, Bellefroid M, Van Lint C. A complex network of transcription factors and epigenetic regulators involved in bovine leukemia virus transcriptional regulation. Retrovirology 2023; 20:11. [PMID: 37268923 DOI: 10.1186/s12977-023-00623-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/09/2023] [Indexed: 06/04/2023] Open
Abstract
Bovine Leukemia Virus (BLV) is the etiological agent of enzootic bovine leukosis, a disease characterized by the neoplastic proliferation of B cells in cattle. While most European countries have introduced efficient eradication programs, BLV is still present worldwide and no treatment is available. A major feature of BLV infection is the viral latency, which enables the escape from the host immune system, the maintenance of a persistent infection and ultimately the tumoral development. BLV latency is a multifactorial phenomenon resulting in the silencing of viral genes due to genetic and epigenetic repressions of the viral promoter located in the 5' Long Terminal Repeat (5'LTR). However, viral miRNAs and antisense transcripts are expressed from two different proviral regions, respectively the miRNA cluster and the 3'LTR. These latter transcripts are expressed despite the viral latency affecting the 5'LTR and are increasingly considered to take part in tumoral development. In the present review, we provide a summary of the experimental evidence that has enabled to characterize the molecular mechanisms regulating each of the three BLV transcriptional units, either through cis-regulatory elements or through epigenetic modifications. Additionally, we describe the recently identified BLV miRNAs and antisense transcripts and their implications in BLV-induced tumorigenesis. Finally, we discuss the relevance of BLV as an experimental model for the closely related human T-lymphotropic virus HTLV-1.
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Affiliation(s)
- Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium.
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Augsornworawat P, Hogrebe NJ, Ishahak M, Schmidt MD, Marquez E, Maestas MM, Veronese-Paniagua DA, Gale SE, Miller JR, Velazco-Cruz L, Millman JR. Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification. Nat Cell Biol 2023; 25:904-916. [PMID: 37188763 PMCID: PMC10264244 DOI: 10.1038/s41556-023-01150-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023]
Abstract
Insulin-producing β cells created from human pluripotent stem cells have potential as a therapy for insulin-dependent diabetes, but human pluripotent stem cell-derived islets (SC-islets) still differ from their in vivo counterparts. To better understand the state of cell types within SC-islets and identify lineage specification deficiencies, we used single-nucleus multi-omic sequencing to analyse chromatin accessibility and transcriptional profiles of SC-islets and primary human islets. Here we provide an analysis that enabled the derivation of gene lists and activity for identifying each SC-islet cell type compared with primary islets. Within SC-islets, we found that the difference between β cells and awry enterochromaffin-like cells is a gradient of cell states rather than a stark difference in identity. Furthermore, transplantation of SC-islets in vivo improved cellular identities overtime, while long-term in vitro culture did not. Collectively, our results highlight the importance of chromatin and transcriptional landscapes during islet cell specification and maturation.
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Affiliation(s)
- Punn Augsornworawat
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Nathaniel J Hogrebe
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Mason D Schmidt
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Erica Marquez
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Marlie M Maestas
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Daniel A Veronese-Paniagua
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Sarah E Gale
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Julia R Miller
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Leonardo Velazco-Cruz
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Price E, Fedida LM, Pugacheva EM, Ji YJ, Loukinov D, Lobanenkov VV. An updated catalog of CTCF variants associated with neurodevelopmental disorder phenotypes. Front Mol Neurosci 2023; 16:1185796. [PMID: 37324587 PMCID: PMC10264798 DOI: 10.3389/fnmol.2023.1185796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction CTCF-related disorder (CRD) is a neurodevelopmental disorder (NDD) caused by monoallelic pathogenic variants in CTCF. The first CTCF variants in CRD cases were documented in 2013. To date, 76 CTCF variants have been further described in the literature. In recent years, due to the increased application of next-generation sequencing (NGS), growing numbers of CTCF variants are being identified, and multiple genotype-phenotype databases cataloging such variants are emerging. Methods In this study, we aimed to expand the genotypic spectrum of CRD, by cataloging NDD phenotypes associated with reported CTCF variants. Here, we systematically reviewed all known CTCF variants reported in case studies and large-scale exome sequencing cohorts. We also conducted a meta-analysis using public variant data from genotype-phenotype databases to identify additional CTCF variants, which we then curated and annotated. Results From this combined approach, we report an additional 86 CTCF variants associated with NDD phenotypes that have not yet been described in the literature. Furthermore, we describe and explain inconsistencies in the quality of reported variants, which impairs the reuse of data for research of NDDs and other pathologies. Discussion From this integrated analysis, we provide a comprehensive and annotated catalog of all currently known CTCF mutations associated with NDD phenotypes, to aid diagnostic applications, as well as translational and basic research.
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Akhtar MS, Akhter N, Talat A, Alharbi RA, Sindi AAA, Klufah F, Alyahyawi HE, Alruwetei A, Ahmad A, Zamzami MA, Deo S, Husain SA, Badi OA, Khan MJ. Association of mutation and expression of the brother of the regulator of imprinted sites (BORIS) gene with breast cancer progression. Oncotarget 2023; 14:528-541. [PMID: 37235839 DOI: 10.18632/oncotarget.28442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION The BORIS, 11 zinc-finger transcription factors, is a member of the cancer-testis antigen (CTA) family. It is mapped to chromosome number 20q13.2 and this region is genetically linked to the early onset of breast cancer. The current study analyzed the correlation between BORIS mutations and the expression of the protein in breast cancer cases. MATERIALS AND METHODS A population-based study including a total of 155 breast cancer tissue samples and an equal number of normal adjacent tissues from Indian female breast cancer patients was carried out. Mutations of the BORIS gene were detected by polymerase chain reaction-single standard confirmation polymorphisms (PCR-SSCP) and automated DNA sequencing and by immunohistochemistry for BORIS protein expression were performed. The observed findings were correlated with several clinicopathological parameters to find out the clinical relevance of associations. RESULTS Of all the cases 16.12% (25/155) showed mutations in the BORIS gene. The observed mutations present on codon 329 are missense, leading to Val> Ile (G>A) change on exon 5 of the BORIS gene. A significant association was observed between mutations of the BORIS gene and some clinicopathological features like nodal status (p = 0.013), estrogen receptor (ER) expression (p = 0.008), progesterone receptor (PR) expression (p = 0.039), clinical stage (p = 0.010) and menopausal status (p = 0.023). The protein expression analysis showed 20.64% (32/155) samples showing low or no expression (+), 34.19% (53/155) with moderate expression (++), and 45.17% (70/155) showing high expression (+++) of BORIS protein. A significant association was observed between the expression of BORIS protein and clinicopathological features like clinical stage (p = 0.013), nodal status (p = 0.049), ER expression (p = 0.039), and PR expression (p = 0.027). When mutation and protein expression were correlated in combination with clinicopathological parameters a significant association was observed in the category of high (+++) level of BORIS protein expression (p = 0.017). CONCLUSION The BORIS mutations and high protein expression occur frequently in carcinoma of the breast suggesting their association with the onset and progression of breast carcinoma. Further, the BORIS has the potential to be used as a biomarker.
