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Dong J, Scott TG, Mukherjee R, Guertin MJ. ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594008. [PMID: 38798607 PMCID: PMC11118474 DOI: 10.1101/2024.05.13.594008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. ZNF143 binds the promoter of nearly all its activated target genes. ZNF143 also binds near the site of genic transcription initiation to directly repress a subset of genes. Although ZNF143 stimulates initiation at ZNF143-repressed genes (i.e. those that increase expression upon ZNF143 depletion), the molecular context of binding leads to cis repression. ZNF143 competes with other more efficient activators for promoter access, physically occludes transcription initiation sites and promoter-proximal sequence elements, and acts as a molecular roadblock to RNA Polymerases during early elongation. The term context specific is often invoked to describe transcription factors that have both activation and repression functions. We define the context and molecular mechanisms of ZNF143-mediated cis activation and repression.
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Affiliation(s)
- Jinhong Dong
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
| | - Thomas G Scott
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rudradeep Mukherjee
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
| | - Michael J Guertin
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America
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2
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024:10.1038/s44320-024-00038-5. [PMID: 38745107 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Kamalyan S, Kyrchanova O, Klimenko N, Babosha V, Vasileva Y, Belova E, Fursenko D, Maksimenko O, Georgiev P. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality. Epigenetics Chromatin 2024; 17:9. [PMID: 38561749 PMCID: PMC10983669 DOI: 10.1186/s13072-024-00534-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. RESULTS Previously, we demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, we observed a strong impact on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. CONCLUSIONS Our findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo.
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Affiliation(s)
- Sofia Kamalyan
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Yulia Vasileva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Dariya Fursenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
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4
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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5
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Zhang M, Huang H, Li J, Wu Q. ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry. Cell Rep 2024; 43:113663. [PMID: 38206813 DOI: 10.1016/j.celrep.2023.113663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.
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Affiliation(s)
- Mo Zhang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Haiyan Huang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China.
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6
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Dong Y, Hu M, Tan K, Dai R. ZNF143 inhibits hepatocyte mitophagy and promotes non-alcoholic fatty liver disease by targeting increased lncRNA NEAT1 expression to activate ROCK2 pathway. Epigenetics 2023; 18:2239592. [PMID: 37566742 PMCID: PMC10424604 DOI: 10.1080/15592294.2023.2239592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is the most common hepatic disorders worldwide. The mitophagy is suggested to be repressed in NAFLD, but the mechanism remains to be elucidated. METHODS NAFLD cell and mouse models were established by treating with free fatty acid (FFA) and feeding a high fat diet (HFD), respectively. QRT-PCR, Western blotting, or IHC measured the expression of ZNF143, lncRNA NEAT1, ROCK2, and lipid formation/mitophagy-related proteins. Cell viability and mitophagy were evaluated by MTT and immunofluorescence. The chloroform-methanol extraction method measured triglyceride and total cholesterol levels. ELISA detected ALT and AST levels. The interactions among ZNF143, lncRNA NEAT1 and SND1 were analysed by ChIP, dual-luciferase reporter, pull-down, and RIP. The lipid droplets were determined by Oil-red O and HE staining. RESULTS ZNF143 and lncRNA NEAT1 were upregulated in hepatic cells treated with FFA (p < 0.01 and p < 0.001). Knockdown of ZNF143 or lncRNA NEAT1 inhibited lipid droplets formation, while promoting mitophagy (p < 0.01 and p < 0.001). ZNF143 promoted lncRNA NEAT1 transcriptional expression through binding to its promoter. LncRNA NEAT1 increased ROCK2 mRNA stability by targeting SND1. LncRNA NEAT1 or ROCK2 overexpression reversed the effect of ZNF143 or lncRNA NEAT1 knockdown on hepatic steatosis and mitophagy (p < 0.01 and p < 0.001). ZNF143 or lncRNA NEAT1 knockdown inhibited HFD-induced steatosis and promoted mitophagy in vivo (p < 0.01 and p < 0.001). CONCLUSION The upregulation of lncRNA NEAT1 caused by ZNF143 promoted NAFLD through inhibiting mitophagy via activating ROCK2 pathway by targeting SND1, providing potential targets for NAFLD therapy.
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Affiliation(s)
- Yujie Dong
- The First Affiliated Hospital, Department of Ultrasound Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Minjie Hu
- The First Affiliated Hospital, Department of Cardiothoracic Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Kewei Tan
- The No.922 Hospital of the People Liberation Army Joint Logistics Support Force, Department of the Laboratory and Blood Transfusion, Hengyang, Hunan421002, China
| | - Rongjuan Dai
- The First Affiliated Hospital, Department of Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
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7
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Winans T, Oaks Z, Choudhary G, Patel A, Huang N, Faludi T, Krakko D, Nolan J, Lewis J, Blair S, Lai Z, Landas SK, Middleton F, Asara JM, Chung SK, Wyman B, Azadi P, Banki K, Perl A. mTOR-dependent loss of PON1 secretion and antiphospholipid autoantibody production underlie autoimmunity-mediated cirrhosis in transaldolase deficiency. J Autoimmun 2023; 140:103112. [PMID: 37742509 PMCID: PMC10957505 DOI: 10.1016/j.jaut.2023.103112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023]
Abstract
Transaldolase deficiency predisposes to chronic liver disease progressing from cirrhosis to hepatocellular carcinoma (HCC). Transition from cirrhosis to hepatocarcinogenesis depends on mitochondrial oxidative stress, as controlled by cytosolic aldose metabolism through the pentose phosphate pathway (PPP). Progression to HCC is critically dependent on NADPH depletion and polyol buildup by aldose reductase (AR), while this enzyme protects from carbon trapping in the PPP and growth restriction in TAL deficiency. Although AR inactivation blocked susceptibility to hepatocarcinogenesis, it enhanced growth restriction, carbon trapping in the non-oxidative branch of the PPP and failed to reverse the depletion of glucose 6-phosphate (G6P) and liver cirrhosis. Here, we show that inactivation of the TAL-AR axis results in metabolic stress characterized by reduced mitophagy, enhanced overall autophagy, activation of the mechanistic target of rapamycin (mTOR), diminished glycosylation and secretion of paraoxonase 1 (PON1), production of antiphospholipid autoantibodies (aPL), loss of CD161+ NK cells, and expansion of CD38+ Ito cells, which are responsive to treatment with rapamycin in vivo. The present study thus identifies glycosylation and secretion of PON1 and aPL production as mTOR-dependent regulatory checkpoints of autoimmunity underlying liver cirrhosis in TAL deficiency.
