1
|
Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024; 15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
Collapse
Affiliation(s)
- Aayush Kant
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zixian Guo
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Wing Shun Li
- Department of Applied Physics, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Vasundhara Agrawal
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Emily Pujadas
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Luay Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- ICREA, Barcelona, 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
2
|
Peng Y, Zhu Y, Wu L, Deng F. Clinical study and genetic analysis of Cornelia de Lange syndrome caused by a novel MAU2 gene variant in a Chinese boy. Mol Genet Genomic Med 2024; 12:e2318. [PMID: 37962004 PMCID: PMC10767608 DOI: 10.1002/mgg3.2318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/24/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is mainly characterized by specific facial features, growth retardation, and bone deformities. Seven genes reportedly cause CdLS. Recent research has reported that loss-of-function variants affecting MAU2, which encodes a regulator of the cohesin complex, can cause CdLS. Thus far, only one MAU2-CdLS case has been reported worldwide. METHODS We detected a novel variant in MAU2 gene, NM_015329, c.526C>T (p.Arg176Trp) in a Chinese patient with CdLS, constructed a plasmid for in vitro transcriptional and protein level analysis, and analyzed the interaction between the MAU2/NIPBL complex using molecular dynamics (MD). RESULTS The results showed that the level of the exogenous MAU2 mutant protein was significantly reduced compared with that of the exogenous wild-type protein. However, MD analysis predicted an increased binding free energy between the MAU2 and NIPBL proteins that may impact the structural stability of the complex. CONCLUSION We investigated a MAU2-CdLS case in a Chinese family, which strengthens the association between MAU2 variants and CdLS phenotypes. We therefore propose that MAU2 be included in the CdLS gene screening list.
Collapse
Affiliation(s)
- Yin Peng
- Department of NephrologyAnhui Provincial Children's HospitalHefeiChina
| | - Ying Zhu
- Department of NephrologyAnhui Provincial Children's HospitalHefeiChina
| | - Lin Wu
- Department of NephrologyAnhui Provincial Children's HospitalHefeiChina
| | - Fang Deng
- Department of NephrologyAnhui Provincial Children's HospitalHefeiChina
| |
Collapse
|
3
|
Kaur P, Lu X, Xu Q, Irvin EM, Pappas C, Zhang H, Finkelstein IJ, Shi Z, Tao YJ, Yu H, Wang H. High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL. J Biol Chem 2023; 299:105296. [PMID: 37774974 PMCID: PMC10656236 DOI: 10.1016/j.jbc.2023.105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023] Open
Abstract
3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. In this study, high-speed atomic force microscopy imaging reveals that cohesin-NIPBL captures DNA through arm extension, assisted by feet (shorter protrusions), and followed by transfer of DNA to its lower compartment (SMC heads, RAD21, SA1, and NIPBL). While binding at the lower compartment, arm extension leads to the capture of a second DNA segment and the initiation of a DNA loop that is independent of ATP hydrolysis. The feet are likely contributed by the C-terminal domains of SA1 and NIPBL and can transiently bind to DNA to facilitate the loading of the cohesin complex onto DNA. Furthermore, high-speed atomic force microscopy imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results advance our understanding of cohesin by establishing direct experimental evidence for a multistep DNA-binding mechanism mediated by dynamic protein conformational changes.
Collapse
Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA.
| | - Xiaotong Lu
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Qi Xu
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang Province, P.R. China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, P.R. China
| | | | - Colette Pappas
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Hongshan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Zhubing Shi
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang Province, P.R. China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, P.R. China
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Hongtao Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang Province, P.R. China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, P.R. China
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA; Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA.
