151
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Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D, Papantonis A. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. SCIENCE ADVANCES 2021; 7:eabg8205. [PMID: 34678064 PMCID: PMC8535795 DOI: 10.1126/sciadv.abg8205] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces marked chromosome condensation, but following reentry into the G1 phase of the cell cycle, chromosomes reestablish their interphase organization. Here, we tested the role of RNA polymerase II (RNAPII) in this transition using a cell line that allows its auxin-mediated degradation. In situ Hi-C showed that RNAPII is required for both compartment and loop establishment following mitosis. RNAPs often counteract loop extrusion, and in their absence, longer and more prominent loops arose. Evidence from chromatin binding, super-resolution imaging, and in silico modeling allude to these effects being a result of RNAPII-mediated cohesin loading upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
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Affiliation(s)
- Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Giada Forte
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Johan A. Slotman
- Optical Imaging Centre, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Michael Chiang
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | | | - Eduardo Gade Gusmao
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | | | | | - Kerstin S. Wendt
- Department of Cell Biology, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Corresponding author.
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152
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Wang H, Huang B, Wang J. Predict long-range enhancer regulation based on protein-protein interactions between transcription factors. Nucleic Acids Res 2021; 49:10347-10368. [PMID: 34570239 PMCID: PMC8501976 DOI: 10.1093/nar/gkab841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/10/2021] [Accepted: 09/10/2021] [Indexed: 12/18/2022] Open
Abstract
Long-range regulation by distal enhancers plays critical roles in cell-type specific transcriptional programs. Computational predictions of genome-wide enhancer-promoter interactions are still challenging due to limited accuracy and the lack of knowledge on the molecular mechanisms. Based on recent biological investigations, the protein-protein interactions (PPIs) between transcription factors (TFs) have been found to participate in the regulation of chromatin loops. Therefore, we developed a novel predictive model for cell-type specific enhancer-promoter interactions by leveraging the information of TF PPI signatures. Evaluated by a series of rigorous performance comparisons, the new model achieves superior performance over other methods. The model also identifies specific TF PPIs that may mediate long-range regulatory interactions, revealing new mechanistic understandings of enhancer regulation. The prioritized TF PPIs are associated with genes in distinct biological pathways, and the predicted enhancer-promoter interactions are strongly enriched with cis-eQTLs. Most interestingly, the model discovers enhancer-mediated trans-regulatory links between TFs and genes, which are significantly enriched with trans-eQTLs. The new predictive model, along with the genome-wide analyses, provides a platform to systematically delineate the complex interplay among TFs, enhancers and genes in long-range regulation. The novel predictions also lead to mechanistic interpretations of eQTLs to decode the genetic associations with gene expression.
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Affiliation(s)
- Hao Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
| | - Binbin Huang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
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153
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154
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Chen Q, Zhang M, Pan X, Yuan X, Zhou L, Yan L, Zeng LH, Xu J, Yang B, Zhang L, Huang J, Lu W, Fukagawa T, Wang F, Yan H. Bub1 and CENP-U redundantly recruit Plk1 to stabilize kinetochore-microtubule attachments and ensure accurate chromosome segregation. Cell Rep 2021; 36:109740. [PMID: 34551298 DOI: 10.1016/j.celrep.2021.109740] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/03/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022] Open
Abstract
Bub1 is required for the kinetochore/centromere localization of two essential mitotic kinases Plk1 and Aurora B. Surprisingly, stable depletion of Bub1 by ∼95% in human cells marginally affects whole chromosome segregation fidelity. We show that CENP-U, which is recruited to kinetochores by the CENP-P and CENP-Q subunits of the CENP-O complex, is required to prevent chromosome mis-segregation in Bub1-depleted cells. Mechanistically, Bub1 and CENP-U redundantly recruit Plk1 to kinetochores to stabilize kinetochore-microtubule attachments, thereby ensuring accurate chromosome segregation. Furthermore, unlike its budding yeast homolog, the CENP-O complex does not regulate centromeric localization of Aurora B. Consistently, depletion of Bub1 or CENP-U sensitizes cells to the inhibition of Plk1 but not Aurora B kinase activity. Taken together, our findings provide mechanistic insight into the regulation of kinetochore function, which may have implications for targeted treatment of cancer cells with mutations perturbing kinetochore recruitment of Plk1 by Bub1 or the CENP-O complex.
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Affiliation(s)
- Qinfu Chen
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China; The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Miao Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuan Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xueying Yuan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Linli Zhou
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lu Yan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ling-Hui Zeng
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China
| | - Junfen Xu
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Long Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Weiguo Lu
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Fangwei Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, The Key Laboratory of Cancer Molecular Cell Biology of Zhejiang Province, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Cancer Center, Zhejiang University, Hangzhou 310058, China.
| | - Haiyan Yan
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China.
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155
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Abstract
The specialized two-stage meiotic cell division program halves a cell's chromosome complement in preparation for sexual reproduction. This reduction in ploidy requires that in meiotic prophase, each pair of homologous chromosomes (homologs) identify one another and form physical links through DNA recombination. Here, we review recent advances in understanding the complex morphological changes that chromosomes undergo during meiotic prophase to promote homolog identification and crossing over. We focus on the structural maintenance of chromosomes (SMC) family cohesin complexes and the meiotic chromosome axis, which together organize chromosomes and promote recombination. We then discuss the architecture and dynamics of the conserved synaptonemal complex (SC), which assembles between homologs and mediates local and global feedback to ensure high fidelity in meiotic recombination. Finally, we discuss exciting new advances, including mechanisms for boosting recombination on particular chromosomes or chromosomal domains and the implications of a new liquid crystal model for SC assembly and structure. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sarah N Ur
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA; ,
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA; , .,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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156
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Robinson J, Raguseo F, Nuccio SP, Liano D, Di Antonio M. DNA G-quadruplex structures: more than simple roadblocks to transcription? Nucleic Acids Res 2021; 49:8419-8431. [PMID: 34255847 PMCID: PMC8421137 DOI: 10.1093/nar/gkab609] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple 'off switches' for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.
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Affiliation(s)
- Jenna Robinson
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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157
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Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods 2021; 18:1046-1055. [PMID: 34480151 PMCID: PMC8446342 DOI: 10.1038/s41592-021-01248-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/18/2021] [Indexed: 01/05/2023]
Abstract
Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project. This analysis systematically evaluates cross-linking chemistry and chromatin fragmentation strategies commonly used in 3C assays and introduces an improved Hi-C protocol for detecting loops and compartments.