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Affiliation(s)
- T Winans
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Z Oaks
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - G Choudhary
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - A Patel
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - N Huang
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - T Faludi
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - D Krakko
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J Nolan
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J Lewis
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Sarah Blair
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Z Lai
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - S K Landas
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - F Middleton
- Departments of Neuroscience, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - S K Chung
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau
| | - B Wyman
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - P Azadi
- University of Georgia, Athens, GA 30602, USA
| | - K Banki
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - A Perl
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Microbiology and Immunology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA.
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8
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Kuang S, Pollard KS. Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563498. [PMID: 37961712 PMCID: PMC10634726 DOI: 10.1101/2023.10.22.563498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. In order to disentangle the cis- and trans-regulatory roles of caRNAs, we compared models with nascent transcripts, trans-located caRNAs, open chromatin data, or DNA sequence alone. Both nascent transcripts and trans-located caRNAs improved the models' predictions, especially at cell-type-specific genomic regions. Analyses of feature importance scores revealed the contribution of caRNAs at TAD boundaries, chromatin loops and nuclear sub-structures such as nuclear speckles and nucleoli to the models' predictions. Furthermore, we identified non-coding RNAs (ncRNAs) known to regulate chromatin structures, such as MALAT1 and NEAT1, as well as several novel RNAs, RNY5, RPPH1, POLG-DT and THBS1-IT, that might modulate chromatin architecture through trans-interactions in HFFc6. Our modeling also suggests that transcripts from Alus and other repetitive elements may facilitate chromatin interactions through trans R-loop formation. Our findings provide new insights and generate testable hypotheses about the roles of caRNAs in shaping chromatin organization.
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Affiliation(s)
- Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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9
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Abstract
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.
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Affiliation(s)
- Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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10
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Zhang P, Wu H. IChrom-Deep: An Attention-Based Deep Learning Model for Identifying Chromatin Interactions. IEEE J Biomed Health Inform 2023; 27:4559-4568. [PMID: 37402191 DOI: 10.1109/jbhi.2023.3292299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Identification of chromatin interactions is crucial for advancing our knowledge of gene regulation. However, due to the limitations of high-throughput experimental techniques, there is an urgent need to develop computational methods for predicting chromatin interactions. In this study, we propose a novel attention-based deep learning model, termed IChrom-Deep, to identify chromatin interactions using sequence features and genomic features. The experimental results based on the datasets of three cell lines demonstrate that the IChrom-Deep achieves satisfactory performance and is superior to the previous methods. We also investigate the effect of DNA sequence and associated features and genomic features on chromatin interactions, and highlight the applicable scenarios of some features, such as sequence conservation and distance. Moreover, we identify a few genomic features that are extremely important across different cell lines, and IChrom-Deep achieves comparable performance with only these significant genomic features versus using all genomic features. It is believed that IChrom-Deep can serve as a useful tool for future studies that seek to identify chromatin interactions.
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11
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Xu H, Yi X, Fan X, Wu C, Wang W, Chu X, Zhang S, Dong X, Wang Z, Wang J, Zhou Y, Zhao K, Yao H, Zheng N, Wang J, Chen Y, Plewczynski D, Sham PC, Chen K, Huang D, Li MJ. Inferring CTCF-binding patterns and anchored loops across human tissues and cell types. PATTERNS (NEW YORK, N.Y.) 2023; 4:100798. [PMID: 37602215 PMCID: PMC10436006 DOI: 10.1016/j.patter.2023.100798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 08/22/2023]
Abstract
CCCTC-binding factor (CTCF) is a transcription regulator with a complex role in gene regulation. The recognition and effects of CTCF on DNA sequences, chromosome barriers, and enhancer blocking are not well understood. Existing computational tools struggle to assess the regulatory potential of CTCF-binding sites and their impact on chromatin loop formation. Here we have developed a deep-learning model, DeepAnchor, to accurately characterize CTCF binding using high-resolution genomic/epigenomic features. This has revealed distinct chromatin and sequence patterns for CTCF-mediated insulation and looping. An optimized implementation of a previous loop model based on DeepAnchor score excels in predicting CTCF-anchored loops. We have established a compendium of CTCF-anchored loops across 52 human tissue/cell types, and this suggests that genomic disruption of these loops could be a general mechanism of disease pathogenesis. These computational models and resources can help investigate how CTCF-mediated cis-regulatory elements shape context-specific gene regulation in cell development and disease progression.