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Affiliation(s)
- Mohammad Salman Akhtar
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naseem Akhter
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Arshi Talat
- Department of Orthodontics and Dentofacial Orthopedics, ITS Dental College, Hospital and Research Centre, Greater Noida, Delhi-NCR, India
| | - Raed A Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Faisal Klufah
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmohsen Alruwetei
- Department of Medical Laboratory, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Svs Deo
- Department of Surgical Oncology, BRA- IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Syed Akhtar Husain
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Osama A Badi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Villaman C, Pollastri G, Saez M, Martin AJ. Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding. Comput Struct Biotechnol J 2023; 21:3024-3031. [PMID: 37266407 PMCID: PMC10229758 DOI: 10.1016/j.csbj.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Motivation One of the most relevant mechanisms involved in the determination of chromatin structure is the formation of structural loops that are also related with the conservation of chromatin states. Many of these loops are stabilized by CCCTC-binding factor (CTCF) proteins at their base. Despite the relevance of chromatin structure and the key role of CTCF, the role of the epigenetic factors that are involved in the regulation of CTCF binding, and thus, in the formation of structural loops in the chromatin, is not thoroughly understood. Results Here we describe a CTCF binding predictor based on Random Forest that employs different epigenetic data and genomic features. Importantly, given the ability of Random Forests to determine the relevance of features for the prediction, our approach also shows how the different types of descriptors impact the binding of CTCF, confirming previous knowledge on the relevance of chromatin accessibility and DNA methylation, but demonstrating the effect of epigenetic modifications on the activity of CTCF. We compared our approach against other predictors and found improved performance in terms of areas under PR and ROC curves (PRAUC-ROCAUC), outperforming current state-of-the-art methods.
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Affiliation(s)
- Camilo Villaman
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | | | - Mauricio Saez
- Centro de Oncología de Precisión, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Chile
| | - Alberto J.M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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Starkova T, Polyanichko A, Tomilin AN, Chikhirzhina E. Structure and Functions of HMGB2 Protein. Int J Mol Sci 2023; 24:ijms24098334. [PMID: 37176041 PMCID: PMC10179549 DOI: 10.3390/ijms24098334] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
High-Mobility Group (HMG) chromosomal proteins are the most numerous nuclear non-histone proteins. HMGB domain proteins are the most abundant and well-studied HMG proteins. They are involved in variety of biological processes. HMGB1 and HMGB2 were the first members of HMGB-family to be discovered and are found in all studied eukaryotes. Despite the high degree of homology, HMGB1 and HMGB2 proteins differ from each other both in structure and functions. In contrast to HMGB2, there is a large pool of works devoted to the HMGB1 protein whose structure-function properties have been described in detail in our previous review in 2020. In this review, we attempted to bring together diverse data about the structure and functions of the HMGB2 protein. The review also describes post-translational modifications of the HMGB2 protein and its role in the development of a number of diseases. Particular attention is paid to its interaction with various targets, including DNA and protein partners. The influence of the level of HMGB2 expression on various processes associated with cell differentiation and aging and its ability to mediate the differentiation of embryonic and adult stem cells are also discussed.
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Affiliation(s)
- Tatiana Starkova
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Alexander Polyanichko
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Alexey N Tomilin
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Elena Chikhirzhina
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
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Hafner A, Park M, Berger SE, Murphy SE, Nora EP, Boettiger AN. Loop stacking organizes genome folding from TADs to chromosomes. Mol Cell 2023; 83:1377-1392.e6. [PMID: 37146570 PMCID: PMC10167645 DOI: 10.1016/j.molcel.2023.04.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/17/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Although population-level analyses revealed significant roles for CTCF and cohesin in mammalian genome organization, their contributions at the single-cell level remain incompletely understood. Here, we used a super-resolution microscopy approach to measure the effects of removal of CTCF or cohesin in mouse embryonic stem cells. Single-chromosome traces revealed cohesin-dependent loops, frequently stacked at their loop anchors forming multi-way contacts (hubs), bridging across TAD boundaries. Despite these bridging interactions, chromatin in intervening TADs was not intermixed, remaining separated in distinct loops around the hub. At the multi-TAD scale, steric effects from loop stacking insulated local chromatin from ultra-long range (>4 Mb) contacts. Upon cohesin removal, the chromosomes were more disordered and increased cell-cell variability in gene expression. Our data revise the TAD-centric understanding of CTCF and cohesin and provide a multi-scale, structural picture of how they organize the genome on the single-cell level through distinct contributions to loop stacking.
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Affiliation(s)
- Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Minhee Park
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Scott E Berger
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Sedona E Murphy
- Department of Developmental Biology, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat Genet 2023; 55:880-890. [PMID: 37142849 PMCID: PMC10181933 DOI: 10.1038/s41588-023-01386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.
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Affiliation(s)
- Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Thomas Conrad
- Genomics Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maja C Stöber
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Life Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Katharina Kasack
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Potsdam, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Eric van Leen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Maria E Stefanova
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Yi Bei
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco Lodrini
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hedwig E Deubzer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Sascha Sauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany.
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Momeni-Boroujeni A, Vanderbilt C, Yousefi E, Abu-Rustum NR, Aghajanian C, Soslow RA, Ellenson LH, Weigelt B, Murali R. Landscape of chromatin remodeling gene alterations in endometrial carcinoma. Gynecol Oncol 2023; 172:54-64. [PMID: 36958196 PMCID: PMC10192087 DOI: 10.1016/j.ygyno.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
OBJECTIVE Chromatin remodeling genes (CRGs) encode components of epigenetic regulatory mechanisms and alterations in these genes have been identified in several tumor types, including gynecologic cancers. In this study, we sought to investigate the prevalence and clinicopathological associations of CRG alterations in endometrial carcinoma (EC). METHODS We performed a retrospective analysis of 660 ECs sequenced using a clinical massively parallel sequencing assay targeting up to 468 genes, including 25 CRGs, and defined the presence of somatic CRG alterations. Clinicopathologic features were obtained for all cases. Immunohistochemical interrogation of ARID1A and PTEN proteins was performed in a subset of samples. RESULTS Of the 660 ECs sequenced, 438 (66.4%) harbored CRG alterations covered by our panel. The most commonly altered CRG was ARID1A (46%), followed by CTCF (21%), KMT2D (18%), KMT2B (17%), BCOR (16%), ARID1B (12%) and SMARCA4 (11%). We found that ARID1A genetic alterations were preferentially bi-allelic and often corresponded to altered ARID1A protein expression in ECs. We further observed that ARID1A alterations were often subclonal when compared to PTEN alterations, which were primarily clonal in ECs harboring both mutations. Finally, CRG alterations were associated with an increased likelihood of myometrial and lymphovascular invasion in endometrioid ECs. CONCLUSION CRG alterations are common in EC and are associated with clinicopathologic features and likely play a crucial role in EC.