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Affiliation(s)
- Betul Akgol Oksuz
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Liyan Yang
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sameer Abraham
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sergey V Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Marlies E Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ankita Nand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hui Mao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rene Maehr
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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158
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Xu B, Wang H, Wright S, Hyle J, Zhang Y, Shao Y, Niu M, Fan Y, Rosikiewicz W, Djekidel MN, Peng J, Lu R, Li C. Acute depletion of CTCF rewires genome-wide chromatin accessibility. Genome Biol 2021; 22:244. [PMID: 34429148 PMCID: PMC8386078 DOI: 10.1186/s13059-021-02466-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/12/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. RESULTS Here, we systematically integrate multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, and CRISPR-Cas9 survival dropout screens, and time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions are frequently located adjacent to CTCF-binding sites at promoter regions and insulator sites associated with enhanced transcription of nearby genes. In addition, we use CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners. We successfully identify 40 candidates, including multiple established partners. Interestingly, many CTCF co-regulators that have alterations of their respective downstream gene expression do not show changes of their own expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. CONCLUSIONS This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.
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Affiliation(s)
- Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shaela Wright
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Judith Hyle
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yang Zhang
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ying Shao
- Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Rui Lu
- Division of Hematology/Oncology, University of Alabama at Birmingham, 1824 6th Ave S WTI 510G, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, 1824 6th Ave S WTI 510G, Birmingham, AL, 35294, USA
| | - Chunliang Li
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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159
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Câmara AS, Schubert V, Mascher M, Houben A. A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species. Nucleic Acids Res 2021; 49:9053-9065. [PMID: 34352103 PMCID: PMC8450114 DOI: 10.1093/nar/gkab648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Centromeres are essential for chromosome movement. In independent taxa, species with holocentric chromosomes exist. In contrast to monocentric species, where no obvious dispersion of centromeres occurs during interphase, the organization of holocentromeres differs between condensed and decondensed chromosomes. During interphase, centromeres are dispersed into a large number of CENH3-positive nucleosome clusters in a number of holocentric species. With the onset of chromosome condensation, the centromeric nucleosomes join and form line-like holocentromeres. Using polymer simulations, we propose a mechanism relying on the interaction between centromeric nucleosomes and structural maintenance of chromosomes (SMC) proteins. Different sets of molecular dynamic simulations were evaluated by testing four parameters: (i) the concentration of Loop Extruders (LEs) corresponding to SMCs, (ii) the distribution and number of centromeric nucleosomes, (iii) the effect of centromeric nucleosomes on interacting LEs and (iv) the assembly of kinetochores bound to centromeric nucleosomes. We observed the formation of a line-like holocentromere, due to the aggregation of the centromeric nucleosomes when the chromosome was compacted into loops. A groove-like holocentromere structure formed after a kinetochore complex was simulated along the centromeric line. Similar mechanisms may also organize a monocentric chromosome constriction, and its regulation may cause different centromere types during evolution.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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160
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Vos ESM, Valdes-Quezada C, Huang Y, Allahyar A, Verstegen MJAM, Felder AK, van der Vegt F, Uijttewaal ECH, Krijger PHL, de Laat W. Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression. Mol Cell 2021; 81:3082-3095.e6. [PMID: 34197738 DOI: 10.1016/j.molcel.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022]
Abstract
To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not rely strictly on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion. Upon boundary inversion, we find that oppositely oriented CTCF terminates extrusion trajectories but does not stall cohesin, while deleted or mutated CTCF sites allow cohesin to extend its trajectory. Enhancer-mediated gene activation occurs independent of paused loop extrusion near the gene promoter. We expand upon the loop extrusion model to propose that cohesin loading and extrusion trajectories originating at an enhancer contribute to gene activation.
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Affiliation(s)
- Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Yike Huang
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Amin Allahyar
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Anna-Karina Felder
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Floor van der Vegt
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Esther C H Uijttewaal
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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161
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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162
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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163
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Golov AK, Golova AV, Gavrilov AA, Razin SV. Sensitivity of cohesin-chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion. Epigenetics Chromatin 2021; 14:36. [PMID: 34321070 PMCID: PMC8320178 DOI: 10.1186/s13072-021-00411-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022] Open
Abstract
Cohesin is a key organizer of chromatin folding in eukaryotic cells. The two main activities of this ring-shaped protein complex are the maintenance of sister chromatid cohesion and the establishment of long-range DNA-DNA interactions through the process of loop extrusion. Although the basic principles of both cohesion and loop extrusion have been described, we still do not understand several crucial mechanistic details. One of such unresolved issues is the question of whether a cohesin ring topologically embraces DNA string(s) during loop extrusion. Here, we show that cohesin complexes residing on CTCF-occupied genomic sites in mammalian cells do not interact with DNA topologically. We assessed the stability of cohesin-dependent loops and cohesin association with chromatin in high-ionic-strength conditions in G1-synchronized HeLa cells. We found that increased salt concentration completely displaces cohesin from those genomic regions that correspond to CTCF-defined loop anchors. Unsurprisingly, CTCF-anchored cohesin loops also dissipate in these conditions. Because topologically engaged cohesin is considered to be salt resistant, our data corroborate a non-topological model of loop extrusion. We also propose a model of cohesin activity throughout the interphase, which essentially equates the termination of non-topological loop extrusion with topological loading of cohesin. This theoretical framework enables a parsimonious explanation of various seemingly contradictory experimental findings.
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Affiliation(s)
- Arkadiy K. Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Mental Health Research Center, Moscow, Russia
| | - Anastasia V. Golova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey A. Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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164
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Garcia P, Fernandez-Hernandez R, Cuadrado A, Coca I, Gomez A, Maqueda M, Latorre-Pellicer A, Puisac B, Ramos FJ, Sandoval J, Esteller M, Mosquera JL, Rodriguez J, Pié J, Losada A, Queralt E. Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome. Nat Commun 2021; 12:4551. [PMID: 34315879 PMCID: PMC8316422 DOI: 10.1038/s41467-021-24808-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. In addition to its canonical role in sister chromatid cohesion, cohesin is implicated in the spatial organization of the genome. Here, we investigate the transcriptome of CdLS patient-derived primary fibroblasts and observe the downregulation of genes involved in development and system skeletal organization, providing a link to the developmental alterations and limb abnormalities characteristic of CdLS patients. Genome-wide distribution studies demonstrate a global reduction of NIPBL at the NIPBL-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at NIPBL-occupied sites at CpG islands potentially due to reduced cohesin translocation along chromosomes, and fewer cohesin peaks colocalize with CTCF.