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Affiliation(s)
- Hang Xu
- Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Human Major Diseases (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Xianfu Yi
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chengyue Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Human Major Diseases (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Human Major Diseases (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiaobao Dong
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhao Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Ke Zhao
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, The University of Hong Kong, Hong Kong 999077, China
| | - Nan Zheng
- Department of Network Security and Informatization, Tianjin Medical University, Tianjin 300070, China
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Yupeng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Dariusz Plewczynski
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, The University of Hong Kong, Hong Kong 999077, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Human Major Diseases (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Dandan Huang
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Human Major Diseases (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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12
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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13
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Dejosez M, Dall'Agnese A, Ramamoorthy M, Platt J, Yin X, Hogan M, Brosh R, Weintraub AS, Hnisz D, Abraham BJ, Young RA, Zwaka TP. Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Rep 2023; 42:112505. [PMID: 37182209 DOI: 10.1016/j.celrep.2023.112505] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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Affiliation(s)
- Marion Dejosez
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Alessandra Dall'Agnese
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mahesh Ramamoorthy
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jesse Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xing Yin
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Megan Hogan
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Ran Brosh
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- St. Jude Research Children's Hospital, Memphis, TN 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA.
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14
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Wang C, Liu X, Liang J, Narita Y, Ding W, Li D, Zhang L, Wang H, Leong MML, Hou I, Gerdt C, Jiang C, Zhong Q, Tang Z, Forney C, Kottyan L, Weirauch MT, Gewurz BE, Zeng MS, Jiang S, Teng M, Zhao B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nat Commun 2023; 14:1598. [PMID: 36949074 PMCID: PMC10033825 DOI: 10.1038/s41467-023-37347-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor virus oncogenesis. RBL and LCL chromatin interaction maps are compared to identify the spatial and temporal genome architectural changes during EBV B cell transformation. EBV induces global genome reorganization where contact domains frequently merge or subdivide during transformation. Repressed B compartments in RBLs frequently switch to active A compartments in LCLs. LCLs gain 40% new contact domain boundaries. Newly gained LCL boundaries have strong CTCF binding at their borders while in RBLs, the same sites have much less CTCF binding. Some LCL CTCF sites also have EBV nuclear antigen (EBNA) leader protein EBNALP binding. LCLs have more local interactions than RBLs at LCL dependency factors and super-enhancer targets. RNA Pol II HiChIP and FISH of RBL and LCL further validate the Hi-C results. EBNA3A inactivation globally alters LCL genome interactions. EBNA3A inactivation reduces CTCF and RAD21 DNA binding. EBNA3C inactivation rewires the looping at the CDKN2A/B and AICDA loci. Disruption of a CTCF site at AICDA locus increases AICDA expression. These data suggest that EBV controls lymphocyte growth by globally reorganizing host genome architecture to facilitate the expression of key oncogenes.
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Affiliation(s)
- Chong Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Xiang Liu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jun Liang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Yohei Narita
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Weiyue Ding
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Difei Li
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Luyao Zhang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Hongbo Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Merrin Man Long Leong
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Isabella Hou
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Catherine Gerdt
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Chang Jiang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Benjamin E Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA.
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
| | - Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA.
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15
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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16
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Kyrchanova OV, Bylino OV, Georgiev PG. Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila. Front Genet 2022; 13:1081088. [PMID: 36531247 PMCID: PMC9751008 DOI: 10.3389/fgene.2022.1081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The spatial organization of chromosomes is involved in regulating the majority of intranuclear processes in higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play a key role in regulation of gene expression in mammals. According to modern views, a cohesin complex mostly determines the architecture of mammalian chromosomes by forming chromatin loops on anchors created by the CTCF DNA-binding architectural protein. The role of the cohesin complex in chromosome architecture is poorly understood in Drosophila, and CTCF is merely one of many Drosophila architectural proteins with a proven potential to organize specific long-range interactions between regulatory elements in the genome. The review compares the mechanisms responsible for long-range interactions and chromosome architecture between mammals and Drosophila.
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17
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Liu S, Cao Y, Cui K, Tang Q, Zhao K. Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops. Nat Commun 2022; 13:6679. [PMID: 36335136 PMCID: PMC9637178 DOI: 10.1038/s41467-022-34276-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022] Open
Abstract
The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation-free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among regulatory elements. Hi-TrAC detects chromatin looping among accessible regions at single nucleosome resolution. With almost half-million identified loops, we reveal a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discover that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we introduce a methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of transcription factors in organizing chromatin loops for genome organization and gene expression.
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Affiliation(s)
- Shuai Liu
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Yaqiang Cao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kairong Cui
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Qingsong Tang
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Keji Zhao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
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18
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Ito S, Das ND, Umehara T, Koseki H. Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation. Cancers (Basel) 2022; 14:cancers14215404. [PMID: 36358822 PMCID: PMC9659172 DOI: 10.3390/cancers14215404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary The physical interactions between enhancers and promoters create chromatin conformations involved in gene regulation. In cancer cells, the chromatin conformations can be altered with uncontrolled deposition of histone marks resulting in varied gene expression. Although it is not entirely comprehensive how chromatin-mediated enhancer–promoter (E–P) interactions with various histone marks can affect gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential to control gene expression. In this review, we focus on emerging views of chromatin conformations associated with the E–P interactions and factors that establish or maintain such interactions, which may regulate gene expression. Abstract Eukaryotic gene expression is regulated through chromatin conformation, in which enhancers and promoters physically interact (E–P interactions). How such chromatin-mediated E–P interactions affect gene expression is not yet fully understood, but the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins such as CCCTC binding factor (CTCF) and cohesin have recently attracted attention. Moreover, accumulated data suggest that E–P interactions are mechanistically involved in biophysical events, including liquid–liquid phase separation, and in biological events, including cancers. In this review, we discuss various mechanisms that regulate eukaryotic gene expression, focusing on emerging views regarding chromatin conformations that are involved in E–P interactions and factors that establish and maintain them.