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Affiliation(s)
- Amir Momeni-Boroujeni
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Chad Vanderbilt
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Elham Yousefi
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, United States of America
| | - Nadeem R Abu-Rustum
- Departments of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Carol Aghajanian
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Robert A Soslow
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Lora H Ellenson
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Britta Weigelt
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Rajmohan Murali
- Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America.
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Caruso LB, Maestri D, Tempera I. Three-Dimensional Chromatin Structure of the EBV Genome: A Crucial Factor in Viral Infection. Viruses 2023; 15:1088. [PMID: 37243174 PMCID: PMC10222312 DOI: 10.3390/v15051088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Epstein-Barr Virus (EBV) is a human gamma-herpesvirus that is widespread worldwide. To this day, about 200,000 cancer cases per year are attributed to EBV infection. EBV is capable of infecting both B cells and epithelial cells. Upon entry, viral DNA reaches the nucleus and undergoes a process of circularization and chromatinization and establishes a latent lifelong infection in host cells. There are different types of latency all characterized by different expressions of latent viral genes correlated with a different three-dimensional architecture of the viral genome. There are multiple factors involved in the regulation and maintenance of this three-dimensional organization, such as CTCF, PARP1, MYC and Nuclear Lamina, emphasizing its central role in latency maintenance.
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Affiliation(s)
| | - Davide Maestri
- The Wistar Institute, Philadelphia, PA 19104, USA; (L.B.C.); (D.M.)
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Italo Tempera
- The Wistar Institute, Philadelphia, PA 19104, USA; (L.B.C.); (D.M.)
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66
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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68
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Wang B, Ji L, Bian Q. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites. Cell Rep 2023; 42:112323. [PMID: 37000624 DOI: 10.1016/j.celrep.2023.112323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.
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Affiliation(s)
- Bao Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Luzhang Ji
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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69
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Moscona R, Janssen SM, Elchebly M, Papadakis AI, Rubin E, Spatz A. BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells. Pigment Cell Melanoma Res 2023; 36:299-313. [PMID: 37082838 DOI: 10.1111/pcmr.13089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023]
Abstract
Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of regulator of imprinted sites (BORIS), also known as CCCTC binding factor-like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of melanoma cells from an intermediate melanocytic state toward a more mesenchymal-like state. However, the mechanism underlying this transcriptional switch remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in melanoma cells harboring an intermediate melanocytic state. The gene set that gained promoter accessibility, following ectopic BORIS expression, showed enrichment for biological processes associated with melanoma invasion, while promoters of genes associated with proliferation showed reduced accessibility. Integration of ATAC-seq and RNA-seq data demonstrated that increased chromatin accessibility was associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes were associated with repressed activity of tumor suppressors and proliferation factors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of melanoma cells toward a mesenchymal-like genetic signature.
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Affiliation(s)
- Roy Moscona
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sanne Marlijn Janssen
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
| | | | | | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alan Spatz
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
- Division of Pathology, Department of Laboratory Medicine, McGill University Health Center, Montréal, Quebec, Canada
- Department of Oncology, McGill University, Montréal, Quebec, Canada
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70
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Iwasaki Y, Aksu C, Reyes M, Ay B, He Q, Bastepe M. The long-range interaction between two GNAS imprinting control regions delineates pseudohypoparathyroidism type 1B pathogenesis. J Clin Invest 2023; 133:e167953. [PMID: 36853809 PMCID: PMC10104902 DOI: 10.1172/jci167953] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2023] Open
Abstract
Genetic defects of GNAS, the imprinted gene encoding the stimulatory G protein α-subunit, are responsible for multiple diseases. Abnormal GNAS imprinting causes pseudohypoparathyroidism type 1B (PHP1B), a prototype of mammalian end-organ hormone resistance. Hypomethylation at the maternally methylated GNAS A/B region is the only shared defect in patients with PHP1B. In autosomal dominant (AD) PHP1B kindreds, A/B hypomethylation is associated with maternal microdeletions at either the GNAS NESP55 differentially methylated region or the STX16 gene located approximately 170 kb upstream. Functional evidence is meager regarding the causality of these microdeletions. Moreover, the mechanisms linking A/B methylation and the putative imprinting control regions (ICRs) NESP-ICR and STX16-ICR remain unknown. Here, we generated a human embryonic stem cell model of AD-PHP1B by introducing ICR deletions using CRISPR/Cas9. With this model, we showed that the NESP-ICR is required for methylation and transcriptional silencing of A/B on the maternal allele. We also found that the SXT16-ICR is a long-range enhancer of NESP55 transcription, which originates from the maternal NESP-ICR. Furthermore, we demonstrated that the STX16-ICR is an embryonic stage-specific enhancer enabled by the direct binding of pluripotency factors. Our findings uncover an essential GNAS imprinting control mechanism and advance the molecular understanding of PHP1B pathogenesis.
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Affiliation(s)
- Yorihiro Iwasaki
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka, Japan
| | - Cagri Aksu
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Reyes
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Birol Ay
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Qing He
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of the Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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71
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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72
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Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D. Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535849. [PMID: 37066361 PMCID: PMC10104055 DOI: 10.1101/2023.04.06.535849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a major role in the compensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto (J. Zhou et al., 2018), and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines.