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Affiliation(s)
- Patricia Garcia
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
| | - Rita Fernandez-Hernandez
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Coca
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Grup de Recerca de Reumatologia, Parc Científic de Barcelona, Barcelona, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP) and Epigenomics Core Facility, Health Research Institute La Fe (IISLaFe), Valencia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Jairo Rodriguez
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
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165
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Kyrchanova O, Klimenko N, Postika N, Bonchuk A, Zolotarev N, Maksimenko O, Georgiev P. Drosophila architectural protein CTCF is not essential for fly survival and is able to function independently of CP190. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194733. [PMID: 34311130 DOI: 10.1016/j.bbagrm.2021.194733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
CTCF is the most likely ancestor of proteins that contain large clusters of C2H2 zinc finger domains (C2H2) and is conserved among most bilateral organisms. In mammals, CTCF functions as the main architectural protein involved in the organization of topology-associated domains (TADs). In vertebrates and Drosophila, CTCF is involved in the regulation of homeotic genes. Previously, it was found that null mutations in the dCTCF gene died as pharate adults, which failed to eclose from their pupal case, or shortly after hatching of adults. Here, we obtained several new null dCTCF mutations and found that the complete inactivation of dCTCF appears is limited mainly to phenotypic manifestations of the Abd-B gene and fertility of adult flies. Many modifiers that are not associated with an independent phenotypic manifestation can significantly enhance the expressivity of the null dCTCF mutations, indicating that other architectural proteins are able to functionally compensate for dCTCF inactivation in Drosophila. We also mapped the 715-735 aa region of dCTCF as being essential for the interaction with the BTB (Broad-Complex, Tramtrack, and Bric a brac) and microtubule-targeting (M) domains of the CP190 protein, which binds to many architectural proteins. However, the mutational analysis showed that the interaction with CP190 was not important for the functional activity of dCTCF in vivo.
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Affiliation(s)
- 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
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Artem Bonchuk
- 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
| | - Nikolay Zolotarev
- 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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166
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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167
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Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol 2021; 22:445-464. [PMID: 33767413 DOI: 10.1038/s41580-021-00349-7] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/02/2023]
Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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168
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Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG. Enhancer release and retargeting activates disease-susceptibility genes. Nature 2021; 595:735-740. [PMID: 34040254 PMCID: PMC11171441 DOI: 10.1038/s41586-021-03577-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/23/2021] [Indexed: 02/04/2023]
Abstract
The functional engagement between an enhancer and its target promoter ensures precise gene transcription1. Understanding the basis of promoter choice by enhancers has important implications for health and disease. Here we report that functional loss of a preferred promoter can release its partner enhancer to loop to and activate an alternative promoter (or alternative promoters) in the neighbourhood. We refer to this target-switching process as 'enhancer release and retargeting'. Genetic deletion, motif perturbation or mutation, and dCas9-mediated CTCF tethering reveal that promoter choice by an enhancer can be determined by the binding of CTCF at promoters, in a cohesin-dependent manner-consistent with a model of 'enhancer scanning' inside the contact domain. Promoter-associated CTCF shows a lower affinity than that at chromatin domain boundaries and often lacks a preferred motif orientation or a partnering CTCF at the cognate enhancer, suggesting properties distinct from boundary CTCF. Analyses of cancer mutations, data from the GTEx project and risk loci from genome-wide association studies, together with a focused CRISPR interference screen, reveal that enhancer release and retargeting represents an overlooked mechanism that underlies the activation of disease-susceptibility genes, as exemplified by a risk locus for Parkinson's disease (NUCKS1-RAB7L1) and three loci associated with cancer (CLPTM1L-TERT, ZCCHC7-PAX5 and PVT1-MYC).
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Affiliation(s)
- Soohwan Oh
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Matteo D'Antonio
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qi Ma
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Sreejith J Nair
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Ohgi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA.
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California San Diego, La Jolla, CA, USA.
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169
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Bartosovic M, Kabbe M, Castelo-Branco G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol 2021; 39:825-835. [PMID: 33846645 PMCID: PMC7611252 DOI: 10.1038/s41587-021-00869-9] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
In contrast to single-cell approaches for measuring gene expression and DNA accessibility, single-cell methods for analyzing histone modifications are limited by low sensitivity and throughput. Here, we combine the CUT&Tag technology, developed to measure bulk histone modifications, with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. We apply single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system and probe histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3). These scCUT&Tag profiles were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. We also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21. Our results indicate that analysis of histone modifications and transcription factor occupancy at single-cell resolution provides unique insights into epigenomic landscapes in the central nervous system.
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Affiliation(s)
- Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden,Corresponding authors: ,
| | - Mukund Kabbe
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, 171 77 Stockholm, Sweden,Corresponding authors: ,
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170
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Surdez D, Zaidi S, Grossetête S, Laud-Duval K, Ferre AS, Mous L, Vourc'h T, Tirode F, Pierron G, Raynal V, Baulande S, Brunet E, Hill V, Delattre O. STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma. Cancer Cell 2021; 39:810-826.e9. [PMID: 33930311 DOI: 10.1016/j.ccell.2021.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/31/2020] [Accepted: 04/02/2021] [Indexed: 12/19/2022]
Abstract
STAG2, a cohesin family gene, is among the most recurrently mutated genes in cancer. STAG2 loss of function (LOF) is associated with aggressive behavior in Ewing sarcoma, a childhood cancer driven by aberrant transcription induced by the EWSR1-FLI1 fusion oncogene. Here, using isogenic Ewing cells, we show that, while STAG2 LOF profoundly changes the transcriptome, it does not significantly impact EWSR1-FLI1, CTCF/cohesin, or acetylated H3K27 DNA binding patterns. In contrast, it strongly alters the anchored dynamic loop extrusion process at boundary CTCF sites and dramatically decreases promoter-enhancer interactions, particularly affecting the expression of genes regulated by EWSR1-FLI1 at GGAA microsatellite neo-enhancers. Down-modulation of cis-mediated EWSR1-FLI1 activity, observed in STAG2-LOF conditions, is associated with enhanced migration and invasion properties of Ewing cells previously observed in EWSR1-FLI1low cells. Our study illuminates a process whereby STAG2-LOF fine-tunes the activity of an oncogenic transcription factor through altered CTCF-anchored loop extrusion and cis-mediated enhancer mechanisms.
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MESH Headings
- Bone Neoplasms/genetics
- Bone Neoplasms/mortality
- Bone Neoplasms/pathology
- CCCTC-Binding Factor/chemistry
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Movement/genetics
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/metabolism
- Enhancer Elements, Genetic
- Gene Expression Regulation, Neoplastic
- Histones/metabolism
- Humans
- Loss of Function Mutation
- Lysine/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/mortality
- Sarcoma, Ewing/pathology
- Cohesins
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Affiliation(s)
- Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France.
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Anna Sole Ferre
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Lieke Mous
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Thomas Vourc'h
- UMR 168, Biology Inspired Physics at Mesoscales, PSL Research University, Institut Curie Research Centre, 75005 Paris, France
| | - Franck Tirode
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Center of Lyon, 69008 Lyon, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France
| | - Virginie Raynal
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Erika Brunet
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France.