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Affiliation(s)
- Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-45-503-9690
| | - Nando Dulal Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
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19
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Witkowski MT, Lee S, Wang E, Lee AK, Talbot A, Ma C, Tsopoulidis N, Brumbaugh J, Zhao Y, Roberts KG, Hogg SJ, Nomikou S, Ghebrechristos YE, Thandapani P, Mullighan CG, Hochedlinger K, Chen W, Abdel-Wahab O, Eyquem J, Aifantis I. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nat Immunol 2022; 23:1424-1432. [PMID: 36138187 PMCID: PMC9611506 DOI: 10.1038/s41590-022-01314-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/11/2022] [Indexed: 02/04/2023]
Abstract
B cell progenitor acute lymphoblastic leukemia (B-ALL) treatment has been revolutionized by T cell-based immunotherapies-including chimeric antigen receptor T cell therapy (CAR-T) and the bispecific T cell engager therapeutic, blinatumomab-targeting surface glycoprotein CD19. Unfortunately, many patients with B-ALL will fail immunotherapy due to 'antigen escape'-the loss or absence of leukemic CD19 targeted by anti-leukemic T cells. In the present study, we utilized a genome-wide CRISPR-Cas9 screening approach to identify modulators of CD19 abundance on human B-ALL blasts. These studies identified a critical role for the transcriptional activator ZNF143 in CD19 promoter activation. Conversely, the RNA-binding protein, NUDT21, limited expression of CD19 by regulating CD19 messenger RNA polyadenylation and stability. NUDT21 deletion in B-ALL cells increased the expression of CD19 and the sensitivity to CD19-specific CAR-T and blinatumomab. In human B-ALL patients treated with CAR-T and blinatumomab, upregulation of NUDT21 mRNA coincided with CD19 loss at disease relapse. Together, these studies identify new CD19 modulators in human B-ALL.
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Affiliation(s)
- Matthew T Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, USA.
| | - Soobeom Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
- Department of Biology, New York University (NYU), New York, NY, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - Anna K Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Alexis Talbot
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Nikolaos Tsopoulidis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Yaqi Zhao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yohana E Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Eyquem
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute of Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
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20
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Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
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Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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21
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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22
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Ye B, Shen W, Zhang C, Yu M, Ding X, Yin M, Wang Y, Guo X, Bai G, Lin K, Shi S, Li P, Zhang Y, Yu G, Zhao Z. The role of ZNF143 overexpression in rat liver cell proliferation. BMC Genomics 2022; 23:483. [PMID: 35780101 PMCID: PMC9250731 DOI: 10.1186/s12864-022-08714-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated. Methods In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression. Results Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity. Conclusion These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08714-2.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Wenlong Shen
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mengli Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xinru Ding
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yahao Wang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Xinjie Guo
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ge Bai
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Kailin Lin
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Shu Shi
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ping Li
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Yan Zhang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Zhihu Zhao
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China.
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23
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Yildirim A, Boninsegna L, Zhan Y, Alber F. Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Cold Spring Harb Perspect Biol 2022; 14:a039693. [PMID: 34400556 PMCID: PMC9248826 DOI: 10.1101/cshperspect.a039693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.
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Affiliation(s)
- Asli Yildirim
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Lorenzo Boninsegna
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yuxiang Zhan
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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24
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Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem 2022; 298:102117. [PMID: 35691341 PMCID: PMC9283939 DOI: 10.1016/j.jbc.2022.102117] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022] Open
Abstract
In mammalian organisms, enhancers can regulate transcription from great genomic distances. How enhancers affect distal gene expression has been a major question in the field of gene regulation. One model to explain how enhancers communicate with their target promoters, the chromatin looping model, posits that enhancers and promoters come in close spatial proximity to mediate communication. Chromatin looping has been broadly accepted as a means for enhancer–promoter communication, driven by accumulating in vitro and in vivo evidence. The genome is now known to be folded into a complex 3D arrangement, created and maintained in part by the interplay of the Cohesin complex and the DNA-binding protein CTCF. In the last few years, however, doubt over the relationship between looping and transcriptional activation has emerged, driven by studies finding that only a modest number of genes are perturbed with acute degradation of looping machinery components. In parallel, newer models describing distal enhancer action have also come to prominence. In this article, we explore the emergence and development of the looping model as a means for enhancer–promoter communication and review the contrasting evidence between historical gene-specific and current global data for the role of chromatin looping in transcriptional regulation. We also discuss evidence for alternative models to chromatin looping and their support in the literature. We suggest that, while there is abundant evidence for chromatin looping as a major mechanism for enhancer function, enhancer–promoter communication is likely mediated by more than one mechanism in an enhancer- and context-dependent manner.
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Affiliation(s)
- Tessa M Popay
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R Dixon
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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25
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Andrieu-Soler C, Soler E. Erythroid Cell Research: 3D Chromatin, Transcription Factors and Beyond. Int J Mol Sci 2022; 23:ijms23116149. [PMID: 35682828 PMCID: PMC9181152 DOI: 10.3390/ijms23116149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Studies of the regulatory networks and signals controlling erythropoiesis have brought important insights in several research fields of biology and have been a rich source of discoveries with far-reaching implications beyond erythroid cells biology. The aim of this review is to highlight key recent discoveries and show how studies of erythroid cells bring forward novel concepts and refine current models related to genome and 3D chromatin organization, signaling and disease, with broad interest in life sciences.
