101
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Alharbi AB, Schmitz U, Bailey CG, Rasko JEJ. CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Res 2021; 49:7825-7838. [PMID: 34181707 PMCID: PMC8373115 DOI: 10.1093/nar/gkab520] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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102
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Cao F, Zhang Y, Cai Y, Animesh S, Zhang Y, Akincilar SC, Loh YP, Li X, Chng WJ, Tergaonkar V, Kwoh CK, Fullwood MJ. Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences. Genome Biol 2021; 22:226. [PMID: 34399797 PMCID: PMC8365954 DOI: 10.1186/s13059-021-02453-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/04/2021] [Indexed: 11/10/2022] Open
Abstract
Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.
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Affiliation(s)
- Fan Cao
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Block N4, 50 Nanyang Avenue, Singapore, 639798 Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Sambhavi Animesh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Semih Can Akincilar
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
| | - Yan Ping Loh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Xinya Li
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore, 119228 Singapore
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, NUH Zone B, Medical Centre, Singapore, 119074 Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117597 Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Block N4, 50 Nanyang Avenue, Singapore, 639798 Singapore
| | - Melissa J. Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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103
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Kojima T, Maeda T, Suzuki A, Yamamori T, Kato Y. Intracellular zinc-dependent TAS2R8 gene expression through CTCF activation. Biomed Res 2021; 41:217-225. [PMID: 33071257 DOI: 10.2220/biomedres.41.217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Taste-2 receptors (TAS2Rs), which belong to the G-protein coupled receptor (GPCR) family, are receptors for bitter taste perception. The aim of this study was to investigate whether zinc deficiency affects the expression of TAS2R genes. The promoter activity of the TAS2R7, TAS2R8, and TAS2R42 genes were determined in Ca9-22 oral squamous cell carcinoma cells cultured in the presence or absence of zinc. Luciferase reporter assays showed that zinc deprivation inhibited TAS2R8 promoter activity, but not the promoter activity of the other two genes. Treatment of the cells with N,N,N',N'-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), an intracellular chelator of Zn2+, in the presence of 10% fetal bovine serum reduced TAS2R8 promoter activity. Truncation/deletion mutants of TAS2R8 promoter-luciferase constructs showed that the region from nucleotide -1152 to nucleotide -925 was critical for intracellular zinc dependency and contained a CCCTC-binding factor (CTCF) binding motif. A chromatin immunoprecipitation (ChiP) assay showed that CTCF bound specifically to this region, a binding abrogated by zinc deficiency, suggesting that CTCF plays a critical role in zinc-dependent bitter taste perception through TAS2R8.
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Affiliation(s)
- Tsuyoshi Kojima
- Departments of Oral Rehabilitation, Ohu University Graduate School of Dentistry
| | - Toyonobu Maeda
- Departments of Oral Rehabilitation, Ohu University Graduate School of Dentistry.,Departments of Oral Function and Molecular Biology, Ohu University School of Dentistry
| | - Atsuko Suzuki
- Departments of Oral Function and Molecular Biology, Ohu University School of Dentistry
| | - Tetsuo Yamamori
- Departments of Oral Rehabilitation, Ohu University Graduate School of Dentistry.,Departments of Prosthetic Dentistry, Ohu University School of Dentistry
| | - Yasumasa Kato
- Departments of Oral Function and Molecular Biology, Ohu University School of Dentistry.,Departments of Oral Physiology and Biochemistry, Ohu University Graduate School of Dentistry
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104
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Exploring chromatin structural roles of non-coding RNAs at imprinted domains. Biochem Soc Trans 2021; 49:1867-1879. [PMID: 34338292 PMCID: PMC8421051 DOI: 10.1042/bst20210758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.
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105
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CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nat Cell Biol 2021; 23:881-893. [PMID: 34326481 DOI: 10.1038/s41556-021-00722-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.
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106
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Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood 2021; 137:1327-1339. [PMID: 33512425 DOI: 10.1182/blood.2020005780] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/05/2020] [Indexed: 11/20/2022] Open
Abstract
While constitutive CCCTC-binding factor (CTCF)-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell-type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell-type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single-nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR-Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell-type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell-type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.
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107
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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108
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Making it or breaking it: DNA methylation and genome integrity. Essays Biochem 2021; 64:687-703. [PMID: 32808652 DOI: 10.1042/ebc20200009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
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109
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Samimi A, Khodayar MJ, Alidadi H, Khodadi E. The Dual Role of ROS in Hematological Malignancies: Stem Cell Protection and Cancer Cell Metastasis. Stem Cell Rev Rep 2021; 16:262-275. [PMID: 31912368 DOI: 10.1007/s12015-019-09949-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND OBJECTIVE Reactive oxygen species (ROS) play crucial role in hematopoiesis, regulation of differentiation, self-renewal, and the balance between quiescence and proliferation of hematopoietic stem cells (HSCs). The HSCs are a small population of undifferentiated cells that reside in the bone marrow (BM) and can undergo self-renewal by giving rise to mature cells. METHODS Relevant literature was identified through a PubMed search (2000-2019) of English-language papers using the following terms: reactive oxygen species, hematopoietic stem cell, leukemic stem cell, leukemia and chemotherapy. RESULTS HSCs are very sensitive to high levels of ROS and increased production of ROS have been attributed to HSC aging. HSC aging induced by both cell intrinsic and extrinsic factors is linked to impaired HSC self-renewal and regeneration. In addition, the elevated ROS levels might even trigger differentiation of Leukemic stem cells (LSCs) and ROS may be involved in the initiation and progression of hematological malignancies, such as leukemia. CONCLUSION Targeting genes involved in ROS in LSCs and HSCs are increasingly being used as a critical target for therapeutic interventions. Appropriate concentration of ROS may be an optimal therapeutic target for treatment of leukemia during chemotherapy, but still more studies are required to better understanding of the of ROS role in blood disorders.
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Affiliation(s)
- Azin Samimi
- Department of Toxicology, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Legal Medicine Organization, Legal Medicine Research Center, Ahvaz, Iran
| | - Mohammad Javad Khodayar
- Department of Toxicology, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hadis Alidadi
- Department of Toxicology, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Elahe Khodadi
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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110
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Cheng X, Joseph A, Castro V, Chen-Liaw A, Skidmore Z, Ueno T, Fujisawa JI, Rauch DA, Challen GA, Martinez MP, Green P, Griffith M, Payton JE, Edwards JR, Ratner L. Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF. PLoS Pathog 2021; 17:e1009577. [PMID: 34019588 PMCID: PMC8174705 DOI: 10.1371/journal.ppat.1009577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/03/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that causes an aggressive T-cell malignancy and a variety of inflammatory conditions. The integrated provirus includes a single binding site for the epigenomic insulator, CCCTC-binding protein (CTCF), but its function remains unclear. In the current study, a mutant virus was examined that eliminates the CTCF-binding site. The mutation did not disrupt the kinetics and levels of virus gene expression, or establishment of or reactivation from latency. However, the mutation disrupted the epigenetic barrier function, resulting in enhanced DNA CpG methylation downstream of the CTCF binding site on both strands of the integrated provirus and H3K4Me3, H3K36Me3, and H3K27Me3 chromatin modifications both up- and downstream of the site. A majority of clonal cell lines infected with wild type HTLV-1 exhibited increased plus strand gene expression with CTCF knockdown, while expression in mutant HTLV-1 clonal lines was unaffected. These findings indicate that CTCF binding regulates HTLV-1 gene expression, DNA and histone methylation in an integration site dependent fashion. Human T-cell leukemia virus type 1 (HTLV-1) is a cause of leukemia and lymphoma as well as several inflammatory medical disorders. The virus integrates in the host cell DNA, and it has a single binding site for a protein designated CTCF. This protein is important in the regulation of many DNA viruses, as well as many properties of normal and malignant cells. In order to define the role of CTCF binding to HTLV, we analyzed a mutant virus lacking the binding site. We found that this mutation variably affected gene expression, DNA and histone modification, suggesting a key role in regulation of virus replication in infected cells.