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73
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Zhang X, Zhu W, Sun H, Ding Y, Liu L. Prediction of CTCF loop anchor based on machine learning. Front Genet 2023; 14:1181956. [PMID: 37077544 PMCID: PMC10106609 DOI: 10.3389/fgene.2023.1181956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction: Various activities in biological cells are affected by three-dimensional genome structure. The insulators play an important role in the organization of higher-order structure. CTCF is a representative of mammalian insulators, which can produce barriers to prevent the continuous extrusion of chromatin loop. As a multifunctional protein, CTCF has tens of thousands of binding sites in the genome, but only a portion of them can be used as anchors of chromatin loops. It is still unclear how cells select the anchor in the process of chromatin looping.Methods: In this paper, a comparative analysis is performed to investigate the sequence preference and binding strength of anchor and non-anchor CTCF binding sites. Furthermore, a machine learning model based on the CTCF binding intensity and DNA sequence is proposed to predict which CTCF sites can form chromatin loop anchors.Results: The accuracy of the machine learning model that we constructed for predicting the anchor of the chromatin loop mediated by CTCF reached 0.8646. And we find that the formation of loop anchor is mainly influenced by the CTCF binding strength and binding pattern (which can be interpreted as the binding of different zinc fingers).Discussion: In conclusion, our results suggest that The CTCF core motif and it’s flanking sequence may be responsible for the binding specificity. This work contributes to understanding the mechanism of loop anchor selection and provides a reference for the prediction of CTCF-mediated chromatin loops.
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Affiliation(s)
- Xiao Zhang
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou, China
| | - Wen Zhu
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou, China
- *Correspondence: Wen Zhu,
| | - Huimin Sun
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| | - Yijie Ding
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou, China
| | - Li Liu
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
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74
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Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Mol Cell 2023; 83:1350-1367.e7. [PMID: 37028419 DOI: 10.1016/j.molcel.2023.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/07/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023]
Abstract
The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes play critical roles in regulating DNA accessibility and gene expression. The three final-form subcomplexes-cBAF, PBAF, and ncBAF-are distinct in biochemical componentry, chromatin targeting, and roles in disease; however, the contributions of their constituent subunits to gene expression remain incompletely defined. Here, we performed Perturb-seq-based CRISPR-Cas9 knockout screens targeting mSWI/SNF subunits individually and in select combinations, followed by single-cell RNA-seq and SHARE-seq. We uncovered complex-, module-, and subunit-specific contributions to distinct regulatory networks and defined paralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-complex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, single-cell subunit perturbation signatures mapped across bulk primary human tumor expression profiles both mirror and predict cBAF loss-of-function status in cancer. Our findings highlight the utility of Perturb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes.
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Affiliation(s)
- Jordan E Otto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Oana Ursu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander P Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evan B Winter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sai Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kristin Qian
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Bonnie Berger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
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75
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Barker R, Biernacka K, Kingshott G, Sewell A, Gwiti P, Martin RM, Lane JA, McGeagh L, Koupparis A, Rowe E, Oxley J, Perks CM, Holly JMP. Associations of CTCF and FOXA1 with androgen and IGF pathways in men with localized prostate cancer. Growth Horm IGF Res 2023; 69-70:101533. [PMID: 37086646 DOI: 10.1016/j.ghir.2023.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023]
Abstract
AIMS To examine associations between the transcription factors CCCTC-binding factor (CTCF) and forkhead box protein A1 (FOXA1) and the androgen receptor (AR) and their association with components of the insulin-like growth factor (IGF)-pathway in a cohort of men with localized prostate cancer. METHODS Using prostate tissue samples collected during the Prostate cancer: Evidence of Exercise and Nutrition Trial (PrEvENT) trial (N = 70 to 92, depending on section availability), we assessed the abundance of CTCF, FOXA1, AR, IGFIR, p-mTOR, PTEN and IGFBP-2 proteins using a modified version of the Allred scoring system. Validation studies were performed using large, publicly available datasets (TCGA) (N = 489). RESULTS We identified a strong correlation between CTCF and AR staining with benign prostate tissue. CTCF also strongly associated with the IGFIR, with PTEN and with phospho-mTOR. FOXA1 was also correlated with staining for the IGF-IR, with IGFBP-2 and with staining for activated phosphor-mTOR. The staining for the IGF-IR was strongly correlated with the AR. CONCLUSION Our findings emphasise the close and complex links between the endocrine controls, well known to play an important role in prostate cancer, and the transcription factors implicated by the recent genetic evidence.
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Affiliation(s)
- Rachel Barker
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Kalina Biernacka
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Georgina Kingshott
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Alex Sewell
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Paida Gwiti
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK; Department of Pathology, North West Anglia NHS Foundation Trust, Peterborough PE3 9GZ, UK
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK; National Institute for Health Research, Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Biomedical Research Unit Offices, University Hospitals Bristol Education Centre, Dental Hospital, Lower Maudlin Street, Bristol BS1 2LY, UK
| | - J Athene Lane
- Bristol Trials Centre, Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Lucy McGeagh
- Supportive Cancer Care Research Group, Faculty of Health and Life Sciences, Oxford Institute of Nursing, Midwifery and Allied Health Research, Oxford Brookes University, Jack Straws Lane, Marston, Oxford OX3 0FL, UK
| | - Anthony Koupparis
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Edward Rowe
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Jon Oxley
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Claire M Perks
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK.
| | - Jeff M P Holly
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
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76
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Thieme E, Bruss N, Sun D, Dominguez EC, Coleman D, Liu T, Roleder C, Martinez M, Garcia-Mansfield K, Ball B, Pirrotte P, Wang L, Xia Z, Danilov AV. CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma. Mol Cancer 2023; 22:64. [PMID: 36998071 PMCID: PMC10061728 DOI: 10.1186/s12943-023-01762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.
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Affiliation(s)
- Elana Thieme
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Nur Bruss
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Duanchen Sun
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA
- grid.27255.370000 0004 1761 1174Present address: School of Mathematics, Shandong University, Jinan, 250100 Shandong China
| | - Edward C. Dominguez
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Daniel Coleman
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Tingting Liu
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Carly Roleder
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Melissa Martinez
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Krystine Garcia-Mansfield
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Brian Ball
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Patrick Pirrotte
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Lili Wang
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Zheng Xia
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Biomedical Engineering Department, Oregon Health & Science University, Portland, OR USA
| | - Alexey V. Danilov
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
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77
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Zhong JY, Niu L, Lin ZB, Bai X, Chen Y, Luo F, Hou C, Xiao CL. High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding. Nat Commun 2023; 14:1250. [PMID: 36878904 PMCID: PMC9988853 DOI: 10.1038/s41467-023-36899-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.