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Affiliation(s)
| | - Eric Soler
- IGMM, Université Montpellier, CNRS, 34093 Montpellier, France;
- Laboratory of Excellence GR-Ex, Université de Paris, 75015 Paris, France
- Correspondence:
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26
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InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification. Genes (Basel) 2022; 13:genes13040621. [PMID: 35456427 PMCID: PMC9026820 DOI: 10.3390/genes13040621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
Mapping chromatin insulator loops is crucial to investigating genome evolution, elucidating critical biological functions, and ultimately quantifying variant impact in diseases. However, chromatin conformation profiling assays are usually expensive, time-consuming, and may report fuzzy insulator annotations with low resolution. Therefore, we propose a weakly supervised deep learning method, InsuLock, to address these challenges. Specifically, InsuLock first utilizes a Siamese neural network to predict the existence of insulators within a given region (up to 2000 bp). Then, it uses an object detection module for precise insulator boundary localization via gradient-weighted class activation mapping (~40 bp resolution). Finally, it quantifies variant impacts by comparing the insulator score differences between the wild-type and mutant alleles. We applied InsuLock on various bulk and single-cell datasets for performance testing and benchmarking. We showed that it outperformed existing methods with an AUROC of ~0.96 and condensed insulator annotations to ~2.5% of their original size while still demonstrating higher conservation scores and better motif enrichments. Finally, we utilized InsuLock to make cell-type-specific variant impacts from brain scATAC-seq data and identified a schizophrenia GWAS variant disrupting an insulator loop proximal to a known risk gene, indicating a possible new mechanism of action for the disease.
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27
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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28
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Wang S, Hu H, Li X. A systematic study of motif pairs that may facilitate enhancer-promoter interactions. J Integr Bioinform 2022; 19:jib-2021-0038. [PMID: 35130376 PMCID: PMC9069648 DOI: 10.1515/jib-2021-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 01/06/2023] Open
Abstract
Pairs of interacting transcription factors (TFs) have previously been shown to bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about such TF pairs. To fill this void, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer-promoter (EP) pairs in seven human cell lines. We discovered 423 motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The developed pipeline, EPmotifPair, together with the predicted motifs and motif pairs, is available at https://doi.org/10.6084/m9.figshare.14192000. Our study provides a comprehensive list of motif pairs that may contribute to EP physical interactions, which facilitate generating meaningful hypotheses for experimental validation.
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Affiliation(s)
- Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA
| | - Xiaoman Li
- Burnett school of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA
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29
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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30
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Shen Y, Zhong Q, Liu T, Wen Z, Shen W, Li L. CharID: a two-step model for universal prediction of interactions between chromatin accessible regions. Brief Bioinform 2022; 23:6514800. [PMID: 35077535 DOI: 10.1093/bib/bbab602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/14/2022] Open
Abstract
Open chromatin regions (OCRs) allow direct interaction between cis-regulatory elements and trans-acting factors. Therefore, predicting all potential OCR-mediated loops is essential for deciphering the regulation mechanism of gene expression. However, existing loop prediction tools are restricted to specific anchor types. Here, we present CharID (Chromatin Accessible Region Interaction Detector), a two-step model that combines neural network and ensemble learning to predict OCR-mediated loops. In the first step, CharID-Anchor, an attention-based hybrid CNN-BiGRU network is constructed to discriminate between the anchor and nonanchor OCRs. In the second step, CharID-Loop uses gradient boosting decision tree with chromosome-split strategy to predict the interactions between anchor OCRs. The performance was assessed in three human cell lines, and CharID showed superior prediction performance compared with other algorithms. In contrast to the methods designed to predict a particular type of loops, CharID can detect varieties of chromatin loops not limited to enhancer-promoter loops or architectural protein-mediated loops. We constructed the OCR-mediated interaction network using the predicted loops and identified hub anchors, which are highlighted by their proximity to housekeeping genes. By analyzing loops containing SNPs associated with cardiovascular disease, we identified an SNP-gene loop indicating the regulation mechanism of the GFOD1. Taken together, CharID universally predicts diverse chromatin loops beyond other state-of-the-art methods, which are limited by anchor types, and experimental techniques, which are limited by sensitivities drastically decaying with the genomic distance of anchors. Finally, we hosted Peaksniffer, a user-friendly web server that provides online prediction, query and visualization of OCRs and associated loops.
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Affiliation(s)
- Yin Shen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Quan Zhong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Tian Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zi Wen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Wei Shen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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31
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Chen C, Sang Y. Phosphomannomutase 2 hyperinsulinemia: Recent advances of genetic pathogenesis, diagnosis, and management. Front Endocrinol (Lausanne) 2022; 13:1102307. [PMID: 36726472 PMCID: PMC9884677 DOI: 10.3389/fendo.2022.1102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 01/17/2023] Open
Abstract
Congenital hyperinsulinemia (CHI), is a clinically heterogeneous disorder that presents as a major cause of persistent and recurrent hypoglycemia during infancy and childhood. There are 16 subtypes of CHI-related genes. Phosphomannomutase 2 hyperinsulinemia (PMM2-HI) is an extremely rare subtype which is first reported in 2017, with only 18 families reported so far. This review provides a structured description of the genetic pathogenesis, and current diagnostic and therapeutic advances of PMM2-HI to increase clinicians' awareness of PMM2-HI.