| |
Collapse
|
4
|
Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
Collapse
Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
| |
Collapse
|
5
|
Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L. Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops. Nucleic Acids Res 2022; 50:2826-2835. [PMID: 35188572 PMCID: PMC8934669 DOI: 10.1093/nar/gkac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022] Open
Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
Collapse
Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
| |
Collapse
|
6
|
Breimann L, Morao AK, Kim J, Sebastian Jimenez D, Maryn N, Bikkasani K, Carrozza MJ, Albritton SE, Kramer M, Street LA, Cerimi K, Schumann VF, Bahry E, Preibisch S, Woehler A, Ercan S. The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding. J Cell Sci 2022; 135:jcs258818. [PMID: 34918745 PMCID: PMC8917352 DOI: 10.1242/jcs.258818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Condensin is a multi-subunit structural maintenance of chromosomes (SMC) complex that binds to and compacts chromosomes. Here, we addressed the regulation of condensin binding dynamics using Caenorhabditis elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes DPY-27 binding to X chromosomes. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C sequencing data from the dpy-21 null mutant showed little change compared to wild-type data, uncoupling Hi-C-measured long-range DNA contacts from transcriptional repression of the X chromosomes. Taken together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.
Collapse
Affiliation(s)
- Laura Breimann
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
- Institute for Biology, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - David Sebastian Jimenez
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Nina Maryn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Krishna Bikkasani
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael J. Carrozza
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sarah E. Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Kustrim Cerimi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Vic-Fabienne Schumann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew Woehler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| |
Collapse
|
7
|
Amândio AR, Beccari L, Lopez-Delisle L, Mascrez B, Zakany J, Gitto S, Duboule D. Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster. Genes Dev 2021; 35:1490-1509. [PMID: 34711654 PMCID: PMC8559674 DOI: 10.1101/gad.348934.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022]
Abstract
Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer-promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates.
Collapse
Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
- Collège de France, 75231 Paris, France
| |
Collapse
|
8
|
García-Gutiérrez P, García-Domínguez M. BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome. Front Mol Biosci 2021; 8:709232. [PMID: 34386522 PMCID: PMC8353280 DOI: 10.3389/fmolb.2021.709232] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental syndrome with complex multisystem phenotypic features. It has been traditionally considered a cohesinopathy together with other phenotypically related diseases because of their association with mutations in subunits of the cohesin complex. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably and, although their precise molecular mechanisms are not well defined yet, the potential pathomechanisms underlying these diverse developmental defects have been theoretically linked to alterations of the cohesin complex function. The cohesin complex plays a critical role in sister chromatid cohesion, but this function is not affected in CdLS. In the last decades, a non-cohesion-related function of this complex on transcriptional regulation has been well established and CdLS pathoetiology has been recently associated to gene expression deregulation. Up to 70% of CdLS cases are linked to mutations in the cohesin-loading factor NIPBL, which has been shown to play a prominent function on chromatin architecture and transcriptional regulation. Therefore, it has been suggested that CdLS can be considered a transcriptomopathy. Actually, CdLS-like phenotypes have been associated to mutations in chromatin-associated proteins, as KMT2A, AFF4, EP300, TAF6, SETD5, SMARCB1, MAU2, ZMYND11, MED13L, PHIP, ARID1B, NAA10, BRD4 or ANKRD11, most of which have no known direct association with cohesin. In the case of BRD4, a critical highly investigated transcriptional coregulator, an interaction with NIPBL has been recently revealed, providing evidence on their cooperation in transcriptional regulation of developmentally important genes. This new finding reinforces the notion of an altered gene expression program during development as the major etiological basis for CdLS. In this review, we intend to integrate the recent available evidence on the molecular mechanisms underlying the clinical manifestations of CdLS, highlighting data that favors a transcription-centered framework, which support the idea that CdLS could be conceptualized as a transcriptomopathy.
Collapse
Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| |
Collapse
|
9
|
Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
Collapse
Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| |
Collapse
|
10
|
Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
Collapse
Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| |
Collapse
|
11
|
Zabolotnaya E, Mela I, Henderson RM, Robinson NP. Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion? Biochem Soc Trans 2020; 48:2359-2376. [PMID: 33300987 PMCID: PMC7752040 DOI: 10.1042/bst20170168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The bacterial SbcC/SbcD DNA repair proteins were identified over a quarter of a century ago. Following the subsequent identification of the homologous Mre11/Rad50 complex in the eukaryotes and archaea, it has become clear that this conserved chromosomal processing machinery is central to DNA repair pathways and the maintenance of genomic stability in all forms of life. A number of experimental studies have explored this intriguing genome surveillance machinery, yielding significant insights and providing conceptual advances towards our understanding of how this complex operates to mediate DNA repair. However, the inherent complexity and dynamic nature of this chromosome-manipulating machinery continue to obfuscate experimental interrogations, and details regarding the precise mechanisms that underpin the critical repair events remain unanswered. This review will summarize our current understanding of the dramatic structural changes that occur in Mre11/Rad50 complex to mediate chromosomal tethering and accomplish the associated DNA processing events. In addition, undetermined mechanistic aspects of the DNA enzymatic pathways driven by this vital yet enigmatic chromosomal surveillance and repair apparatus will be discussed. In particular, novel and putative models of DNA damage recognition will be considered and comparisons will be made between the modes of action of the Rad50 protein and other related ATPases of the overarching SMC superfamily.