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Affiliation(s)
- Jia-Yong Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Longjian Niu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.,School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhuo-Bin Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xin Bai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, 29634-0974, USA
| | - Chunhui Hou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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78
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Gandhi J, Mantilla JG, Ricciotti RW, Chen EY, Liu YJ, Bandhlish A. Myoepithelial carcinoma of the parotid gland with a novel CTCF::NCOA2 fusion. Genes Chromosomes Cancer 2023; 62:161-166. [PMID: 36331420 DOI: 10.1002/gcc.23101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
We describe a case of a myoepithelial carcinoma of the superficial parotid gland in a 46-year-old male harboring a novel CTCF::NCOA2 gene fusion. To our knowledge, this novel gene fusion has not been described previously in myoepithelial carcinoma. A 46-year-old male patient presented with a mass involving the superficial left parotid gland with extension into the external auditory canal (EAC) and erosion of the conchal cartilage. Histologically, the neoplasm was composed of uniform spindled, epithelioid/ovoid cells arranged in cords and nests within hyalinized to myxoid stroma. On immunohistochemistry (IHC), the tumor cells demonstrated patchy and variable staining for low molecular weight cytokeratin (CAM5.2), pan-cytokeratin (OSCAR), and S-100. Overall, the morphological and immunohistochemical attributes supported a locally aggressive tumor of myoepithelial differentiation consistent with myoepithelial carcinoma. Molecular analysis using a custom 115-gene gene panel by targeted RNA sequencing, showed an in-frame CTCF::NCOA2 fusion. In addition to reporting this novel fusion in myoepithelial carcinoma, we also discuss relevant differential diagnosis, and provide a brief review of NCOA2 gene function in both normal and neoplastic contexts.
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Affiliation(s)
- Jatin Gandhi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, Emory University School of Medicine, Atlanta, Washington, USA
| | - Jose G Mantilla
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Robert W Ricciotti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Eleanor Y Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Anshu Bandhlish
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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79
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de Morales HGV, Wang HLV, Garber K, Cheng X, Corces VG, Li H. Expansion of the genotypic and phenotypic spectrum of CTCF-related disorder guides clinical management: 43 new subjects and a comprehensive literature review. Am J Med Genet A 2023; 191:718-729. [PMID: 36454652 PMCID: PMC9928606 DOI: 10.1002/ajmg.a.63065] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/22/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
Monoallelic variants of CTCF cause an autosomal dominant neurodevelopmental disorder with a wide range of features, including impacts on the brain, growth, and craniofacial development. A growing number of subjects with CTCF-related disorder (CRD) have been identified due to the increased application of exome sequencing, and further delineation of the clinical spectrum of CRD is needed. Here, we examined the clinical features, including facial profiles, and genotypic spectrum of 107 subjects with identified CTCF variants, including 43 new and 64 previously described subjects. Among the 43 new subjects, 23 novel variants were reported. The cardinal clinical features in subjects with CRD included intellectual disability/developmental delay (91%) with speech delay (65%), motor delay (53%), feeding difficulties/failure to thrive (66%), ocular abnormalities (56%), musculoskeletal anomalies (53%), and behavioral problems (52%). Other congenital anomalies were also reported, but none of them were common. Our findings expanded the genotypic and phenotypic spectrum of CRD that will guide genetic counseling, management, and surveillance care for patients with CRD. Additionally, a newly built facial gestalt on the Face2Gene tool will facilitate prompt recognition of CRD by physicians and shorten a patient's diagnostic odyssey.
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Affiliation(s)
| | - Hsiao-Lin V. Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Kathryn Garber
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX. 77030
| | - Victor G. Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
| | - Hong Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA. 30322
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA. 30322
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80
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Reactivation of Epstein-Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites on the Viral Genome. J Virol 2023; 97:e0189422. [PMID: 36744959 PMCID: PMC9972995 DOI: 10.1128/jvi.01894-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability of Epstein-Barr virus (EBV) to switch between latent and lytic infection is key to its long-term persistence, yet the molecular mechanisms behind this switch remain unclear. To investigate transcriptional events during the latent-to-lytic switch, we utilized Precision nuclear Run On followed by deep Sequencing (PRO-Seq) to map cellular RNA polymerase (Pol) activity to single-nucleotide resolution on the host and EBV genome in three different models of EBV latency and reactivation. In latently infected Mutu-I Burkitt lymphoma (BL) cells, Pol activity was enriched at the Qp promoter, the EBER region, and the BHLF1/LF3 transcripts. Upon reactivation with phorbol ester and sodium butyrate, early-phase Pol activity occurred bidirectionally at CTCF sites within the LMP-2A, EBER-1, and RPMS1 loci. PRO-Seq analysis of Akata cells reactivated from latency with anti-IgG and a lymphoblastoid cell line (LCL) reactivated with small molecule C60 showed a similar pattern of early bidirectional transcription initiating around CTCF binding sites, although the specific CTCF sites and viral genes were different for each latency model. The functional importance of CTCF binding, transcription, and reactivation was confirmed using an EBV mutant lacking the LMP-2A CTCF binding site. This virus was unable to reactivate and had disrupted Pol activity at multiple CTCF binding sites relative to the wild-type (WT) virus. Overall, these data suggest that CTCF regulates the viral early transcripts during reactivation from latency. These activities likely help maintain the accessibility of the viral genome to initiate productive replication. IMPORTANCE The ability of EBV to switch between latent and lytic infection is key to its long-term persistence in memory B cells, and its ability to persist in proliferating cells is strongly linked to oncogenesis. During latency, most viral genes are epigenetically silenced, and the virus must overcome this repression to reactivate lytic replication. Reactivation occurs once the immediate early (IE) EBV lytic genes are expressed. However, the molecular mechanisms behind the switch from the latent transcriptional program to begin transcription of the IE genes remain unknown. In this study, we mapped RNA Pol positioning and activity during latency and reactivation. Unexpectedly, Pol activity accumulated at distinct regions characteristic of transcription initiation on the EBV genome previously shown to be associated with CTCF. We propose that CTCF binding at these regions retains Pol to maintain a stable latent chromosome conformation and a rapid response to various reactivation signals.