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Affiliation(s)
- Xiaogang Cheng
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ancy Joseph
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Victor Castro
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Alice Chen-Liaw
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Zachary Skidmore
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Takaharu Ueno
- Department of Microbiology, Kansai Medical University, Osaka, Japan
| | | | - Daniel A. Rauch
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Grant A. Challen
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Michael P. Martinez
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Patrick Green
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jacqueline E. Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John R. Edwards
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Phamacogenomics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
- * E-mail:
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111
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DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift. Commun Biol 2021; 4:598. [PMID: 34011964 PMCID: PMC8134454 DOI: 10.1038/s42003-021-02116-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/14/2021] [Indexed: 12/27/2022] Open
Abstract
Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift. Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.
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112
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Chyr J, Zhang Z, Chen X, Zhou X. PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. Comput Struct Biotechnol J 2021; 19:2870-2880. [PMID: 34093998 PMCID: PMC8142020 DOI: 10.1016/j.csbj.2021.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 10/26/2022] Open
Abstract
Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. In our study, we addressed the relationship between multi-omics data and higher-order chromatin structures using a newly developed machine-learning model called PredTAD. Our tool uses already-available and cost-effective datatypes such as transcription factor and histone modification ChIPseq data. Specifically, PredTAD utilizes both epigenetic and genetic features as well as neighboring information to classify the entire human genome as boundary or non-boundary regions. Our tool can predict boundary changes between normal and breast cancer genomes. Among the most important features for predicting boundary alterations were CTCF, subunits of cohesin (RAD21 and SMC3), and chromosome number, suggesting their roles in conserved and dynamic boundaries formation. Upon further analysis, we observed that genes near altered TAD boundaries were found to be involved in several important breast cancer signaling pathways such as Ras, Jak-STAT, and estrogen signaling pathways. We also discovered a TAD boundary alteration that contributes to RET oncogene overexpression. PredTAD can also successfully predict TAD boundary changes in other conditions and diseases. In conclusion, our newly developed machine learning tool allowed for a more complete understanding of the dynamic 3D chromatin structures involved in signaling pathway activation, altered gene expression, and disease state in breast cancer cells.
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Affiliation(s)
- Jacqueline Chyr
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Zhigang Zhang
- School of Information Management and Statistics, Hubei University of Economics, Wuhan, Hubei 430205 China
| | - Xi Chen
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
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113
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Kaneko S, Mitsuyama T, Shiraishi K, Ikawa N, Shozu K, Dozen A, Machino H, Asada K, Komatsu M, Kukita A, Sone K, Yoshida H, Motoi N, Hayami S, Yoneoka Y, Kato T, Kohno T, Natsume T, von Keudell G, Saloura V, Yamaue H, Hamamoto R. Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential. Cancers (Basel) 2021; 13:cancers13092126. [PMID: 33924956 PMCID: PMC8125448 DOI: 10.3390/cancers13092126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Although chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) using formalin-fixed paraffin-embedded tissue (FFPE) has been reported, it remained elusive whether they retained accurate transcription factor binding. Here, we developed a method to identify the binding sites of the insulator transcription factor CTCF and the genome-wide distribution of histone modifications involved in transcriptional activation. Importantly, we provide evidence that the ChIP-seq datasets obtained from FFPE samples are similar to or even better than the data for corresponding fresh-frozen samples, indicating that FFPE samples are compatible with ChIP-seq analysis. H3K27ac ChIP-seq analyses of 69 FFPE samples using a dual-arm robot revealed that driver mutations in EGFR were distinguishable from pan-negative cases and were relatively homogeneous as a group in lung adenocarcinomas. Thus, our results demonstrate that FFPE samples are an important source for epigenomic research, enabling the study of histone modifications, nuclear chromatin structure, and clinical data.
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Affiliation(s)
- Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
- Correspondence: (S.K.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
| | - Toutai Mitsuyama
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (K.S.); (T.K.)
| | - Noriko Ikawa
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
| | - Kanto Shozu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
| | - Ai Dozen
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
| | - Hidenori Machino
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Masaaki Komatsu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Asako Kukita
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; (A.K.); (K.S.)
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; (A.K.); (K.S.)
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan; (H.Y.); (N.M.)
| | - Noriko Motoi
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan; (H.Y.); (N.M.)
| | - Shinya Hayami
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama 641-0011, Japan; (S.H.); (H.Y.)
| | - Yutaka Yoneoka
- Department of Gynecology, National Cancer Center Hospital, Tokyo 104-0045, Japan; (Y.Y.); (T.K.)
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center Hospital, Tokyo 104-0045, Japan; (Y.Y.); (T.K.)
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (K.S.); (T.K.)
| | - Toru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 100-8921, Japan;
- Robotic Biology Institute, Inc., Tokyo 135-0064, Japan
| | | | - Vassiliki Saloura
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA;
| | - Hiroki Yamaue
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama 641-0011, Japan; (S.H.); (H.Y.)
| | - Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (N.I.); (K.S.); (A.D.); (H.M.); (K.A.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
- Correspondence: (S.K.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
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Pinsach-Abuin M, del Olmo B, Pérez-Agustin A, Mates J, Allegue C, Iglesias A, Ma Q, Merkurjev D, Konovalov S, Zhang J, Sheikh F, Telenti A, Brugada J, Brugada R, Gymrek M, di Iulio J, Garcia-Bassets I, Pagans S. Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants. Cell Rep Med 2021; 2:100250. [PMID: 33948580 PMCID: PMC8080235 DOI: 10.1016/j.xcrm.2021.100250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/07/2021] [Accepted: 03/23/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide association studies (GWASs) are instrumental in identifying loci harboring common single-nucleotide variants (SNVs) that affect human traits and diseases. GWAS hits emerge in clusters, but the focus is often on the most significant hit in each trait- or disease-associated locus. The remaining hits represent SNVs in linkage disequilibrium (LD) and are considered redundant and thus frequently marginally reported or exploited. Here, we interrogate the value of integrating the full set of GWAS hits in a locus repeatedly associated with cardiac conduction traits and arrhythmia, SCN5A-SCN10A. Our analysis reveals 5 common 7-SNV haplotypes (Hap1-5) with 2 combinations associated with life-threatening arrhythmia-Brugada syndrome (the risk Hap1/1 and protective Hap2/3 genotypes). Hap1 and Hap2 share 3 SNVs; thus, this analysis suggests that assuming redundancy among clustered GWAS hits can lead to confounding disease-risk associations and supports the need to deconstruct GWAS data in the context of haplotype composition.
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Affiliation(s)
- Mel·lina Pinsach-Abuin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Bernat del Olmo
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Adrian Pérez-Agustin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jesus Mates
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Catarina Allegue
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Anna Iglesias
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sergiy Konovalov
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jing Zhang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Farah Sheikh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Josep Brugada
- Arrhythmia Unit, Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ramon Brugada
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
- Cardiology Service, Hospital Universitari Dr. Josep Trueta, Girona, Spain
| | - Melissa Gymrek
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Julia di Iulio
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
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115
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Xiang JF, Corces VG. Regulation of 3D chromatin organization by CTCF. Curr Opin Genet Dev 2021; 67:33-40. [PMID: 33259986 PMCID: PMC8084898 DOI: 10.1016/j.gde.2020.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 01/12/2023]
Abstract
Studies of nuclear architecture using chromosome conformation capture methods have provided a detailed view of how chromatin folds in the 3D nuclear space. New variants of this technology now afford unprecedented resolution and allow the identification of ever smaller folding domains that offer new insights into the mechanisms by which this organization is established and maintained. Here we review recent results in this rapidly evolving field with an emphasis on CTCF function, with the goal of gaining a mechanistic understanding of the principles by which chromatin is folded in the eukaryotic nucleus.