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171
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van Ruiten MS, Rowland BD. On the choreography of genome folding: A grand pas de deux of cohesin and CTCF. Curr Opin Cell Biol 2021; 70:84-90. [PMID: 33545664 DOI: 10.1016/j.ceb.2020.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 02/06/2023]
Abstract
Cohesin and CTCF are key to the 3D folding of interphase chromosomes. Cohesin forms chromatin loops via loop extrusion, a process that involves the formation and enlargement of DNA loops. The architectural protein CTCF controls this process by acting as an anchor for chromatin looping. How CTCF controls cohesin has long been a mystery. Recent work shows that CTCF dictates chromatin looping via a direct interaction of its N-terminus with cohesin. CTCF's ability to regulate chromatin looping turns out to also be partially dependent on several RNA-binding domains. In this review, we discuss recent insights and consider how cohesin and CTCF together may orchestrate the folding of the genome into chromosomal loops.
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Affiliation(s)
- Marjon S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands.
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172
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Peters JM. How DNA loop extrusion mediated by cohesin enables V(D)J recombination. Curr Opin Cell Biol 2021; 70:75-83. [PMID: 33422934 DOI: 10.1016/j.ceb.2020.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 12/16/2022]
Abstract
'Structural maintenance of chromosomes' (SMC) complexes are required for the folding of genomic DNA into loops. Theoretical considerations and single-molecule experiments performed with the SMC complexes cohesin and condensin indicate that DNA folding occurs via loop extrusion. Recent work indicates that this process is essential for the assembly of antigen receptor genes by V(D)J recombination in developing B and T cells of the vertebrate immune system. Here, I review how recent studies of the mouse immunoglobulin heavy chain locus Igh have provided evidence for this hypothesis and how the formation of chromatin loops by cohesin and regulation of this process by CTCF and Wapl might ensure that all variable gene segments in this locus (VH segments) participate in recombination with a re-arranged DJH segment, to ensure generation of a maximally diverse repertoire of B-cell receptors and antibodies.
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Affiliation(s)
- Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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173
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Schang LM, Hu M, Cortes EF, Sun K. Chromatin-mediated epigenetic regulation of HSV-1 transcription as a potential target in antiviral therapy. Antiviral Res 2021; 192:105103. [PMID: 34082058 PMCID: PMC8277756 DOI: 10.1016/j.antiviral.2021.105103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
The ability to establish, and reactivate from, latent infections is central to the biology and pathogenesis of HSV-1. It also poses a strong challenge to antiviral therapy, as latent HSV-1 genomes do not replicate or express any protein to be targeted. Although the processes regulating the establishment and maintenance of, and reactivation from, latency are not fully elucidated, the current general consensus is that epigenetics play a major role. A unifying model postulates that whereas HSV-1 avoids or counteracts chromatin silencing in lytic infections, it becomes silenced during latency, silencing which is somewhat disrupted during reactivation. Many years of work by different groups using a variety of approaches have also shown that the lytic HSV-1 chromatin is distinct and has unique biophysical properties not shared with most cellular chromatin. Nonetheless, the lytic and latent viral chromatins are typically enriched in post translational modifications or histone variants characteristic of active or repressed transcription, respectively. Moreover, a variety of small molecule epigenetic modulators inhibit viral replication and reactivation from latency. Despite these successes in culture and animal models, it is not obvious how epigenetic modulation would be used in antiviral therapy if the same epigenetic mechanisms governed viral and cellular gene expression. Recent work has highlighted several important differences between the viral and cellular chromatins, which appear to be of consequence to their respective epigenetic regulations. In this review, we will discuss the distinctiveness of the viral chromatin, and explore whether it is regulated by mechanisms unique enough to be exploited in antiviral therapy.
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Affiliation(s)
- Luis M Schang
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
| | - MiYao Hu
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA; Departments of Biochemistry and Medical Microbiology and Immunology, University of Alberta. 470 MSB, Edmonton, AB, T6G 2H7, Canada.
| | - Esteban Flores Cortes
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
| | - Kairui Sun
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
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174
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Sergeant MJ, Hughes JR, Hentges L, Lunter G, Downes DJ, Taylor S. Multi Locus View: an extensible web-based tool for the analysis of genomic data. Commun Biol 2021; 4:623. [PMID: 34035422 PMCID: PMC8149710 DOI: 10.1038/s42003-021-02097-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/31/2021] [Indexed: 01/10/2023] Open
Abstract
Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualisations. Interpretation is normally made at a high level without the ability to visualise the underlying data in detail. Conventional genome browsers are limited to browsing single locations and do not allow for interactions with the dataset as a whole. Multi Locus View (MLV), a web-based tool, has been developed to allow users to fluidly interact with genomics datasets at multiple scales. The user is able to browse the raw data, cluster, and combine the data with other analysis and annotate the data. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available at https://mlv.molbiol.ox.ac.uk .
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Affiliation(s)
- Martin J Sergeant
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lance Hentges
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerton Lunter
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- University Medical Centre Groningen, Department of Epidemiology, University of Groningen, Groningen, The Netherlands
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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175
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Ulianov SV, Razin SV. The two waves in single-cell 3D genomics. Semin Cell Dev Biol 2021; 121:143-152. [PMID: 34030950 DOI: 10.1016/j.semcdb.2021.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
For decades, biochemical methods for the analysis of genome structure and function provided cell-population-averaged data that allowed general principles and tendencies to be disclosed. Microscopy-based studies, which immanently involve single-cell analysis, did not provide sufficient spatial resolution to investigate the particularly small details of 3D genome folding. Nevertheless, these studies demonstrated that mutual positions of chromosome territories within cell nuclei and individual genomic loci within chromosomal territories can vary significantly in individual cells. The development of new technologies in biochemistry and the advent of super-resolution microscopy in the last decade have made possible the full-scale study of 3D genome organization in individual cells. Maps of the 3D genome build based on C-data and super-resolution microscopy are highly consistent and, therefore, biologically relevant. The internal structures of individual chromosomes, loci, and topologically associating domains (TADs) are resolved as well as cell-cycle dynamics. 3D modeling allows one to investigate the physical mechanisms underlying genome folding. Finally, joint profiling of genome topology and epigenetic features will allow 3D genomics to handle complex cell-to-cell heterogeneity. In this review, we summarize the present state of studies into 3D genome organization in individual cells, analyze the technical problems of single-cell studies, and outline perspectives of 3D genomics.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
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176
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van der Weide RH, van den Brand T, Haarhuis JHI, Teunissen H, Rowland BD, de Wit E. Hi-C analyses with GENOVA: a case study with cohesin variants. NAR Genom Bioinform 2021; 3:lqab040. [PMID: 34046591 PMCID: PMC8140737 DOI: 10.1093/nargab/lqab040] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conformation capture-approaches like Hi-C can elucidate chromosome structure at a genome-wide scale. Hi-C datasets are large and require specialised software. Here, we present GENOVA: a user-friendly software package to analyse and visualise chromosome conformation capture (3C) data. GENOVA is an R-package that includes the most common Hi-C analyses, such as compartment and insulation score analysis. It can create annotated heatmaps to visualise the contact frequency at a specific locus and aggregate Hi-C signal over user-specified genomic regions such as ChIP-seq data. Finally, our package supports output from the major mapping-pipelines. We demonstrate the capabilities of GENOVA by analysing Hi-C data from HAP1 cell lines in which the cohesin-subunits SA1 and SA2 were knocked out. We find that ΔSA1 cells gain intra-TAD interactions and increase compartmentalisation. ΔSA2 cells have longer loops and a less compartmentalised genome. These results suggest that cohesinSA1 forms longer loops, while cohesinSA2 plays a role in forming and maintaining intra-TAD interactions. Our data supports the model that the genome is provided structure in 3D by the counter-balancing of loop formation on one hand, and compartmentalization on the other hand. By differentially controlling loops, cohesinSA1 and cohesinSA2 therefore also affect nuclear compartmentalization. We show that GENOVA is an easy to use R-package, that allows researchers to explore Hi-C data in great detail.