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81
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Khurana I, Kaipananickal H, Maxwell S, Birkelund S, Syreeni A, Forsblom C, Okabe J, Ziemann M, Kaspi A, Rafehi H, Jørgensen A, Al-Hasani K, Thomas MC, Jiang G, Luk AO, Lee HM, Huang Y, Thewjitcharoen Y, Nakasatien S, Himathongkam T, Fogarty C, Njeim R, Eid A, Hansen TW, Tofte N, Ottesen EC, Ma RC, Chan JC, Cooper ME, Rossing P, Groop PH, El-Osta A. Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes. J Clin Invest 2023; 133:160959. [PMID: 36633903 PMCID: PMC9927943 DOI: 10.1172/jci160959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Diabetic nephropathy (DN) is a polygenic disorder with few risk variants showing robust replication in large-scale genome-wide association studies. To understand the role of DNA methylation, it is important to have the prevailing genomic view to distinguish key sequence elements that influence gene expression. This is particularly challenging for DN because genome-wide methylation patterns are poorly defined. While methylation is known to alter gene expression, the importance of this causal relationship is obscured by array-based technologies since coverage outside promoter regions is low. To overcome these challenges, we performed methylation sequencing using leukocytes derived from participants of the Finnish Diabetic Nephropathy (FinnDiane) type 1 diabetes (T1D) study (n = 39) that was subsequently replicated in a larger validation cohort (n = 296). Gene body-related regions made up more than 60% of the methylation differences and emphasized the importance of methylation sequencing. We observed differentially methylated genes associated with DN in 3 independent T1D registries originating from Denmark (n = 445), Hong Kong (n = 107), and Thailand (n = 130). Reduced DNA methylation at CTCF and Pol2B sites was tightly connected with DN pathways that include insulin signaling, lipid metabolism, and fibrosis. To define the pathophysiological significance of these population findings, methylation indices were assessed in human renal cells such as podocytes and proximal convoluted tubule cells. The expression of core genes was associated with reduced methylation, elevated CTCF and Pol2B binding, and the activation of insulin-signaling phosphoproteins in hyperglycemic cells. These experimental observations also closely parallel methylation-mediated regulation in human macrophages and vascular endothelial cells.
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Affiliation(s)
- Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Scott Maxwell
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sørine Birkelund
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Anne Jørgensen
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Keith Al-Hasani
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Merlin C. Thomas
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | | | - Andrea O.Y. Luk
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Heung Man Lee
- Department of Medicine and Therapeutics,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | | | | | - Christopher Fogarty
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rachel Njeim
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Assaad Eid
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Nete Tofte
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Ronald C.W. Ma
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Juliana C.N. Chan
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark E. Cooper
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Herlev, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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82
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Choudhary MNK, Quaid K, Xing X, Schmidt H, Wang T. Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. Nat Commun 2023; 14:634. [PMID: 36746940 PMCID: PMC9902604 DOI: 10.1038/s41467-023-36364-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders, and RNA-DNA interactions. These play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific families and subfamilies of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate sustained interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to shaping 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.
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Affiliation(s)
- Mayank N K Choudhary
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Kara Quaid
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Heather Schmidt
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Ting Wang
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA.
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83
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Fan C, Chen K, Wang Y, Ball EV, Stenson PD, Mort M, Bacolla A, Kehrer-Sawatzki H, Tainer JA, Cooper DN, Zhao H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet 2023; 142:245-274. [PMID: 36344696 PMCID: PMC10290229 DOI: 10.1007/s00439-022-02500-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5'UTRs and 5'genes but were not significantly different from controls in introns, 3'UTRs and 3'genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5'genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx ( http://biomed.nscc-gz.cn/zhaolab/geneprediction/# ) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.
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Affiliation(s)
- Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
| | - Ken Chen
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Yukai Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | | | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.
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84
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Hyle J, Djekidel MN, Williams J, Wright S, Shao Y, Xu B, Li C. Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation. Genome Biol 2023; 24:14. [PMID: 36698211 PMCID: PMC9878928 DOI: 10.1186/s13059-022-02843-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/29/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF. RESULTS We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. CONCLUSIONS By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.
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Affiliation(s)
- Judith Hyle
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Mohamed Nadhir Djekidel
- grid.240871.80000 0001 0224 711XCenter for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Justin Williams
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Shaela Wright
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Ying Shao
- grid.240871.80000 0001 0224 711XDepartment of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Beisi Xu
- grid.240871.80000 0001 0224 711XCenter for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Chunliang Li
- grid.240871.80000 0001 0224 711XDepartment of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
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85
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Zablon HA, VonHandorf A, Puga A. Mechanisms of chromate carcinogenesis by chromatin alterations. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2023; 96:1-23. [PMID: 36858770 DOI: 10.1016/bs.apha.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a dynamic environment, organisms must constantly mount an adaptive response to new environmental conditions in order to survive. Novel patterns of gene expression, driven by attendant changes in chromatin architecture, aid in adaptation and survival. Critical mechanisms in the control of gene transcription govern new spatiotemporal chromatin-chromatin interactions that make regulatory DNA elements accessible to the transcription factors that control the response. Consequently, agents that disrupt chromatin structure are likely to have a direct impact on the transcriptional programs of cells and organisms and to drive alterations in fundamental physiological processes. In this regard, hexavalent chromium (Cr(VI)) is of special interest because it interacts directly with cellular proteins, DNA, and other macromolecules, and is likely to upset cell functions that may cause generalized damage to the organism. Here, we will highlight chromium-mediated mechanisms that disrupt chromatin architecture and discuss how these mechanisms are integral to its carcinogenic properties. Emerging evidence indicates that Cr(VI) targets euchromatin, particularly in genomic locations flanking the binding sites of the essential transcription factors CTCF and AP1, and, in so doing, they disrupt nucleosomal architecture. Ultimately, the ensuing changes, if occurring in critical regulatory domains, may establish a new chromatin state, either toxic or adaptive, that will be governed by the corresponding gene transcription changes in key biological processes associated with that state.
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Affiliation(s)
- Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew VonHandorf
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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86
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Fritz AJ, Ghule PN, Toor R, Dillac L, Perelman J, Boyd J, Lian JB, Gordon JA, Frietze S, Van Wijnen A, Stein JL, Stein GS. Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle. Crit Rev Eukaryot Gene Expr 2023; 33:85-97. [PMID: 37017672 PMCID: PMC10826887 DOI: 10.1615/critreveukaryotgeneexpr.2022046190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Rabail Toor
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Louis Dillac
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Jonah Perelman
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Joseph Boyd
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Johnathan A.R. Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Seth Frietze
- University of Vermont Cancer Center, Burlington, Vermont, USA
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Andre Van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
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87
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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88
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Osman A, Lindén M, Österlund T, Vannas C, Andersson L, Escobar M, Ståhlberg A, Åman P. Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP. Exp Cell Res 2023; 422:113418. [PMID: 36402425 DOI: 10.1016/j.yexcr.2022.113418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene in several types of cancer. DDIT3 was originally believed to act as a dominant-negative inhibitor by forming heterodimers with other bZIP transcription factors, preventing their DNA binding and transactivating functions. DDIT3 has, however, been reported to bind DNA and regulate target genes. Here, we employed ChIP sequencing combined with microarray-based expression analysis to identify direct binding motifs and target genes of DDIT3. The results reveal DDIT3 binding to motifs similar to other bZIP transcription factors, known to form heterodimers with DDIT3. Binding to a class III satellite DNA repeat sequence was also detected. DDIT3 acted as a DNA-binding transcription factor and bound mainly to the promotor region of regulated genes. ChIP sequencing analysis of histone H3K27 methylation and acetylation showed a strong overlap between H3K27-acetylated marks and DDIT3 binding. These results support a role for DDIT3 as a transcriptional regulator of H3K27ac-marked genes in transcriptionally active chromatin.