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Affiliation(s)
- Jian-Feng Xiang
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA
| | - Victor G Corces
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA.
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116
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Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, Feng FY, Boutros PC, Lupien M, Zoubeidi A, Wang L, Walsh MJ, Wang T, Ren S, Wei GH, He HH. CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer. Nat Commun 2021; 12:1781. [PMID: 33741908 PMCID: PMC7979745 DOI: 10.1038/s41467-021-21867-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/18/2021] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) risk-associated SNPs are enriched in noncoding cis-regulatory elements (rCREs), yet their modi operandi and clinical impact remain elusive. Here, we perform CRISPRi screens of 260 rCREs in PCa cell lines. We find that rCREs harboring high risk SNPs are more essential for cell proliferation and H3K27ac occupancy is a strong indicator of essentiality. We also show that cell-line-specific essential rCREs are enriched in the 8q24.21 region, with the rs11986220-containing rCRE regulating MYC and PVT1 expression, cell proliferation and tumorigenesis in a cell-line-specific manner, depending on DNA methylation-orchestrated occupancy of a CTCF binding site in between this rCRE and the MYC promoter. We demonstrate that CTCF deposition at this site as measured by DNA methylation level is highly variable in prostate specimens, and observe the MYC eQTL in the 8q24.21 locus in individuals with low CTCF binding. Together our findings highlight a causal mechanism synergistically driven by a risk SNP and DNA methylation-mediated 3D genome architecture, advocating for the integration of genetics and epigenetics in assessing risks conferred by genetic predispositions.
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Affiliation(s)
- Musaddeque Ahmed
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Fraser Soares
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Ji-Han Xia
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Yue Yang
- Changhai Hospital, Shanghai, China
| | - Jing Li
- Changhai Hospital, Shanghai, China
| | - Haiyang Guo
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Peiran Su
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Miranda Wang
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Nayeema Akhtar
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Kathleen E Houlahan
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Almudena Bosch
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stanley Zhou
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Junjie T Hua
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sujun Chen
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jessica Petricca
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yong Zeng
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
| | - Alastair Davies
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Michael Fraser
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Vector Institute, Toronto, ON, Canada
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mathieu Lupien
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Amina Zoubeidi
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center, School of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Housheng Hansen He
- Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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117
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Genomic Space of MGMT in Human Glioma Revisited: Novel Motifs, Regulatory RNAs, NRF1, 2, and CTCF Involvement in Gene Expression. Int J Mol Sci 2021; 22:ijms22052492. [PMID: 33801310 PMCID: PMC7958331 DOI: 10.3390/ijms22052492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The molecular regulation of increased MGMT expression in human brain tumors, the associated regulatory elements, and linkages of these to its epigenetic silencing are not understood. Because the heightened expression or non-expression of MGMT plays a pivotal role in glioma therapeutics, we applied bioinformatics and experimental tools to identify the regulatory elements in the MGMT and neighboring EBF3 gene loci. Results: Extensive genome database analyses showed that the MGMT genomic space was rich in and harbored many undescribed RNA regulatory sequences and recognition motifs. We extended the MGMT’s exon-1 promoter to 2019 bp to include five overlapping alternate promoters. Consensus sequences in the revised promoter for (a) the transcriptional factors CTCF, NRF1/NRF2, GAF, (b) the genetic switch MYC/MAX/MAD, and (c) two well-defined p53 response elements in MGMT intron-1, were identified. A putative protein-coding or non-coding RNA sequence was located in the extended 3′ UTR of the MGMT transcript. Eleven non-coding RNA loci coding for miRNAs, antisense RNA, and lncRNAs were identified in the MGMT-EBF3 region and six of these showed validated potential for curtailing the expression of both MGMT and EBF3 genes. ChIP analysis verified the binding site in MGMT promoter for CTCF which regulates the genomic methylation and chromatin looping. CTCF depletion by a pool of specific siRNA and shRNAs led to a significant attenuation of MGMT expression in human GBM cell lines. Computational analysis of the ChIP sequence data in ENCODE showed the presence of NRF1 in the MGMT promoter and this occurred only in MGMT-proficient cell lines. Further, an enforced NRF2 expression markedly augmented the MGMT mRNA and protein levels in glioma cells. Conclusions: We provide the first evidence for several new regulatory components in the MGMT gene locus which predict complex transcriptional and posttranscriptional controls with potential for new therapeutic avenues.
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118
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AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding. Blood 2021; 136:339-352. [PMID: 32232485 DOI: 10.1182/blood.2019002326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022] Open
Abstract
CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.
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119
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Jefferys SR, Burgos SD, Peterson JJ, Selitsky SR, Turner AMW, James LI, Tsai YH, Coffey AR, Margolis DM, Parker J, Browne EP. Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors. PLoS Pathog 2021; 17:e1009346. [PMID: 33635929 PMCID: PMC7946360 DOI: 10.1371/journal.ppat.1009346] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/10/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
Transcriptional silencing of HIV in CD4 T cells generates a reservoir of latently infected cells that can reseed infection after interruption of therapy. As such, these cells represent the principal barrier to curing HIV infection, but little is known about their characteristics. To further our understanding of the molecular mechanisms of latency, we characterized a primary cell model of HIV latency in which infected cells adopt heterogeneous transcriptional fates. In this model, we observed that latency is a stable, heritable state that is transmitted through cell division. Using Assay of Transposon-Accessible Chromatin sequencing (ATACseq) we found that latently infected cells exhibit greatly reduced proviral accessibility, indicating the presence of chromatin-based structural barriers to viral gene expression. By quantifying the activity of host cell transcription factors, we observe elevated activity of Forkhead and Kruppel-like factor transcription factors (TFs), and reduced activity of AP-1, RUNX and GATA TFs in latently infected cells. Interestingly, latency reversing agents with different mechanisms of action caused distinct patterns of chromatin reopening across the provirus. We observe that binding sites for the chromatin insulator CTCF are highly enriched in the differentially open chromatin of infected CD4 T cells. Furthermore, depletion of CTCF inhibited HIV latency, identifying this factor as playing a key role in the initiation or enforcement of latency. These data indicate that HIV latency develops preferentially in cells with a distinct pattern of TF activity that promotes a closed proviral structure and inhibits viral gene expression. Furthermore, these findings identify CTCF as a novel regulator of HIV latency. HIV is able to persist during antiviral therapy by entering a state of viral latency, in which viral gene expression is greatly reduced. These latently infected cells can re-seed infection if therapy is interrupted, and thus represent a major obstacle to an HIV cure. Identifying the mechanisms that lead to this state will help to identify strategies to block or eliminate HIV latency, leading to a cure for infection. By observing HIV gene expression in infected CD4 T cells, we isolated cells in which HIV has entered latency and identified characteristics that distinguish them from cells with active viral replication. We found that latently infected cells have elevated activity of specific transcription factors including Forkhead TFs and Kruppel-like factors. We also identify CTCF, a protein responsible for mediating insulation of genome domains from each other, as being required for the establishment of HIV latency. Developing agents to target these factors may lead to new strategies to eliminate the HIV reservoir.