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Affiliation(s)
- Robin H van der Weide
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Judith H I Haarhuis
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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177
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Su Z, Liu G, Zhang B, Lin Z, Huang D. Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene. Genes (Basel) 2021; 12:genes12050759. [PMID: 34067766 PMCID: PMC8156488 DOI: 10.3390/genes12050759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/15/2021] [Indexed: 02/05/2023] Open
Abstract
The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.
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Affiliation(s)
- Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
- Correspondence: (Z.S.); (D.H.)
| | - Guangyu Liu
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Bin Zhang
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Ze Lin
- Department of Central Laboratory, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Dongyang Huang
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
- Correspondence: (Z.S.); (D.H.)
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178
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Cohesin subunit Rad21 binds to the HSV-1 genome near CTCF insulator sites during latency in vivo. J Virol 2021; 95:JVI.00364-21. [PMID: 33692212 PMCID: PMC8139716 DOI: 10.1128/jvi.00364-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Herpes Simplex Virus 1 (HSV-1) is a human pathogen that has the ability to establish a lifelong infection in the host. During latency, HSV-1 genomes are chromatinized and are abundantly associated with histones in sensory neurons, yet the mechanisms that govern the latent-lytic transition remain unclear. We hypothesize that the latent-lytic switch is controlled by CTCF insulators, positioned within the HSV-1 latent genome. CTCF insulators, together with the cohesin complex, have the ability to establish and maintain chromtin loops that allow distance separated gene regions to be spatially oriented for transcriptional control. In this current study, we demonstrated that the cohesin subunit Rad21 was recruited to latent HSV-1 genomes near four of the CTCF insulators during latency. We showed that the CTCF insulator known as CTRS1/2, positioned downstream from the essential transactivating IE region of ICP4 was only enriched in Rad21 prior to but not during latency, suggesting that the CTRS1/2 insulator is not required for the maintenance of latency. Further, deletion of the CTRL2 insulator, positioned downstream from the LAT enhancer, resulted in a loss of Rad21 enrichment at insulators flanking the ICP4 region at early times post-infection in mice ganglia, suggesting that these insulators are interdependent. Finally, deletion of the CTRL2 insulator resulted in a loss of Rad21 enrichment at the CTRL2 insulator in a cell-type specific manner, and this loss of Rad21 enrichment was correlated to decreased LAT expression, suggesting that Rad21 recruitment to viral genomes is important for efficient gene expression.ImportanceCTCF insulators are important for transcriptional control and increasing evidence suggests that that CTCF insulators, together with the cohesin complex, regulate viral transcription in DNA viruses. The CTCF-cohesin interaction is important for the formation of chromatin loops, structures that orient distance separated elements in close spatial proximity for transcriptional control. Herpes Simplex Virus 1 (HSV-1) has seven putative CTCF insulators that flank the LAT and the IE, indicating that CTCF insulators play a role in the transition from latency to reactivation. Contributions from the work presented here include the finding that CTCF insulators in HSV-1 genomes are differentially enriched in the cohesin subunit Rad21, suggesting that CTCF-cohesin interactions could be establishing and anchoring chromatin loop structures to control viral transcription.
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179
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Oudelaar AM, Beagrie RA, Kassouf MT, Higgs DR. The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization. Curr Opin Genet Dev 2021; 67:18-24. [PMID: 33221670 PMCID: PMC8100094 DOI: 10.1016/j.gde.2020.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023]
Abstract
The mammalian globin gene clusters provide a paradigm for studying the relationship between genome structure and function. As blood stem cells undergo lineage specification and differentiation to form red blood cells, the chromatin structure and expression of the α-globin cluster change. The gradual activation of the α-globin genes in well-defined cell populations has enabled investigation of the structural and functional roles of its enhancers, promoters and boundary elements. Recent studies of gene regulatory processes involving these elements at the mouse α-globin cluster have brought new insights into the general principles underlying the three-dimensional structure of the genome and its relationship to gene expression throughout time.
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Affiliation(s)
| | - Robert A Beagrie
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mira T Kassouf
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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180
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Abstract
Single-cell sequencing-based methods for profiling gene transcript levels have revealed substantial heterogeneity in expression levels among morphologically indistinguishable cells. This variability has important functional implications for tissue biology and disease states such as cancer. Mapping of epigenomic information such as chromatin accessibility, nucleosome positioning, histone tail modifications and enhancer-promoter interactions in both bulk-cell and single-cell samples has shown that these characteristics of chromatin state contribute to expression or repression of associated genes. Advances in single-cell epigenomic profiling methods are enabling high-resolution mapping of chromatin states in individual cells. Recent studies using these techniques provide evidence that variations in different aspects of chromatin organization collectively define gene expression heterogeneity among otherwise highly similar cells.
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Affiliation(s)
- Benjamin Carter
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
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181
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Xiang JF, Corces VG. Regulation of 3D chromatin organization by CTCF. Curr Opin Genet Dev 2021; 67:33-40. [PMID: 33259986 PMCID: PMC8084898 DOI: 10.1016/j.gde.2020.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 01/12/2023]
Abstract
Studies of nuclear architecture using chromosome conformation capture methods have provided a detailed view of how chromatin folds in the 3D nuclear space. New variants of this technology now afford unprecedented resolution and allow the identification of ever smaller folding domains that offer new insights into the mechanisms by which this organization is established and maintained. Here we review recent results in this rapidly evolving field with an emphasis on CTCF function, with the goal of gaining a mechanistic understanding of the principles by which chromatin is folded in the eukaryotic nucleus.