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32
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Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X. A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nat Commun 2021; 12:7139. [PMID: 34880227 PMCID: PMC8654995 DOI: 10.1038/s41467-021-27055-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023] Open
Abstract
Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Zhong Wu
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jin Zhou
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dinesh K A Ramadurai
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yifei Yan
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Alison M Taylor
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Peter S Choi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada.
| | - Xiaoyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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33
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The genetic architecture of DNA replication timing in human pluripotent stem cells. Nat Commun 2021; 12:6746. [PMID: 34799581 PMCID: PMC8604924 DOI: 10.1038/s41467-021-27115-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome's replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) - sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation.
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34
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Stilianoudakis SC, Marshall MA, Dozmorov MG. preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution. Bioinformatics 2021; 38:621-630. [PMID: 34741515 PMCID: PMC8756196 DOI: 10.1093/bioinformatics/btab743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Chromosome conformation capture technologies (Hi-C) revealed extensive DNA folding into discrete 3D domains, such as Topologically Associating Domains and chromatin loops. The correct binding of CTCF and cohesin at domain boundaries is integral in maintaining the proper structure and function of these 3D domains. 3D domains have been mapped at the resolutions of 1 kilobase and above. However, it has not been possible to define their boundaries at the resolution of boundary-forming proteins. RESULTS To predict domain boundaries at base-pair resolution, we developed preciseTAD, an optimized transfer learning framework trained on high-resolution genome annotation data. In contrast to current TAD/loop callers, preciseTAD-predicted boundaries are strongly supported by experimental evidence. Importantly, this approach can accurately delineate boundaries in cells without Hi-C data. preciseTAD provides a powerful framework to improve our understanding of how genomic regulators are shaping the 3D structure of the genome at base-pair resolution. AVAILABILITY AND IMPLEMENTATION preciseTAD is an R/Bioconductor package available at https://bioconductor.org/packages/preciseTAD/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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35
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [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: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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36
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Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nat Methods 2021; 18:1075-1081. [PMID: 34354266 PMCID: PMC8446310 DOI: 10.1038/s41592-021-01224-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the activation induced by directing aTFs to distal transcriptional enhancers is substantially less robust and consistent. Here we show that long-range activation using CRISPR-based aTFs in human cells can be made more efficient and reliable by concurrently targeting an aTF to the target gene promoter. We used this strategy to direct target gene choice for enhancers capable of regulating more than one promoter and to achieve allele-selective activation of human genes by targeting aTFs to single-nucleotide polymorphisms embedded in distally located sequences. Our results broaden the potential applications of the epigenetic editing toolbox for research and therapeutics.
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Affiliation(s)
- Y. Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Joy E. Horng
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,These authors contributed equally
| | - Nicholas T. Perry
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,These authors contributed equally
| | - Hayley T. Schultz
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Qiuming Yao
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luli S. Zou
- Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin J. Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA,Correspondence and requests for materials should be addressed to J. Keith Joung.
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37
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Biswas A, Narlikar L. A universal framework for detecting cis-regulatory diversity in DNA regulatory regions. Genome Res 2021; 31:1646-1662. [PMID: 34285090 PMCID: PMC8415372 DOI: 10.1101/gr.274563.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 07/09/2021] [Indexed: 12/02/2022]
Abstract
High-throughput sequencing-based assays measure different biochemical activities pertaining to gene regulation, genome-wide. These activities include transcription factor (TF)–DNA binding, enhancer activity, open chromatin, and more. A major goal is to understand underlying sequence components, or motifs, that can explain the measured activity. It is usually not one motif but a combination of motifs bound by cooperatively acting proteins that confers activity to such regions. Furthermore, regions can be diverse, governed by different combinations of TFs/motifs. Current approaches do not take into account this issue of combinatorial diversity. We present a new statistical framework, cisDIVERSITY, which models regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves. Because cisDIVERSITY does not rely on knowledge of motifs, modules, cell type, or organism, it is general enough to be applied to regions reported by most high-throughput assays. For example, in enhancer predictions resulting from different assays—GRO-cap, STARR-seq, and those measuring chromatin structure—cisDIVERSITY discovers distinct modules and combinations of TF binding sites, some specific to the assay. From protein–DNA binding data, cisDIVERSITY identifies potential cofactors of the profiled TF, whereas from ATAC-seq data, it identifies tissue-specific regulatory modules. Finally, analysis of single-cell ATAC-seq data suggests that regions open in one cell-state encode information about future states, with certain modules staying open and others closing down in the next time point.
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Affiliation(s)
- Anushua Biswas
- CSIR-National Chemical Laboratory, Academy of Scientific and Innovative Research
| | - Leelavati Narlikar
- CSIR-National Chemical Laboratory, Academy of Scientific and Innovative Research
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38
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Zwaka TP, Skowronska M, Richman R, Dejosez M. Ronin overexpression induces cerebellar degeneration in a mouse model of ataxia. Dis Model Mech 2021; 14:269269. [PMID: 34165550 PMCID: PMC8246265 DOI: 10.1242/dmm.044834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a group of genetically heterogeneous inherited neurodegenerative disorders characterized by progressive ataxia and cerebellar degeneration. Here, we used a mouse model to test a possible connection between SCA and Ronin (Thap11), a polyglutamine-containing transcriptional regulator encoded in a region of human chromosome 16q22.1 that has been genetically linked to SCA type 4. We report that transgenic expression of Ronin in mouse cerebellar Purkinje cells leads to detrimental loss of these cells and the development of severe ataxia as early as 10 weeks after birth. Mechanistically, we find that several SCA-causing genes harbor Ronin DNA-binding motifs and are transcriptionally deregulated in transgenic animals. In addition, ectopic expression of Ronin in embryonic stem cells significantly increases the protein level of Ataxin-1, the protein encoded by Atxn1, alterations of which cause SCA type 1. This increase is also seen in the cerebellum of transgenic animals, although the latter was not statistically significant. Hence, our data provide evidence for a link between Ronin and SCAs, and suggest that Ronin may be involved in the development of other neurodegenerative diseases. Summary: Ronin is a polyglutamine protein encoded in a region of human chromosome 16q22.1 linked to spinocerebellar ataxia type 4. Overexpression of Ronin in mouse cerebellar Purkinje cells leads to their loss and ataxia.