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Affiliation(s)
- Stuart R. Jefferys
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Samuel D. Burgos
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jackson J. Peterson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara R. Selitsky
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anne-Marie W. Turner
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lindsey I. James
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yi-Hsuan Tsai
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alisha R. Coffey
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joel Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Edward P. Browne
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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120
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Luo X, Zhang T, Zhai Y, Wang F, Zhang S, Wang G. Effects of DNA Methylation on TFs in Human Embryonic Stem Cells. Front Genet 2021; 12:639461. [PMID: 33708244 PMCID: PMC7940757 DOI: 10.3389/fgene.2021.639461] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/14/2021] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism for gene regulation. The conventional view of DNA methylation is that DNA methylation could disrupt protein-DNA interactions and repress gene expression. Several recent studies reported that DNA methylation could alter transcription factors (TFs) binding sequence specificity in vitro. Here, we took advantage of the large sets of ChIP-seq data for TFs and whole-genome bisulfite sequencing data in many cell types to perform a systematic analysis of the protein-DNA methylation in vivo. We observed that many TFs could bind methylated DNA regions, especially in H1-hESC cells. By locating binding sites, we confirmed that some TFs could bind to methylated CpGs directly. The different proportion of CpGs at TF binding specificity motifs in different methylation statuses shows that some TFs are sensitive to methylation and some could bind to the methylated DNA with different motifs, such as CEBPB and CTCF. At the same time, TF binding could interactively alter local DNA methylation. The TF hypermethylation binding sites extensively overlap with enhancers. And we also found that some DNase I hypersensitive sites were specifically hypermethylated in H1-hESC cells. At last, compared with TFs' binding regions in multiple cell types, we observed that CTCF binding to high methylated regions in H1-hESC were not conservative. These pieces of evidence indicate that TFs that bind to hypermethylation DNA in H1-hESC cells may associate with enhancers to regulate special biological functions.
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Affiliation(s)
- Ximei Luo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianjiao Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yixiao Zhai
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Fang Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shumei Zhang
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Guohua Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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121
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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122
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Noble AJ, Pearson JF, Boden JM, Horwood LJ, Gemmell NJ, Kennedy MA, Osborne AJ. A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing. PeerJ 2021; 9:e10762. [PMID: 33614276 PMCID: PMC7881719 DOI: 10.7717/peerj.10762] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
The Illumina Infinium® MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are often used for hypothesis generation or pilot studies, the natural conclusion to which is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system at some loci. However, BSAS correlated less well with EPIC array data in some instances, and most notably, when the magnitude of change via EPIC array was greater than 5%. Therefore, our data suggests that BSAS can be used to validate EPIC array data, but each locus must be compared on an individual basis, before being taken forward into large scale screening. Further, BSAS does offer advantages compared to the probe-based EPIC array; BSAS amplifies a region of the genome (∼500 bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system.
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Affiliation(s)
- Alexandra J Noble
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Sciences, University of Otago, Christchurch, New Zealand
| | - Joseph M Boden
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - L John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, Univeristy of Otago, Dunedin, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Sciences, University of Otago, Christchurch, New Zealand
| | - Amy J Osborne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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123
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Quilter CR, Harvey KM, Bauer J, Skinner BM, Gomez M, Shrivastava M, Doel AM, Drammeh S, Dunger DB, Moore SE, Ong KK, Prentice AM, Bernstein RM, Sargent CA, Affara NA. Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA. FASEB Bioadv 2021; 3:205-230. [PMID: 33842847 PMCID: PMC8019263 DOI: 10.1096/fba.2020-00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Low birthweight and reduced height gain during infancy (stunting) may arise at least in part from adverse early life environments that trigger epigenetic reprogramming that may favor survival. We examined differential DNA methylation patterns using targeted methyl sequencing of regions regulating gene activity in groups of rural Gambian infants: (a) low and high birthweight (DNA from cord blood (n = 16 and n = 20, respectively), from placental trophoblast tissue (n = 21 and n = 20, respectively), and DNA from peripheral blood collected from infants at 12 months of age (n = 23 and n = 17, respectively)), and, (b) the top 10% showing rapid postnatal length gain (high, n = 20) and the bottom 10% showing slow postnatal length gain (low, n = 20) based on z score change between birth and 12 months of age (LAZ) (DNA from peripheral blood collected from infants at 12 months of age). Using BiSeq analysis to identify significant methylation marks, for birthweight, four differentially methylated regions (DMRs) were identified in trophoblast DNA, compared to 68 DMRs in cord blood DNA, and 54 DMRs in 12‐month peripheral blood DNA. Twenty‐five DMRs were observed to be associated with high and low length for age (LAZ) at 12 months. With the exception of five loci (associated with two different genes), there was no overlap between these groups of methylation marks. Of the 194 CpG methylation marks contained within DMRs, 106 were located to defined gene regulatory elements (promoters, CTCF‐binding sites, transcription factor‐binding sites, and enhancers), 58 to gene bodies (introns or exons), and 30 to intergenic DNA. Distinct methylation patterns associated with birthweight between comparison groups were observed in DNA collected at birth (at the end of intrauterine growth window) compared to those established by 12 months (near the infancy/childhood growth transition). The longitudinal differences in methylation patterns may arise from methylation adjustments, changes in cellular composition of blood or both that continue during the critical postnatal growth period, and in response to early nutritional and infectious environmental exposures with impacts on growth and longer‐term health outcomes.
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Affiliation(s)
- Claire R Quilter
- Department of Pathology University of Cambridge Cambridge UK.,Present address: East Midlands & East of England NHS Genomic Laboratory Hub, Genomics Laboratories Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Kerry M Harvey
- Department of Pathology University of Cambridge Cambridge UK
| | - Julien Bauer
- Department of Pathology University of Cambridge Cambridge UK
| | - Benjamin M Skinner
- Department of Pathology University of Cambridge Cambridge UK.,School of Life Sciences University of Essex Colchester UK
| | - Maria Gomez
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Kennedy Institute of Rheumatology University of Oxford Oxford UK
| | - Manu Shrivastava
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Oxford University Hospitals Oxford UK
| | - Andrew M Doel
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Saikou Drammeh
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - David B Dunger
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK
| | - Sophie E Moore
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Ken K Ong
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK.,Department of Paediatrics University of Cambridge School of Clinical Medicine Cambridge UK.,Institute of Metabolic Science Cambridge Biomedical Campus Cambridge Cambridge UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Robin M Bernstein
- Growth and Development Lab Department of Anthropology University of Colorado Boulder CO USA.,Institute of Behavioural Science University of Colorado Boulder CO USA
| | | | - Nabeel A Affara
- Department of Pathology University of Cambridge Cambridge UK
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124
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Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 2021; 28:152-161. [PMID: 33398174 PMCID: PMC7913465 DOI: 10.1038/s41594-020-00539-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/06/2020] [Indexed: 01/28/2023]
Abstract
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.