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Affiliation(s)
- Jian-Feng Xiang
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA
| | - Victor G Corces
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA.
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182
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Wang W, Song F, Feng X, Chu X, Dai H, Tian J, Fang X, Song F, Liu B, Li L, Li X, Zhao Y, Zheng H, Chen K. Functional Interrogation of Enhancer Connectome Prioritizes Candidate Target Genes at Ovarian Cancer Susceptibility Loci. Front Genet 2021; 12:646179. [PMID: 33815481 PMCID: PMC8017555 DOI: 10.3389/fgene.2021.646179] [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: 12/25/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Identifying causal regulatory variants and their target genes from the majority of non-coding disease-associated genetic loci is the main challenge in post-Genome-Wide Association Studies (GWAS) functional studies. Although chromosome conformation capture (3C) and its derivative technologies have been successfully applied to nominate putative causal genes for non-coding variants, many GWAS target genes have not been identified yet. This study generated a high-resolution contact map from epithelial ovarian cancer (EOC) cells with two H3K27ac-HiChIP libraries and analyzed the underlying gene networks for 15 risk loci identified from the largest EOC GWAS. By combinatory analysis of 4,021 fine-mapped credible variants of EOC GWAS and high-resolution contact map, we obtained 162 target genes that mainly enriched in cancer related pathways. Compared with GTEx eQTL genes in ovarian tissue and annotated proximal genes, 132 HiChIP targets were first identified for EOC causal variants. More than half of the credible variants (CVs) involved interactions that were over 185 kb in distance, indicating that long-range transcriptional regulation is an important mechanism for the function of GWAS variants in EOC. We also found that many HiChIP gene targets showed significantly differential expressions between normal ovarian and EOC tumor samples. We validated one of these targets by manipulating the rs9303542 located region with CRISPR-Cas9 deletion and dCas9-VP64 activation experiments and found altered expression of HOXB7 and HOXB8 at 17q21.32. This study presents a systematic analysis to identify putative target genes for causal variants of EOC, providing an in-depth investigation of the mechanisms of non-coding regulatory variants in the etiology and pathogenesis of ovarian cancer.
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Affiliation(s)
- Wei Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jing Tian
- Department of Gynecological Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xuan Fang
- The Third Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangchun Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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183
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Kang MA, Lee JS. A Newly Assigned Role of CTCF in Cellular Response to Broken DNAs. Biomolecules 2021; 11:363. [PMID: 33673494 PMCID: PMC7997455 DOI: 10.3390/biom11030363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023] Open
Abstract
Best known as a transcriptional factor, CCCTC-binding factor (CTCF) is a highly conserved multifunctional DNA-binding protein with 11 zinc fingers. It functions in diverse genomic processes, including transcriptional activation/repression, insulation, genome imprinting and three-dimensional genome organization. A big surprise has recently emerged with the identification of CTCF engaging in the repair of DNA double-strand breaks (DSBs) and in the maintenance of genome fidelity. This discovery now adds a new dimension to the multifaceted attributes of this protein. CTCF facilitates the most accurate DSB repair via homologous recombination (HR) that occurs through an elaborate pathway, which entails a chain of timely assembly/disassembly of various HR-repair complexes and chromatin modifications and coordinates multistep HR processes to faithfully restore the original DNA sequences of broken DNA sites. Understanding the functional crosstalks between CTCF and other HR factors will illuminate the molecular basis of various human diseases that range from developmental disorders to cancer and arise from impaired repair. Such knowledge will also help understand the molecular mechanisms underlying the diverse functions of CTCF in genome biology. In this review, we discuss the recent advances regarding this newly assigned versatile role of CTCF and the mechanism whereby CTCF functions in DSB repair.
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Affiliation(s)
| | - Jong-Soo Lee
- Department of Life Sciences, Ajou University, Suwon 16499, Korea;
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184
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What do Transcription Factors Interact With? J Mol Biol 2021; 433:166883. [PMID: 33621520 DOI: 10.1016/j.jmb.2021.166883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Although we have made significant progress, we still possess a limited understanding of how genomic and epigenomic information directs gene expression programs through sequence-specific transcription factors (TFs). Extensive research has settled on three general classes of TF targets in metazoans: promoter accessibility via chromatin regulation (e.g., SAGA), assembly of the general transcription factors on promoter DNA (e.g., TFIID), and recruitment of RNA polymerase (Pol) II (e.g., Mediator) to establish a transcription pre-initiation complex (PIC). Here we discuss TFs and their targets. We also place this in the context of our current work with Saccharomyces (yeast), where we find that promoters typically lack an architecture that supports TF function. Moreover, yeast promoters that support TF binding also display interactions with cofactors like SAGA and Mediator, but not TFIID. It is unknown to what extent all genes in metazoans require TFs and their cofactors.
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185
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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186
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Lin D, Sanders J, Noble WS. HiCRep.py: fast comparison of Hi-C contact matrices in Python. Bioinformatics 2021; 37:2996-2997. [PMID: 33576390 PMCID: PMC8479650 DOI: 10.1093/bioinformatics/btab097] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/17/2020] [Accepted: 02/08/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Hi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to assess experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high-resolution Hi-C data or on large single-cell Hi-C datasets. RESULTS We introduce a Python implementation of HiCRep and demonstrate that it is much faster and consumes much less memory than the existing R implementation. Furthermore, we give examples of HiCRep's ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data. AVAILABILITY AND IMPLEMENTATION HiCRep.py and its documentation are available with a GPL license at https://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dejun Lin
- Department of Genome Sciences, University of Washington, Seattle, WA 98040, USA
| | - Justin Sanders
- Department of Computer Science, Brown University, Providence, RI 02912, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98040, USA,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98040, USA,To whom correspondence should be addressed.
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187
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Bertero A, Rosa-Garrido M. Three-dimensional chromatin organization in cardiac development and disease. J Mol Cell Cardiol 2021; 151:89-105. [PMID: 33242466 PMCID: PMC11056610 DOI: 10.1016/j.yjmcc.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Recent technological advancements in the field of chromatin biology have rewritten the textbook on nuclear organization. We now appreciate that the folding of chromatin in the three-dimensional space (i.e. its 3D "architecture") is non-random, hierarchical, and highly complex. While 3D chromatin structure is partially encoded in the primary sequence and thereby broadly conserved across cell types and states, a substantial portion of the genome seems to be dynamic during development or in disease. Moreover, there is growing evidence that at least some of the 3D structure of chromatin is functionally linked to gene regulation, both being modulated by and impacting on multiple nuclear processes (including DNA replication, transcription, and RNA splicing). In recent years, these new concepts have nourished several investigations about the functional role of 3D chromatin topology dynamics in the heart during development and disease. This review aims to provide a comprehensive overview of our current understanding in this field, and to discuss how this knowledge can inform further research as well as clinical practice.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA.
| | - Manuel Rosa-Garrido
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, 650 Charles Young Dr, Los Angeles, CA 90095, USA.