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Affiliation(s)
- Thomas P Zwaka
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marta Skowronska
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ronald Richman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marion Dejosez
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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39
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Agelopoulos M, Foutadakis S, Thanos D. The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression. Front Immunol 2021; 12:682397. [PMID: 34149720 PMCID: PMC8212036 DOI: 10.3389/fimmu.2021.682397] [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: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 01/05/2023] Open
Abstract
Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.
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Affiliation(s)
| | | | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
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40
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Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases. Int J Mol Sci 2021; 22:ijms22084187. [PMID: 33919522 PMCID: PMC8073710 DOI: 10.3390/ijms22084187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Man-Chun Wong
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan;
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 81148, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
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41
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Sabirov M, Kyrchanova O, Pokholkova GV, Bonchuk A, Klimenko N, Belova E, Zhimulev IF, Maksimenko O, Georgiev P. Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster. Epigenetics Chromatin 2021; 14:16. [PMID: 33752739 PMCID: PMC7983404 DOI: 10.1186/s13072-021-00391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background Pita is required for Drosophila development and binds specifically to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-finger architectural proteins, which also includes Su(Hw) and the conserved among higher eukaryotes CTCF. The architectural proteins maintain the active state of regulatory elements and the long-distance interactions between them. In particular, Pita is involved in the formation of several boundaries between regulatory domains that controlled the expression of three hox genes in the Bithorax complex (BX-C). The CP190 protein is recruited to chromatin through interaction with the architectural proteins. Results Using in vitro pull-down analysis, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. Then we constructed transgenic lines expressing the Pita protein of the wild-type and mutant variants lacking CP190-interacting regions. We have demonstrated that CP190-interacting region of the Pita can maintain nucleosome-free open chromatin and is critical for Pita-mediated enhancer blocking activity in BX-C. At the same time, interaction with CP190 is not required for the in vivo function of the mutant Pita protein, which binds to the same regions of the genome as the wild-type protein. Unexpectedly, we found that CP190 was still associated with the most of genome regions bound by the mutant Pita protein, which suggested that other architectural proteins were continuing to recruit CP190 to these regions. Conclusions The results directly demonstrate role of CP190 in insulation and support a model in which the regulatory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00391-x.
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Affiliation(s)
- Marat Sabirov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Galina V Pokholkova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.
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42
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Luzhin AV, Golov AK, Gavrilov AA, Velichko AK, Ulianov SV, Razin SV, Kantidze OL. LASCA: loop and significant contact annotation pipeline. Sci Rep 2021; 11:6361. [PMID: 33737718 PMCID: PMC7973524 DOI: 10.1038/s41598-021-85970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/09/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail to identify chromatin loops in animal species with substantially different genome architecture. This paper presents the loop and significant contact annotation (LASCA) pipeline, which uses Weibull distribution-based modeling to effectively identify loops and enhancer–promoter interactions in Hi-C data from evolutionarily distant species: from yeast and worms to mammals. Available at: https://github.com/ArtemLuzhin/LASCA_pipeline.
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Affiliation(s)
- Artem V Luzhin
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Arkadiy K Golov
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Artem K Velichko
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia.
| | - Omar L Kantidze
- Institute of Gene Biology Russian Academy of Science, Moscow, Russia.
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43
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Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations. Nat Commun 2021; 12:499. [PMID: 33479238 PMCID: PMC7820432 DOI: 10.1038/s41467-020-20830-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
The human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating control elements and cis-regulatory elements, such as promoters, enhancers, and anchors of chromatin interactions. Uneven distribution of these features within chromosomes gives rise to clusters, such as topologically associating domains (TADs), lamina-associated domains, clusters of cis-regulatory elements or large organized chromatin lysine (K) domains (LOCKs). Here we show that LOCKs from diverse histone modifications discriminate primitive from differentiated cell types. Active LOCKs (H3K4me1, H3K4me3 and H3K27ac) cover a higher fraction of the genome in primitive compared to differentiated cell types while repressive LOCKs (H3K9me3, H3K27me3 and H3K36me3) do not. Active LOCKs in differentiated cells lie proximal to highly expressed genes while active LOCKs in primitive cells tend to be bivalent. Genes proximal to bivalent LOCKs are minimally expressed in primitive cells. Furthermore, bivalent LOCKs populate TAD boundaries and are preferentially bound by regulators of chromatin interactions, including CTCF, RAD21 and ZNF143. Together, our results argue that LOCKs discriminate primitive from differentiated cell populations.