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Affiliation(s)
- Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Haruhiko Ishii
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Xiong Xiong
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Simona Bianco
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - Franz Meitinger
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James D. Hocker
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mattia Conte
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - David Gorkin
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Miao Yu
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Mario Nicodemi
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Departments of Chemistry, Biochemistry, and Bioengineering, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA,Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA,Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA,Correspondence to:
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125
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Rienzo M, Sorrentino A, Di Zazzo E, Di Donato M, Carafa V, Marino MM, De Rosa C, Gazzerro P, Castoria G, Altucci L, Casamassimi A, Abbondanza C. Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. Front Oncol 2021; 10:583533. [PMID: 33585202 PMCID: PMC7880127 DOI: 10.3389/fonc.2020.583533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Positive Regulatory Domain (PRDM) gene family members commonly express two main molecular variants, the PR-plus isoform usually acting as tumor suppressor and the PR-minus one functioning as oncogene. Accordingly, PRDM2/RIZ encodes for RIZ1 (PR-plus) and RIZ2 (PR-minus). In human cancers, genetic or epigenetic modifications induce RIZ1 silencing with an expression level imbalance in favor of RIZ2 that could be relevant for tumorigenesis. Additionally, in estrogen target cells and tissues, estradiol increases RIZ2 expression level with concurrent increase of cell proliferation and survival. Several attempts to study RIZ2 function in HeLa or MCF-7 cells by its over-expression were unsuccessful. Thus, we over-expressed RIZ2 in HEK-293 cells, which are both RIZ1 and RIZ2 positive but unresponsive to estrogens. The forced RIZ2 expression increased cell viability and growth, prompted the G2-to-M phase transition and organoids formation. Accordingly, microarray analysis revealed that RIZ2 regulates several genes involved in mitosis. Consistently, RIZ silencing in both estrogen-responsive MCF-7 and -unresponsive MDA-MB-231 cells induced a reduction of cell proliferation and an increase of apoptosis rate. Our findings add novel insights on the putative RIZ2 tumor-promoting functions, although additional attempts are warranted to depict the underlying molecular mechanism.
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Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Michela Marino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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126
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Zimak J, Wagoner ZW, Nelson N, Waechtler B, Schlosser H, Kopecky M, Wu J, Zhao W. Epigenetic silencing directs expression heterogeneity of stably integrated multi-transcript unit genetic circuits. Sci Rep 2021; 11:2424. [PMID: 33510302 PMCID: PMC7844226 DOI: 10.1038/s41598-021-81975-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
We report that epigenetic silencing causes the loss of function of multi-transcript unit constructs that are integrated using CRISPR-Cas9. Using a modular two color reporter system flanked by selection markers, we demonstrate that expression heterogeneity does not correlate with sequence alteration but instead correlates with chromosomal accessibility. We partially reverse this epigenetic silencing via small-molecule inhibitors of methylation and histone deacetylation. We then correlate each heterogeneously-expressing phenotype with its expected epigenetic state by employing ATAC-seq. The stability of each expression phenotype is reinforced by selective pressure, which indicates that ongoing epigenetic remodeling can occur for over one month after integration. Collectively, our data suggests that epigenetic silencing limits the utility of multi-transcript unit constructs that are integrated via double-strand repair pathways. Our research implies that mammalian synthetic biologists should consider localized epigenetic outcomes when designing complex genetic circuits.
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Affiliation(s)
- Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Zachary W Wagoner
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nellie Nelson
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Brooke Waechtler
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hana Schlosser
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Morgan Kopecky
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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127
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Strelnikov VV, Kuznetsova EB, Tanas AS, Rudenko VV, Kalinkin AI, Poddubskaya EV, Kekeeva TV, Chesnokova GG, Trotsenko ID, Larin SS, Kutsev SI, Zaletaev DV, Nemtsova MV, Simonova OA. Abnormal promoter DNA hypermethylation of the integrin, nidogen, and dystroglycan genes in breast cancer. Sci Rep 2021; 11:2264. [PMID: 33500458 PMCID: PMC7838398 DOI: 10.1038/s41598-021-81851-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Cell transmembrane receptors and extracellular matrix components play a pivotal role in regulating cell activity and providing for the concerted integration of cells in the tissue structures. We have assessed DNA methylation in the promoter regions of eight integrin genes, two nidogen genes, and the dystroglycan gene in normal breast tissues and breast carcinomas (BC). The protein products of these genes interact with the basement membrane proteins LAMA1, LAMA2, and LAMB1; abnormal hypermethylation of the LAMA1, LAMA2, and LAMB1 promoters in BC has been described in our previous publications. In the present study, the frequencies of abnormal promoter hypermethylation in BC were 13% for ITGA1, 31% for ITGA4, 4% for ITGA7, 39% for ITGA9, 38% for NID1, and 41% for NID2. ITGA2, ITGA3, ITGA6, ITGB1, and DAG1 promoters were nonmethylated in normal and BC samples. ITGA4, ITGA9, and NID1 promoter hypermethylation was associated with the HER2 positive tumors, and promoter hypermethylation of ITGA1, ITGA9, NID1 and NID2 was associated with a genome-wide CpG island hypermethylated BC subtype. Given that ITGA4 is not expressed in normal breast, one might suggest that its abnormal promoter hypermethylation in cancer is non-functional and is thus merely a passenger epimutation. Yet, this assumption is not supported by our finding that it is not associated with a hypermethylated BC subtype. ITGA4 acquires expression in a subset of breast carcinomas, and methylation of its promoter may be preventive against expression in some tumors. Strong association of abnormal ITGA4 hypermethylation with the HER2 positive tumors (p = 0.0025) suggests that simultaneous presence of both HER2 and integrin α4 receptors is not beneficial for tumor cells. This may imply HER2 and integrin α4 signaling pathways interactions that are yet to be discovered.
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Affiliation(s)
- Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.
| | - Ekaterina B Kuznetsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Viktoria V Rudenko
- Molecular Genetic Diagnostics Laboratory 2, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Alexey I Kalinkin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Elena V Poddubskaya
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia.,VitaMed LLC, Seslavinskaya St 10, 121309, Moscow, Russia
| | - Tatiana V Kekeeva
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Galina G Chesnokova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Ivan D Trotsenko
- Institute of Medicine, Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya St 6, 117198, Moscow, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Federal Scientific Clinical Centre of Pediatric Hematology Oncology Immunology Named After Dmitry Rogachev, Samory Mashela St 1, 117997, Moscow, Russia.,Gene Therapy Laboratory, Institute of Gene Biology, Vavilova St 34/5, 119334, Moscow, Russia
| | - Sergey I Kutsev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Marina V Nemtsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Olga A Simonova
- Molecular Genetic Diagnostics Laboratory 2, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
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128
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Guo L, Lee YT, Zhou Y, Huang Y. Targeting epigenetic regulatory machinery to overcome cancer therapy resistance. Semin Cancer Biol 2021; 83:487-502. [PMID: 33421619 PMCID: PMC8257754 DOI: 10.1016/j.semcancer.2020.12.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
Drug resistance, either intrinsic or acquired, represents a major hurdle to achieving optimal therapeutic outcomes during cancer treatment. In addition to acquisition of resistance-conferring genetic mutations, accumulating evidence suggests an intimate involvement of the epigenetic machinery in this process as well. Recent studies have revealed that epigenetic reprogramming, such as altered expression or relocation of DNA/histone modulators accompanied with chromatin structure remodeling, can lead to transcriptional plasticity in tumor cells, thereby driving their transformation towards a persistent state. These "persisters" represent a pool of slow-growing cells that can either re-expand when treatment is discontinued or acquire permanent resistance. Targeting epigenetic reprogramming or plasticity represents a new strategy to prevent the emergence of drug-refractory populations and to enable more consistent clinical responses. With the growing numbers of drugs or drug candidates developed to target epigenetic regulators, more and more epigenetic therapies are under preclinical evaluation, early clinical trials or approved by FDA as single agent or in combination with existing antitumor drugs. In this review, we highlight latest discoveries in the mechanistic understanding of epigenetically-induced drug resistance. In parallel, we discuss the potential of combining epigenetic drugs with existing anticancer regimens as a promising strategy for overcoming cancer drug resistance.