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188
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Dai HQ, Hu H, Lou J, Ye AY, Ba Z, Zhang X, Zhang Y, Zhao L, Yoon HS, Chapdelaine-Williams AM, Kyritsis N, Chen H, Johnson K, Lin S, Conte A, Casellas R, Lee CS, Alt FW. Loop extrusion mediates physiological Igh locus contraction for RAG scanning. Nature 2021; 590:338-343. [PMID: 33442057 PMCID: PMC9037962 DOI: 10.1038/s41586-020-03121-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023]
Abstract
RAG endonuclease initiates Igh V(D)J recombination in progenitor B cells by binding a JH-recombination signal sequence (RSS) within a recombination centre (RC) and then linearly scanning upstream chromatin, presented by loop extrusion mediated by cohesin, for convergent D-RSSs1,2. The utilization of convergently oriented RSSs and cryptic RSSs is intrinsic to long-range RAG scanning3. Scanning of RAG from the DJH-RC-RSS to upstream convergent VH-RSSs is impeded by D-proximal CTCF-binding elements (CBEs)2-5. Primary progenitor B cells undergo a mechanistically undefined contraction of the VH locus that is proposed to provide distal VHs access to the DJH-RC6-9. Here we report that an inversion of the entire 2.4-Mb VH locus in mouse primary progenitor B cells abrogates rearrangement of both VH-RSSs and normally convergent cryptic RSSs, even though locus contraction still occurs. In addition, this inversion activated both the utilization of cryptic VH-RSSs that are normally in opposite orientation and RAG scanning beyond the VH locus through several convergent CBE domains to the telomere. Together, these findings imply that broad deregulation of CBE impediments in primary progenitor B cells promotes RAG scanning of the VH locus mediated by loop extrusion. We further found that the expression of wings apart-like protein homologue (WAPL)10, a cohesin-unloading factor, was low in primary progenitor B cells compared with v-Abl-transformed progenitor B cell lines that lacked contraction and RAG scanning of the VH locus. Correspondingly, depletion of WAPL in v-Abl-transformed lines activated both processes, further implicating loop extrusion in the locus contraction mechanism.
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Affiliation(s)
- Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
| | - Hongli Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jiangman Lou
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhaoqing Ba
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yiwen Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lijuan Zhao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hye Suk Yoon
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aimee M. Chapdelaine-Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nia Kyritsis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Huan Chen
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kerstin Johnson
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sherry Lin
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, and Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, and Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Cheng-Sheng Lee
- Institute of Molecular and Cellular Biology, Department of Life Sciences, Hsinchu, Taiwan, 30013, R.O.C.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Correspondence: ; ; . Correspondence and requests for materials should be addressed to F.W.A
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189
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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: 40] [Impact Index Per Article: 13.3] [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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190
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Singh P, Pesenti ME, Maffini S, Carmignani S, Hedtfeld M, Petrovic A, Srinivasamani A, Bange T, Musacchio A. BUB1 and CENP-U, Primed by CDK1, Are the Main PLK1 Kinetochore Receptors in Mitosis. Mol Cell 2021; 81:67-87.e9. [PMID: 33248027 PMCID: PMC7837267 DOI: 10.1016/j.molcel.2020.10.040] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/08/2020] [Accepted: 10/28/2020] [Indexed: 02/02/2023]
Abstract
Reflecting its pleiotropic functions, Polo-like kinase 1 (PLK1) localizes to various sub-cellular structures during mitosis. At kinetochores, PLK1 contributes to microtubule attachments and mitotic checkpoint signaling. Previous studies identified a wealth of potential PLK1 receptors at kinetochores, as well as requirements for various mitotic kinases, including BUB1, Aurora B, and PLK1 itself. Here, we combine ectopic localization, in vitro reconstitution, and kinetochore localization studies to demonstrate that most and likely all of the PLK1 is recruited through BUB1 in the outer kinetochore and centromeric protein U (CENP-U) in the inner kinetochore. BUB1 and CENP-U share a constellation of sequence motifs consisting of a putative PP2A-docking motif and two neighboring PLK1-docking sites, which, contingent on priming phosphorylation by cyclin-dependent kinase 1 and PLK1 itself, bind PLK1 and promote its dimerization. Our results rationalize previous observations and describe a unifying mechanism for recruitment of PLK1 to human kinetochores.
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Affiliation(s)
- Priyanka Singh
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marion E Pesenti
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Sara Carmignani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marius Hedtfeld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Anupallavi Srinivasamani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitätsstrasse, 45141 Essen, Germany.
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191
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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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192
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Niu L, Shen W, Shi Z, Tan Y, He N, Wan J, Sun J, Zhang Y, Huang Y, Wang W, Fang C, Li J, Zheng P, Cheung E, Chen Y, Li L, Hou C. Three-dimensional folding dynamics of the Xenopus tropicalis genome. Nat Genet 2021; 53:1075-1087. [PMID: 34099928 PMCID: PMC8270788 DOI: 10.1038/s41588-021-00878-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023]
Abstract
Animal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.
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Affiliation(s)
- Longjian Niu
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Shen
- grid.35155.370000 0004 1790 4137Department of Bioinformatics, Huazhong Agricultural University, Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Zhaoying Shi
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yongjun Tan
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Na He
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Wan
- grid.35155.370000 0004 1790 4137Department of Bioinformatics, Huazhong Agricultural University, Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Jialei Sun
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuedong Zhang
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yingzhang Huang
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenjing Wang
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chao Fang
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China ,grid.437123.00000 0004 1794 8068Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, China
| | - Jiashuo Li
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Piaopiao Zheng
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Edwin Cheung
- grid.437123.00000 0004 1794 8068Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, China ,grid.437123.00000 0004 1794 8068Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, China
| | - Yonglong Chen
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Li Li
- grid.35155.370000 0004 1790 4137Department of Bioinformatics, Huazhong Agricultural University, Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Chunhui Hou
- grid.263817.9Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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193
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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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194
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Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cell Mol Life Sci 2021; 78:7519-7536. [PMID: 34657170 PMCID: PMC8629902 DOI: 10.1007/s00018-021-03946-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022]
Abstract
CCCTC-binding factor (CTCF) plays fundamental roles in transcriptional regulation and chromatin architecture maintenance. CTCF is also a tumour suppressor frequently mutated in cancer, however, the structural and functional impact of mutations have not been examined. We performed molecular and structural characterisation of five cancer-specific CTCF missense zinc finger (ZF) mutations occurring within key intra- and inter-ZF residues. Functional characterisation of CTCF ZF mutations revealed a complete (L309P, R339W, R377H) or intermediate (R339Q) abrogation as well as an enhancement (G420D) of the anti-proliferative effects of CTCF. DNA binding at select sites was disrupted and transcriptional regulatory activities abrogated. Molecular docking and molecular dynamics confirmed that mutations in residues specifically contacting DNA bases or backbone exhibited loss of DNA binding. However, R339Q and G420D were stabilised by the formation of new primary DNA bonds, contributing to gain-of-function. Our data confirm that a spectrum of loss-, change- and gain-of-function impacts on CTCF zinc fingers are observed in cell growth regulation and gene regulatory activities. Hence, diverse cellular phenotypes of mutant CTCF are clearly explained by examining structure-function relationships.