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Affiliation(s)
- Ayman Osman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Malin Lindén
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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89
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Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol 2023; 30:38-51. [PMID: 36550219 PMCID: PMC9851908 DOI: 10.1038/s41594-022-00892-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-dimensional interaction preferences and which, to our knowledge, has not previously been characterized. We find that heterochromatin marked by H3K9me3, HP1α and HP1β correlates with strong compartmentalization. We demonstrate that disruption of DNA methyltransferase activity greatly remodels genome compartmentalization whereby domains lose H3K9me3-HP1α/β binding and acquire the neutrally interacting state while retaining late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the silent portion of the genome and establishes connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.
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Affiliation(s)
- George Spracklin
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Nezar Abdennur
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Neil Chowdhury
- Program for Research in Mathematics, Engineering and Science for High School Students (PRIMES), MIT, Cambridge, MA, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, USA.
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90
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Shah R, Gallardo CM, Jung YH, Clock B, Dixon JR, McFadden WM, Majumder K, Pintel DJ, Corces VG, Torbett BE, Tedbury PR, Sarafianos SG. Activation of HIV-1 proviruses increases downstream chromatin accessibility. iScience 2022; 25:105490. [PMID: 36505924 PMCID: PMC9732416 DOI: 10.1016/j.isci.2022.105490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
It is unclear how the activation of HIV-1 transcription affects chromatin structure. We interrogated chromatin organization both genome-wide and nearby HIV-1 integration sites using Hi-C and ATAC-seq. In conjunction, we analyzed the transcription of the HIV-1 genome and neighboring genes. We found that long-range chromatin contacts did not differ significantly between uninfected cells and those harboring an integrated HIV-1 genome, whether the HIV-1 genome was actively transcribed or inactive. Instead, the activation of HIV-1 transcription changes chromatin accessibility immediately downstream of the provirus, demonstrating that HIV-1 can alter local cellular chromatin structure. Finally, we examined HIV-1 and neighboring host gene transcripts with long-read sequencing and found populations of chimeric RNAs both virus-to-host and host-to-virus. Thus, multiomics profiling revealed that the activation of HIV-1 transcription led to local changes in chromatin organization and altered the expression of neighboring host genes.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Christian M. Gallardo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yoonhee H. Jung
- Department of Biology, Emory University, Atlanta, GA 30329, USA
| | - Ben Clock
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William M. McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Kinjal Majumder
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | | | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
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91
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Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ, Phanstiel DH, Love MI. CTCF: an R/bioconductor data package of human and mouse CTCF binding sites. BIOINFORMATICS ADVANCES 2022; 2:vbac097. [PMID: 36699364 PMCID: PMC9793704 DOI: 10.1093/bioadv/vbac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data. Availability and implementation https://bioconductor.org/packages/CTCF. Companion website: https://dozmorovlab.github.io/CTCF/; Code to reproduce the analyses: https://github.com/dozmorovlab/CTCF.dev. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stuart Lee
- Department of Econometrics and Business Statistics, Monash University, Clayton, NC 3168, Australia,Molecular Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA,Department of Pediatrics, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA,Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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92
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Zhao X, Zhu S, Peng W, Xue HH. The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2269-2278. [PMID: 36469845 PMCID: PMC9731349 DOI: 10.4049/jimmunol.2200625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 01/04/2023]
Abstract
T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.
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Affiliation(s)
- Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ 07018
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93
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Gaspar AD, Cuddapah S. Nickel-induced alterations to chromatin structure and function. Toxicol Appl Pharmacol 2022; 457:116317. [PMID: 36400264 PMCID: PMC9722551 DOI: 10.1016/j.taap.2022.116317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Nickel (Ni), a heavy metal is prevalent in the atmosphere due to both natural and anthropogenic activities. Ni is a carcinogen implicated in the development of lung and nasal cancers in humans. Furthermore, Ni exposure is associated with a number of chronic lung diseases in humans including asthma, chronic bronchitis, emphysema, pulmonary fibrosis, pulmonary edema and chronic obstructive pulmonary disease (COPD). While Ni compounds are weak mutagens, a number of studies have demonstrated the potential of Ni to alter the epigenome, suggesting epigenomic dysregulation as an important underlying cause for its pathogenicity. In the eukaryotic nucleus, the DNA is organized in a three-dimensional (3D) space through assembly of higher order chromatin structures. Such an organization is critically important for transcription and other biological activities. Accumulating evidence suggests that by negatively affecting various cellular regulatory processes, Ni could potentially affect chromatin organization. In this review, we discuss the role of Ni in altering the chromatin architecture, which potentially plays a major role in Ni pathogenicity.
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Affiliation(s)
- Adrian Domnic Gaspar
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Suresh Cuddapah
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA.
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94
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Al-Maslamani NA, Oldershaw R, Tew S, Curran J, D’Hooghe P, Yamamoto K, Horn HF. Chondrocyte De-Differentiation: Biophysical Cues to Nuclear Alterations. Cells 2022; 11:cells11244011. [PMID: 36552775 PMCID: PMC9777101 DOI: 10.3390/cells11244011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Autologous chondrocyte implantation (ACI) is a cell therapy to repair cartilage defects. In ACI a biopsy is taken from a non-load bearing area of the knee and expanded in-vitro. The expansion process provides the benefit of generating a large number of cells required for implantation; however, during the expansion these cells de-differentiate and lose their chondrocyte phenotype. In this review we focus on examining the de-differentiation phenotype from a mechanobiology and biophysical perspective, highlighting some of the nuclear mechanics and chromatin changes in chondrocytes seen during the expansion process and how this relates to the gene expression profile. We propose that manipulating chondrocyte nuclear architecture and chromatin organization will highlight mechanisms that will help to preserve the chondrocyte phenotype.