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Affiliation(s)
- Lei Guo
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yi-Tsang Lee
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
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129
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Xu L, Zheng Y, Li X, Wang A, Huo D, Li Q, Wang S, Luo Z, Liu Y, Xu F, Wu X, Wu M, Zhou Y. Abnormal neocortex arealization and Sotos-like syndrome-associated behavior in Setd2 mutant mice. SCIENCE ADVANCES 2021; 7:7/1/eaba1180. [PMID: 33523829 PMCID: PMC7775761 DOI: 10.1126/sciadv.aba1180] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Proper formation of area identities of the cerebral cortex is crucial for cognitive functions and social behaviors of the brain. It remains largely unknown whether epigenetic mechanisms, including histone methylation, regulate cortical arealization. Here, we removed SETD2, the methyltransferase for histone 3 lysine-36 trimethylation (H3K36me3), in the developing dorsal forebrain in mice and showed that Setd2 is required for proper cortical arealization and the formation of cortico-thalamo-cortical circuits. Moreover, Setd2 conditional knockout mice exhibit defects in social interaction, motor learning, and spatial memory, reminiscent of patients with the Sotos-like syndrome bearing SETD2 mutations. SETD2 maintains the expression of clustered protocadherin (cPcdh) genes in an H3K36me3 methyltransferase-dependent manner. Aberrant cortical arealization was recapitulated in cPcdh heterozygous mice. Together, our study emphasizes epigenetic mechanisms underlying cortical arealization and pathogenesis of the Sotos-like syndrome.
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Affiliation(s)
- Lichao Xu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yue Zheng
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xuejing Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Andi Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Dawei Huo
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Qinglan Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Shikang Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Zhiyuan Luo
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Ying Liu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xudong Wu
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Min Wu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
| | - Yan Zhou
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
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Hall AW, Chaffin M, Roselli C, Lin H, Lubitz SA, Bianchi V, Geeven G, Bedi K, Margulies KB, de Laat W, Tucker NR, Ellinor PT. Epigenetic Analyses of Human Left Atrial Tissue Identifies Gene Networks Underlying Atrial Fibrillation. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2020; 13:e003085. [PMID: 33155827 PMCID: PMC8240092 DOI: 10.1161/circgen.120.003085] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Atrial fibrillation (AF) often arises from structural abnormalities in the left atria (LA). Annotation of the noncoding genome in human LA is limited, as are effects on gene expression and chromatin architecture. Many AF-associated genetic variants reside in noncoding regions; this knowledge gap impairs efforts to understand the molecular mechanisms of AF and cardiac conduction phenotypes. METHODS We generated a model of the LA noncoding genome by profiling 7 histone post-translational modifications (active: H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K36me3; repressive: H3K27me3, H3K9me3), CTCF binding, and gene expression in samples from 5 individuals without structural heart disease or AF. We used MACS2 to identify peak regions (P<0.01), applied a Markov model to classify regulatory elements, and annotated this model with matched gene expression data. We intersected chromatin states with expression quantitative trait locus, DNA methylation, and HiC chromatin interaction data from LA and left ventricle. Finally, we integrated genome-wide association data for AF and electrocardiographic traits to link disease-related variants to genes. RESULTS Our model identified 21 epigenetic states, encompassing regulatory motifs, such as promoters, enhancers, and repressed regions. Genes were regulated by proximal chromatin states; repressive states were associated with a significant reduction in gene expression (P<2×10-16). Chromatin states were differentially methylated, promoters were less methylated than repressed regions (P<2×10-16). We identified over 15 000 LA-specific enhancers, defined by homeobox family motifs, and annotated several cardiovascular disease susceptibility loci. Intersecting AF and PR genome-wide association studies loci with long-range chromatin conformation data identified a gene interaction network dominated by NKX2-5, TBX3, ZFHX3, and SYNPO2L. CONCLUSIONS Profiling the noncoding genome provides new insights into the gene expression and chromatin regulation in human LA tissue. These findings enabled identification of a gene network underlying AF; our experimental and analytic approach can be extended to identify molecular mechanisms for other cardiac diseases and traits.
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Affiliation(s)
- Amelia Weber Hall
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Steven A. Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Geert Geeven
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kenneth Bedi
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kenneth B. Margulies
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nathan R. Tucker
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
- Masonic Medical Research Institute, Utica, NY
| | - Patrick T. Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
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Chen L, Gu X, Huang X, Liu R, Li J, Hu Y, Li G, Zeng T, Tian Y, Hu X, Lu L, Li N. Two cis-regulatory SNPs upstream of ABCG2 synergistically cause the blue eggshell phenotype in the duck. PLoS Genet 2020; 16:e1009119. [PMID: 33186356 PMCID: PMC7688135 DOI: 10.1371/journal.pgen.1009119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 11/25/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
Avian eggshell color is an interesting genetic trait. Here, we report that the blue eggshell color of the domestic duck is caused by two cis-regulatory G to A transitions upstream of ABCG2, which encodes an efflux transporter. The juxtaposed blue eggshell allele A-A exhibited higher promoter activity and stronger nuclear protein binding capacity than the white eggshell allele G-G. Transcription factor analysis suggested differential binding capability of CTCF between blue eggshell and white eggshell alleles. Knockdown of CTCF expression significantly decreased the promoter activity of the blue eggshell but not the white eggshell allele. DNA methylation analysis revealed similar high methylation of the region upstream of the CTCF binding sites in both blue-eggshelled and white-eggshelled ducks. However, DNA methylation levels downstream of the binding sites were decreased and 35% lower in blue-eggshelled ducks than in white-eggshelled ducks. Consistent with the in vitro regulatory pattern of causative sites, ABCG2 exhibited higher expression in uteruses of blue-eggshelled ducks and also showed polarized distribution in their endometrial epithelial cells, distributing at the apical surface of endometrial epithelial cells and with orientation toward the uterine cavity, where the eggshell is pigmented. In conclusion, our results suggest that two cis-regulatory SNPs upstream of ABCG2 are the causative mutations for blue eggshells in ducks. The blue eggshell variant up-regulated ABCG2 expression through recruiting CTCF binding, which may function as a barrier element to shield the downstream region from high methylation levels present upstream. ABCG2 was identified as the only candidate causative gene for blue eggshells; it may function as an efflux transporter of biliverdin to the uterine cavity. Avian eggshell color is an interesting genetic trait that has been related to numerous interesting biological functions, such as crypsis, mimicry, and protection from ultraviolet radiation. In ducks, blue eggshells are a dominant Mendelian trait. The color is preferred by customers and has become one of the main breeding targets in laying ducks in China. In this study, we identified that duck blue eggshells are likely caused by two cis-regulatory variations that synergistically up-regulate ABCG2 expression in the uterus. ABCG2 was identified as the only candidate causative gene for blue eggshell; it may function as an efflux transporter of biliverdin to the uterine cavity, where the eggshell is pigmented. Our study provides useful molecular markers for breeding of blue-eggshelled ducks.
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Affiliation(s)
- Li Chen
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaorong Gu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xuetao Huang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rui Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Jinxiu Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yiqing Hu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Guoqin Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yong Tian
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
- * E-mail: (XH); (LL); (NL)
| | - Lizhi Lu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (XH); (LL); (NL)
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
- * E-mail: (XH); (LL); (NL)
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132
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Rovirosa L, Ramos-Morales A, Javierre BM. The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer. Front Immunol 2020; 11:592087. [PMID: 33117405 PMCID: PMC7575776 DOI: 10.3389/fimmu.2020.592087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Associations between blood cancer and genetic predisposition, including both inherited variants and acquired mutations and epimutations, have been well characterized. However, the majority of these variants affect noncoding regions, making their mechanisms difficult to hypothesize and hindering the translation of these insights into patient benefits. Fueled by unprecedented progress in next-generation sequencing and computational integrative analysis, studies have started applying combinations of epigenetic, genome architecture, and functional assays to bridge the gap between noncoding variants and blood cancer. These complementary tools have not only allowed us to understand the potential malignant role of these variants but also to differentiate key variants, cell-types, and conditions from misleading ones. Here, we briefly review recent studies that have provided fundamental insights into our understanding of how noncoding mutations at enhancers predispose and promote blood malignancies in the context of spatial genome architecture.