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195
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Datta S, Lecomte L, Haering CH. Structural insights into DNA loop extrusion by SMC protein complexes. Curr Opin Struct Biol 2020; 65:102-109. [DOI: 10.1016/j.sbi.2020.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
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196
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Kim Y, Yu H. Shaping of the 3D genome by the ATPase machine cohesin. Exp Mol Med 2020; 52:1891-1897. [PMID: 33268833 PMCID: PMC8080590 DOI: 10.1038/s12276-020-00526-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023] Open
Abstract
The spatial organization of the genome is critical for fundamental biological processes, including transcription, genome replication, and segregation. Chromatin is compacted and organized with defined patterns and proper dynamics during the cell cycle. Aided by direct visualization and indirect genome reconstruction tools, recent discoveries have advanced our understanding of how interphase chromatin is dynamically folded at the molecular level. Here, we review the current understanding of interphase genome organization with a focus on the major regulator of genome structure, the cohesin complex. We further discuss how cohesin harnesses the energy of ATP hydrolysis to shape the genome by extruding chromatin loops.
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Affiliation(s)
- Yoori Kim
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China.
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197
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Hansen AS. CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism. Nucleus 2020; 11:132-148. [PMID: 32631111 PMCID: PMC7566886 DOI: 10.1080/19491034.2020.1782024] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/10/2023] Open
Abstract
Mammalian genome structure is closely linked to function. At the scale of kilobases to megabases, CTCF and cohesin organize the genome into chromatin loops. Mechanistically, cohesin is proposed to extrude chromatin loops bidirectionally until it encounters occupied CTCF DNA-binding sites. Curiously, loops form predominantly between CTCF binding sites in a convergent orientation. How CTCF interacts with and blocks cohesin extrusion in an orientation-specific manner has remained a mechanistic mystery. Here, we review recent papers that have shed light on these processes and suggest a multi-step interaction between CTCF and cohesin. This interaction may first involve a pausing step, where CTCF halts cohesin extrusion, followed by a stabilization step of the CTCF-cohesin complex, resulting in a chromatin loop. Finally, we discuss our own recent studies on an internal RNA-Binding Region (RBRi) in CTCF to elucidate its role in regulating CTCF clustering, target search mechanisms and chromatin loop formation and future challenges.
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Affiliation(s)
- Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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198
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Valletta M, Russo R, Baglivo I, Russo V, Ragucci S, Sandomenico A, Iaccarino E, Ruvo M, De Feis I, Angelini C, Iachettini S, Biroccio A, Pedone PV, Chambery A. Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF. Int J Mol Sci 2020; 21:E8950. [PMID: 33255744 PMCID: PMC7728349 DOI: 10.3390/ijms21238950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/18/2022] Open
Abstract
The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases, and BRG1, further supports the interplay between master regulators of mammalian genome folding. Here, we report a comprehensive LC-MS/MS mapping of the components of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature, and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4-8 of CTCF, thus, suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.
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Affiliation(s)
- Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Emanuela Iaccarino
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Italia De Feis
- Istituto per le Applicazioni del Calcolo IAC ‘M. Picone’, National Research Council, 80131 Napoli, Italy; (I.D.F.); (C.A.)
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo IAC ‘M. Picone’, National Research Council, 80131 Napoli, Italy; (I.D.F.); (C.A.)
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Roma, Italy; (S.I.); (A.B.)
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Roma, Italy; (S.I.); (A.B.)
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
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199
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Oudelaar AM, Higgs DR. The relationship between genome structure and function. Nat Rev Genet 2020; 22:154-168. [PMID: 33235358 DOI: 10.1038/s41576-020-00303-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Precise patterns of gene expression in metazoans are controlled by three classes of regulatory elements: promoters, enhancers and boundary elements. During differentiation and development, these elements form specific interactions in dynamic higher-order chromatin structures. However, the relationship between genome structure and its function in gene regulation is not completely understood. Here we review recent progress in this field and discuss whether genome structure plays an instructive role in regulating gene expression or is a reflection of the activity of the regulatory elements of the genome.
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Affiliation(s)
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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200
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Gu B, Comerci CJ, McCarthy DG, Saurabh S, Moerner WE, Wysocka J. Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging. Mol Cell 2020; 80:699-711.e7. [PMID: 33091336 PMCID: PMC7725164 DOI: 10.1016/j.molcel.2020.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/30/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022]
Abstract
CCCTC-binding factor (CTCF) and cohesin play critical roles in organizing mammalian genomes into topologically associating domains (TADs). Here, by combining genetic engineering with quantitative super-resolution stimulated emission depletion (STED) microscopy, we demonstrate that in living cells, CTCF forms clusters typically containing 2-8 molecules. A fraction of CTCF clusters, enriched for those with ≥3 molecules, are coupled with cohesin complexes with a characteristic physical distance suggestive of a defined molecular interaction. Acute degradation of the cohesin unloader WAPL or transcriptional inhibition (TI) result in increased CTCF clustering. Furthermore, the effect of TI on CTCF clusters is alleviated by the acute loss of the cohesin subunit SMC3. Our study provides quantitative characterization of CTCF clusters in living cells, uncovers the opposing effects of cohesin and transcription on CTCF clustering, and highlights the power of quantitative super-resolution microscopy as a tool to bridge the gap between biochemical and genomic methodologies in chromatin research.
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Affiliation(s)
- Bo Gu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Colin J Comerci
- Department of Chemistry, Stanford University, Stanford, CA, USA; Biophysics Program, Stanford University, Stanford, CA, USA
| | | | - Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA; Biophysics Program, Stanford University, Stanford, CA, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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