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Kyrchanova O, Georgiev P. Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes. Int J Mol Sci 2021; 22:ijms22020671. [PMID: 33445415 PMCID: PMC7828040 DOI: 10.3390/ijms22020671] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
In higher eukaryotes, enhancers determine the activation of developmental gene transcription in specific cell types and stages of embryogenesis. Enhancers transform the signals produced by various transcription factors within a given cell, activating the transcription of the targeted genes. Often, developmental genes can be associated with dozens of enhancers, some of which are located at large distances from the promoters that they regulate. Currently, the mechanisms underlying specific distance interactions between enhancers and promoters remain poorly understood. This review briefly describes the properties of enhancers and discusses the mechanisms of distance interactions and potential proteins involved in this process.
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Zhou Q, Yu M, Tirado-Magallanes R, Li B, Kong L, Guo M, Tan ZH, Lee S, Chai L, Numata A, Benoukraf T, Fullwood MJ, Osato M, Ren B, Tenen DG. ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun 2021; 12:43. [PMID: 33397967 PMCID: PMC7782510 DOI: 10.1038/s41467-020-20282-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/23/2020] [Indexed: 12/28/2022] Open
Abstract
CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin-chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF-bound promoter-enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF-bound promoter-enhancer loops are also disrupted after excision of ZNF143. ZNF143-CTCF-bound promoter-enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation is that ZNF143 is a critical factor for CTCF-bound promoter-enhancer loops.
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Affiliation(s)
- Qiling Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- YLL School of Medicine, National University of Singapore, 119228, Singapore, Singapore
| | - Miao Yu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Roberto Tirado-Magallanes
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Lingshi Kong
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Mingrui Guo
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- YLL School of Medicine, National University of Singapore, 119228, Singapore, Singapore
| | - Zi Hui Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Sanghoon Lee
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Akihiko Numata
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, A1B 3V6, Canada
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Department of Cellular & Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore.
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.
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Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers. Acta Naturae 2021; 13:31-46. [PMID: 33959385 PMCID: PMC8084297 DOI: 10.32607/actanaturae.11206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
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Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | | - E. V. Belova
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
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Lanchantin J, Qi Y. Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data. Bioinformatics 2020; 36:i659-i667. [PMID: 33381816 DOI: 10.1093/bioinformatics/btaa793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial structure of DNA, is highly influential in the chromatin profile. Deep neural networks have achieved state of the art performance on chromatin profile prediction by using short windows of DNA sequences independently. These methods, however, ignore the long-range dependencies when predicting the chromatin profiles because modeling the 3D genome is challenging. RESULTS In this work, we introduce ChromeGCN, a graph convolutional network for chromatin profile prediction by fusing both local sequence and long-range 3D genome information. By incorporating the 3D genome, we relax the independent and identically distributed assumption of local windows for a better representation of DNA. ChromeGCN explicitly incorporates known long-range interactions into the modeling, allowing us to identify and interpret those important long-range dependencies in influencing chromatin profiles. We show experimentally that by fusing sequential and 3D genome data using ChromeGCN, we get a significant improvement over the state-of-the-art deep learning methods as indicated by three metrics. Importantly, we show that ChromeGCN is particularly useful for identifying epigenetic effects in those DNA windows that have a high degree of interactions with other DNA windows. AVAILABILITY AND IMPLEMENTATION https://github.com/QData/ChromeGCN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jack Lanchantin
- Department of Computer Science, University of Virginia, Charlottesville, VA 22903, USA
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA 22903, USA
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Maji A, Padinhateeri R, Mitra MK. The Accidental Ally: Nucleosome Barriers Can Accelerate Cohesin-Mediated Loop Formation in Chromatin. Biophys J 2020; 119:2316-2325. [PMID: 33181117 PMCID: PMC7732762 DOI: 10.1016/j.bpj.2020.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 01/26/2023] Open
Abstract
An important question in the context of the three-dimensional organization of chromosomes is the mechanism of formation of large loops between distant basepairs. Recent experiments suggest that the formation of loops might be mediated by loop extrusion factor proteins such as cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low-effective-diffusion constants leads to times that are unphysically large. The puzzle then is the following: how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle and show that although at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration they can reduce loop formation times because of a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.
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Affiliation(s)
- Ajoy Maji
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
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Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell 2020; 28:488-501.e10. [PMID: 33242413 DOI: 10.1016/j.stem.2020.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/17/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Abstract
Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.
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Affiliation(s)
- Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa 236-0004, Japan
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erwin Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ken Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael D Taylor
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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50
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Liu L, Zhang LR, Dao FY, Yang YC, Lin H. A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:347-354. [PMID: 33425492 PMCID: PMC7779541 DOI: 10.1016/j.omtn.2020.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/11/2020] [Indexed: 12/30/2022]
Abstract
The pairwise interaction between transcription factors (TFs) plays an important role in enhancer-promoter loop formation. Although thousands of TFs in the human genome have been found, only a few TF pairs have been demonstrated to be related to loop formation. It is still a challenge to determine which TF pairs could be involved in the enhancer-promoter regulation network. This work describes a computational framework to identify TF pairs in enhancer-promoter regulation. By integrating different levels of data derived from Promoter Capture Hi-C, chromatin immunoprecipitation sequencing (ChIP-seq) of histone marks, RNA-seq, protein-protein interaction (PPI), and TF motif, we identified 361 significant TF pairs and constructed a TF interaction network. From the network, we found several hub-TFs, which may have important roles in the regulation of long-range interactions. Our studies extended TF pairs identified in other experimental and computational approaches. These findings will help the further study of long-range interactions between enhancers and promoters.
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Affiliation(s)
- Li Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li-Rong Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Fu-Ying Dao
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yan-Chao Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Hao Lin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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