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Affiliation(s)
- Llorenç Rovirosa
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Alberto Ramos-Morales
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain.,Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
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133
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Zhou Q, Wang Z, Li J, Sung WK, Li G. MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification. BMC Bioinformatics 2020; 21:451. [PMID: 33045983 PMCID: PMC7552496 DOI: 10.1186/s12859-020-03798-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data. Results In this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes. Conclusions This study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.
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Affiliation(s)
- Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ze Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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134
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Halstead MM, Kern C, Saelao P, Wang Y, Chanthavixay G, Medrano JF, Van Eenennaam AL, Korf I, Tuggle CK, Ernst CW, Zhou H, Ross PJ. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics 2020; 21:698. [PMID: 33028202 PMCID: PMC7541309 DOI: 10.1186/s12864-020-07078-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/17/2020] [Indexed: 12/25/2022] Open
Abstract
Background Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Results Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. Conclusions The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
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Affiliation(s)
- Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Colin Kern
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Perot Saelao
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ying Wang
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Juan F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Ian Korf
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, 48824, MI, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
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135
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Fang C, Rao S, Crispino JD, Ntziachristos P. Determinants and role of chromatin organization in acute leukemia. Leukemia 2020; 34:2561-2575. [PMID: 32690881 PMCID: PMC7999176 DOI: 10.1038/s41375-020-0981-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
DNA is compacted into higher order structures that have major implications in gene regulation. These structures allow for long-range interactions of DNA elements, such as the association of promoters with their cognate enhancers. In recent years, mutations in genes that control these structures, including the cohesin-complex and the insulator-binding protein CTCF, have been found in a spectrum of hematologic disorders, and especially in acute leukemias. Cohesin and CTCF are critical for mediating looping and establishing boundaries within chromatin. Cells that harbor mutations in these genes display aberrant chromatin architecture and resulting differences in gene expression that contribute to leukemia initiation and progression. Here, we provide detailed discussion of the nature of 3D interactions and the way that they are disrupted in acute leukemia. Continued research in this area will provide new insights into the mechanisms of leukemogenesis and may shed light on novel treatment strategies.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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Verheul TCJ, van Hijfte L, Perenthaler E, Barakat TS. The Why of YY1: Mechanisms of Transcriptional Regulation by Yin Yang 1. Front Cell Dev Biol 2020; 8:592164. [PMID: 33102493 PMCID: PMC7554316 DOI: 10.3389/fcell.2020.592164] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
First described in 1991, Yin Yang 1 (YY1) is a transcription factor that is ubiquitously expressed throughout mammalian cells. It regulates both transcriptional activation and repression, in a seemingly context-dependent manner. YY1 has a well-established role in the development of the central nervous system, where it is involved in neurogenesis and maintenance of homeostasis in the developing brain. In neurodevelopmental and neurodegenerative disease, the crucial role of YY1 in cellular processes in the central nervous system is further underscored. In this mini-review, we discuss the various mechanisms leading to the transcriptional activating and repressing roles of YY1, including its role as a traditional transcription factor, its interactions with cofactors and chromatin modifiers, the role of YY1 in the non-coding genome and 3D chromatin organization and the possible implications of the phase-separation mechanism on YY1 function. We provide examples on how these processes can be involved in normal development and how alterations can lead to various diseases.
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Affiliation(s)
- Thijs C J Verheul
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Levi van Hijfte
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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137
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Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Genome Med 2020; 12:81. [PMID: 32977850 PMCID: PMC7519528 DOI: 10.1186/s13073-020-00779-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. RESULTS We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. CONCLUSION Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.
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Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Lourdes Ortiz-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Elena López-Isac
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Alfredo Guillén-Del-Castillo
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
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138
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Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR. Association of CNVs with methylation variation. NPJ Genom Med 2020; 5:41. [PMID: 33062306 PMCID: PMC7519119 DOI: 10.1038/s41525-020-00145-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/04/2020] [Indexed: 12/03/2022] Open
Abstract
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.
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Affiliation(s)
- Xinghua Shi
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Saranya Radhakrishnan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Jia Wen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Jin Yun Chen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Junjie Chen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Brianna Ashlyn Lam
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Barbara E Stranger
- Department of Pharmacology, Northwestern University, Chicago, Illinois 60611 USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032 USA.,Department of Life Sciences, Ewha Womans University, Seoul, 03760 South Korea.,Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Sunita R Setlur
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
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139
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Fang C, Wang Z, Han C, Safgren SL, Helmin KA, Adelman ER, Serafin V, Basso G, Eagen KP, Gaspar-Maia A, Figueroa ME, Singer BD, Ratan A, Ntziachristos P, Zang C. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. Genome Biol 2020; 21:247. [PMID: 32933554 PMCID: PMC7493976 DOI: 10.1186/s13059-020-02152-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human cancers. RESULTS To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions, partially with DNA methylation changes, and rarely with sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events exhibit enhancer activities and are induced by oncogenic transcription factors. We validate these findings in T cell acute lymphoblastic leukemia cell lines and patient samples and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena. CONCLUSIONS Specific CTCF binding events occur in human cancers. Cancer-specific CTCF binding can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stephanie L Safgren
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kathryn A Helmin
- Department of Medicine, Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Emmalee R Adelman
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Italian Institute for Genomic Medicine, 10060, Torino, Italy
| | - Kyle P Eagen
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexandre Gaspar-Maia
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Benjamin D Singer
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
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140
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Alharbi AB, Schmitz U, Marshall AD, Vanichkina D, Nagarajah R, Vellozzi M, Wong JJ, Bailey CG, Rasko JE. Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner. RNA Biol 2020; 18:93-103. [PMID: 32816606 PMCID: PMC7834090 DOI: 10.1080/15476286.2020.1796052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of Ctcf dosage on AS has not been investigated. We examined the effect of Ctcf haploinsufficiency on gene expression and AS in five tissues from Ctcf hemizygous (Ctcf+/-) mice. Reduced Ctcf levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in Ctcf+/- liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of CTCF haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University , Makkah, Saudi Arabia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - Amy D Marshall
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Darya Vanichkina
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Sydney Informatics Hub, University of Sydney , Darlington, Australia
| | - Rajini Nagarajah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Melissa Vellozzi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Justin Jl Wong
- Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia
| | - John Ej Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney , Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney , Camperdown, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital , Camperdown, Australia
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141