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Affiliation(s)
- Noor A. Al-Maslamani
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
- Correspondence:
| | - Rachel Oldershaw
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Simon Tew
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Jude Curran
- Department of Mechanical, Materials and Aerospace Engineering, School of Engineering, University of Liverpool, Liverpool L69 3GH, UK
| | - Pieter D’Hooghe
- Department of Orthopaedic Surgery, Aspetar Orthopaedic and Sports Medicine Hospital, Doha P.O. Box 29222, Qatar
| | - Kazuhiro Yamamoto
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Henning F. Horn
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
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95
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Jiang L, Liu Y, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Luo X, Liu Z, Chae H, Que Q, Liu Z. CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants. Transgenic Res 2022; 31:647-660. [PMID: 36053433 DOI: 10.1007/s11248-022-00326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/15/2022] [Indexed: 01/20/2023]
Abstract
Insulators in vertebrates play a role in genome architecture and orchestrate temporo-spatial enhancer-promoter interactions. In plants, insulators and their associated binding factors have not been documented as of yet, largely as a result of a lack of characterized insulators. In this study, we took a comprehensive strategy to identify and validate the enhancer-blocking insulator CW198. We show that a 1.08-kb CW198 fragment from Arabidopsis can, when interposed between an enhancer and a promoter, efficiently abrogate the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and tobacco plants. In plants, both transcriptional crosstalk and spreading of histone modifications were rarely detectable across CW198, which resembles the insulation property observed across the CTCF insulator in the mammalian genome. Taken together, our findings support that CW198 acts as an enhancer-blocking insulator in both Arabidopsis and tobacco. The significance of the present findings and their relevance to the mitigation of mutual interference between enhancers and promoters, as well as multiple promoters in transgenes, is discussed.
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Affiliation(s)
- Li Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhifeng Wen
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingjun Yang
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.,Forestry College, Henan University of Science and Technology, Luoyang, 471023, China
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Dennis Bennett
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhifang Yu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Josh Cohn
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Hyunsook Chae
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Zongrang Liu
- USDA-ARS, -Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA.
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96
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Mandal M, Banerjee I, Mandal M. Nanoparticle-mediated gene therapy as a novel strategy for the treatment of retinoblastoma. Colloids Surf B Biointerfaces 2022; 220:112899. [DOI: 10.1016/j.colsurfb.2022.112899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022]
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97
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From Nucleus to Organs: Insights of Aryl Hydrocarbon Receptor Molecular Mechanisms. Int J Mol Sci 2022; 23:ijms232314919. [PMID: 36499247 PMCID: PMC9738205 DOI: 10.3390/ijms232314919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a markedly established regulator of a plethora of cellular and molecular processes. Its initial role in the detoxification of xenobiotic compounds has been partially overshadowed by its involvement in homeostatic and organ physiology processes. In fact, the discovery of its ability to bind specific target regulatory sequences has allowed for the understanding of how AHR modulates such processes. Thereby, AHR presents functions in transcriptional regulation, chromatin architecture modifications and participation in different key signaling pathways. Interestingly, such fields of influence end up affecting organ and tissue homeostasis, including regenerative response both to endogenous and exogenous stimuli. Therefore, from classical spheres such as canonical transcriptional regulation in embryonic development, cell migration, differentiation or tumor progression to modern approaches in epigenetics, senescence, immune system or microbiome, this review covers all aspects derived from the balance between regulation/deregulation of AHR and its physio-pathological consequences.
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98
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Hirayama T, Kadooka Y, Tarusawa E, Saitoh S, Nakayama H, Hoshino N, Nakama S, Fukuishi T, Kawanishi Y, Umeshima H, Tomita K, Yoshimura Y, Galjart N, Hashimoto K, Ohno N, Yagi T. CTCF loss induces giant lamellar bodies in Purkinje cell dendrites. Acta Neuropathol Commun 2022; 10:172. [PMID: 36447271 PMCID: PMC9706876 DOI: 10.1186/s40478-022-01478-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
CCCTC-binding factor (CTCF) has a key role in higher-order chromatin architecture that is important for establishing and maintaining cell identity by controlling gene expression. In the mature cerebellum, CTCF is highly expressed in Purkinje cells (PCs) as compared with other cerebellar neurons. The cerebellum plays an important role in motor function by regulating PCs, which are the sole output neurons, and defects in PCs cause motor dysfunction. However, the role of CTCF in PCs has not yet been explored. Here we found that the absence of CTCF in mouse PCs led to progressive motor dysfunction and abnormal dendritic morphology in those cells, which included dendritic self-avoidance defects and a proximal shift in the climbing fibre innervation territory on PC dendrites. Furthermore, we found the peculiar lamellar structures known as "giant lamellar bodies" (GLBs), which have been reported in PCs of patients with Werdnig-Hoffman disease, 13q deletion syndrome, and Krabbe disease. GLBs are localized to PC dendrites and are assumed to be associated with neurodegeneration. They have been noted, however, only in case reports following autopsy, and reports of their existence have been very limited. Here we show that GLBs were reproducibly formed in PC dendrites of a mouse model in which CTCF was deleted. GLBs were not noted in PC dendrites at infancy but instead developed over time. In conjunction with GLB development in PC dendrites, the endoplasmic reticulum was almost absent around the nuclei, the mitochondria were markedly swollen and their cristae had decreased drastically, and almost all PCs eventually disappeared as severe motor deficits manifested. Our results revealed the important role of CTCF during normal development and in maintaining PCs and provide new insights into the molecular mechanism of GLB formation during neurodegenerative disease.
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Affiliation(s)
- Teruyoshi Hirayama
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan ,grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yuuki Kadooka
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Etsuko Tarusawa
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Sei Saitoh
- grid.467811.d0000 0001 2272 1771Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787 Japan ,grid.256115.40000 0004 1761 798XDepartment of Anatomy II and Cell Biology, Fujita Health University School of Medicine, 1-98 Dengakubo, Kutsukake-cho, Toyoake, 470-1192 Japan
| | - Hisako Nakayama
- grid.410818.40000 0001 0720 6587Department of Physiology, Division of Neurophysiology, School of Medicine, Tokyo Women’s Medical University, Tokyo, 162-8666 Japan ,grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Natsumi Hoshino
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Soichiro Nakama
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Takahiro Fukuishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yudai Kawanishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Hiroki Umeshima
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Koichi Tomita
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yumiko Yoshimura
- grid.467811.d0000 0001 2272 1771Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan ,grid.275033.00000 0004 1763 208XDepartment of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 Japan
| | - Niels Galjart
- grid.5645.2000000040459992XDepartment of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Kouichi Hashimoto
- grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Nobuhiko Ohno
- grid.467811.d0000 0001 2272 1771Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan ,grid.410804.90000000123090000Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Takeshi Yagi
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
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99
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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100
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Zelenka T, Klonizakis A, Tsoukatou D, Papamatheakis DA, Franzenburg S, Tzerpos P, Tzonevrakis IR, Papadogkonas G, Kapsetaki M, Nikolaou C, Plewczynski D, Spilianakis C. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun 2022; 13:6954. [PMID: 36376298 PMCID: PMC9663569 DOI: 10.1038/s41467-022-34345-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Despina Tsoukatou
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, HU-4032, Hungary
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming", 16672, Vari, Greece
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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