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Zhang C, Zhao N, Zhang X, Xiao J, Li J, Lv D, Zhou W, Li Y, Xu J, Li X. SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis. Brief Bioinform 2020; 22:5890509. [PMID: 32778890 DOI: 10.1093/bib/bbaa162] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a tool to comprehensively assess the impact of DMFEs on prognosis. Therefore, we developed SurvivalMeth (http://bio-bigdata.hrbmu.edu.cn/survivalmeth) to explore the prognosis-related DMFEs, which documented many kinds of DMFEs, including 309,465 CpG island-related elements, 104,748 transcript-related elements, 77,634 repeat elements, as well as cell-type specific 1,689,653 super enhancers (SE) and 1,304,902 CTCF binding regions for analysis. SurvivalMeth is a convenient tool which collected DNA methylation profiles of 36 cancers and allowed users to query their genes of interest in different datasets for prognosis. Furthermore, SurvivalMeth not only integrated different combinations, including single DMFE, multiple DMFEs, SEs and clinical data, to perform survival analysis on preupload data but also allowed for uploading customized DNA methylation profile of DMFEs from various diseases to analyze. SurvivalMeth provided a comprehensive resource and automated analysis for prognostic DMFEs, including DMFE methylation level, correlation analysis, clinical analysis, differential analysis, DMFE annotation, survival-related detailed result and visualization of survival analysis. In summary, we believe that SurvivalMeth will facilitate prognostic research of DMFEs in diverse cancers.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Ning Zhao
- School of Life Sciences and Technology at Harbin Institute of Technology
| | - Xue Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Jun Xiao
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Junyi Li
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Dezhong Lv
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Yongsheng Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Juan Xu
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xia Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
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142
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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143
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Matthews BJ, Waxman DJ. Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics Chromatin 2020; 13:30. [PMID: 32680543 PMCID: PMC7368777 DOI: 10.1186/s13072-020-00350-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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144
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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145
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Freeman DM, Wang Z. Epigenetic Vulnerability of Insulator CTCF Motifs at Parkinson's Disease-Associated Genes in Response to Neurotoxicant Rotenone. Front Genet 2020; 11:627. [PMID: 32774342 PMCID: PMC7381335 DOI: 10.3389/fgene.2020.00627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/26/2020] [Indexed: 11/27/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a regulatory protein that binds DNA to control spatial organization and transcription. The sequence-specific binding of CTCF is variable and is impacted by nearby epigenetic patterns. It has been demonstrated that non-coding genetic variants cluster with CTCF sites in topological associating domains and thus can affect CTCF activity on gene expression. Therefore, environmental factors that alter epigenetic patterns at CTCF binding sites may dictate the interaction of non-coding genetic variants with regulatory proteins. To test this mechanism, we treated human cell line HEK293 with rotenone for 24 h and characterized its effect on global epigenetic patterns specifically at regulatory regions of Parkinson's disease (PD) risk loci. We used RNA sequencing to examine changes in global transcription and identified over 2000 differentially expressed genes (DEGs, >1.5-fold change, FDR < 0.05). Among these DEGs, 13 were identified as PD-associated genes according to Genome-wide association studies meta-data. We focused on eight genes that have non-coding risk variants and a prominent CTCF binding site. We analyzed methylation of a total of 165 CGs surrounding CTCF binding sites and detected differential methylation (|>1%|, q < 0.05) in 45 CGs at 7 PD-associated genes. Of these 45 CGs, 47% were hypomethylated and 53% were hypermethylated. Interestingly, 5 out of the 7 genes had correlated gene upregulation with CG hypermethylation at CTCF and gene downregulation with CG hypomethylation at CTCF. We also investigated active H3K27ac surrounding the same CTCF binding sites within these seven genes. We observed a significant increase in H3K27ac in four genes (FDR < 0.05). Three genes (PARK2, GPRIN3, FER) showed increased CTCF binding in response to rotenone. Our data indicate that rotenone alters regulatory regions of PD-associated genes through changes in epigenetic patterns, and these changes impact high-order chromatin organization to increase the influence of non-coding variants on genome integrity and cellular survival.
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Affiliation(s)
| | - Zhibin Wang
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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146
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Damaschke NA, Gawdzik J, Avilla M, Yang B, Svaren J, Roopra A, Luo JH, Yu YP, Keles S, Jarrard DF. CTCF loss mediates unique DNA hypermethylation landscapes in human cancers. Clin Epigenetics 2020; 12:80. [PMID: 32503656 PMCID: PMC7275597 DOI: 10.1186/s13148-020-00869-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Background The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization. Despite evidence linking CTCF to the protection of epigenetic states through barrier insulation, the impact of CTCF loss on genome-wide DNA methylation sites in human cancer remains undefined. Results Here, we demonstrate that prostate and breast cancers within The Cancer Genome Atlas (TCGA) exhibit frequent copy number loss of CTCF and that this loss is associated with increased DNA methylation events that occur preferentially at CTCF binding sites. CTCF sites differ among tumor types and result in tissue-specific methylation patterns with little overlap between breast and prostate cancers. DNA methylation and transcriptome profiling in vitro establish that forced downregulation of CTCF leads to spatially distinct DNA hypermethylation surrounding CTCF binding sites, loss of CTCF binding, and decreased gene expression that is also seen in human tumors. DNA methylation inhibition reverses loss of expression at these CTCF-regulated genes. Conclusion These findings establish CTCF loss as a major mediator in directing localized DNA hypermethylation events in a tissue-specific fashion and further support its role as a driver of the cancer phenotype.
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Affiliation(s)
- Nathan A Damaschke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joseph Gawdzik
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Mele Avilla
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bing Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - John Svaren
- Waisman Center and Department of Comparative Biosciences, University of Wisconsin, Madison, WI, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin, Madison, WI, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sunduz Keles
- Department of Biostatistic and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - David F Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA. .,University of Wisconsin Carbone Comprehensive Cancer Center, Madison, WI, USA. .,Environmental and Molecular Toxicology, University of Wisconsin, Madison, WI, USA. .,7037 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI, 53705, USA.
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147
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Sensitivity of transcription factors to DNA methylation. Essays Biochem 2020; 63:727-741. [PMID: 31755929 PMCID: PMC6923324 DOI: 10.1042/ebc20190033] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022]
Abstract
Dynamic binding of transcription factors (TFs) to regulatory elements controls transcriptional states throughout organism development. Epigenetics modifications, such as DNA methylation mostly within cytosine-guanine dinucleotides (CpGs), have the potential to modulate TF binding to DNA. Although DNA methylation has long been thought to repress TF binding, a more recent model proposes that TF binding can also inhibit DNA methylation. Here, we review the possible scenarios by which DNA methylation and TF binding affect each other. Further in vivo experiments will be required to generalize these models.
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148
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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Chang S, Bartolomei MS. Modeling human epigenetic disorders in mice: Beckwith-Wiedemann syndrome and Silver-Russell syndrome. Dis Model Mech 2020; 13:dmm044123. [PMID: 32424032 PMCID: PMC7272347 DOI: 10.1242/dmm.044123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting, a phenomenon in which the two parental alleles are regulated differently, is observed in mammals, marsupials and a few other species, including seed-bearing plants. Dysregulation of genomic imprinting can cause developmental disorders such as Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). In this Review, we discuss (1) how various (epi)genetic lesions lead to the dysregulation of clinically relevant imprinted loci, and (2) how such perturbations may contribute to the developmental defects in BWS and SRS. Given that the regulatory mechanisms of most imprinted clusters are well conserved between mice and humans, numerous mouse models of BWS and SRS have been generated. These mouse models are key to understanding how mutations at imprinted loci result in pathological phenotypes in humans, although there are some limitations. This Review focuses on how the biological findings obtained from innovative mouse models explain the clinical features of BWS and SRS.
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Affiliation(s)
- Suhee Chang
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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150
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Krismer K, Guo Y, Gifford DK. IDR2D identifies reproducible genomic interactions. Nucleic Acids Res 2020; 48:e31. [PMID: 32009147 PMCID: PMC7102997 DOI: 10.1093/nar/gkaa030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/19/2019] [Accepted: 01/22/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https://idr2d.mit.edu.
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Affiliation(s)
- Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yuchun Guo
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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