Collapse
Affiliation(s)
| | - Ioanna Mela
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | | | - Nicholas P. Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, U.K
| |
Collapse
|
12
|
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]
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Abstract
Mutations of the cohesin complex in human cancer were first discovered ~10 years ago. Since then, researchers worldwide have demonstrated that cohesin is among the most commonly mutated protein complexes in cancer. Inactivating mutations in genes encoding cohesin subunits are common in bladder cancers, paediatric sarcomas, leukaemias, brain tumours and other cancer types. Also in those 10 years, the prevailing view of the functions of cohesin in cell biology has undergone a revolutionary transformation. Initially, the predominant view of cohesin was as a ring that encircled and cohered replicated chromosomes until its cleavage triggered the metaphase-to-anaphase transition. As such, early studies focused on the role of tumour-derived cohesin mutations in the fidelity of chromosome segregation and aneuploidy. However, over the past 5 years the cohesin field has shifted dramatically, and research now focuses on the primary role of cohesin in generating, maintaining and regulating the intra-chromosomal DNA looping events that modulate 3D genome organization and gene expression. This Review focuses on recent discoveries in the cohesin field that provide insight into the role of cohesin inactivation in cancer pathogenesis, and opportunities for exploiting these findings for the clinical benefit of patients with cohesin-mutant cancers.
Collapse
Affiliation(s)
- Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC, USA.
| |
Collapse
|
15
|
Kong M, Cutts EE, Pan D, Beuron F, Kaliyappan T, Xue C, Morris EP, Musacchio A, Vannini A, Greene EC. Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA. Mol Cell 2020; 79:99-114.e9. [PMID: 32445620 PMCID: PMC7335352 DOI: 10.1016/j.molcel.2020.04.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/08/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential for genome organization from bacteria to humans, but their mechanisms of action remain poorly understood. Here, we characterize human SMC complexes condensin I and II and unveil the architecture of the human condensin II complex, revealing two putative DNA-entrapment sites. Using single-molecule imaging, we demonstrate that both condensin I and II exhibit ATP-dependent motor activity and promote extensive and reversible compaction of double-stranded DNA. Nucleosomes are incorporated into DNA loops during compaction without being displaced from the DNA, indicating that condensin complexes can readily act upon nucleosome-bound DNA molecules. These observations shed light on critical processes involved in genome organization in human cells.
Collapse
Affiliation(s)
- Muwen Kong
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Thangavelu Kaliyappan
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
16
|
Loop extrusion: theory meets single-molecule experiments. Curr Opin Cell Biol 2020; 64:124-138. [PMID: 32534241 DOI: 10.1016/j.ceb.2020.04.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/20/2022]
Abstract
Chromosomes are organized as chromatin loops that promote segregation, enhancer-promoter interactions, and other genomic functions. Loops were hypothesized to form by 'loop extrusion,' by which structural maintenance of chromosomes (SMC) complexes, such as condensin and cohesin, bind to chromatin, reel it in, and extrude it as a loop. However, such exotic motor activity had never been observed. Following an explosion of indirect evidence, recent single-molecule experiments directly imaged DNA loop extrusion by condensin and cohesin in vitro. These experiments observe rapid (kb/s) extrusion that requires ATP hydrolysis and stalls under pN forces. Surprisingly, condensin extrudes loops asymmetrically, challenging previous models. Extrusion by cohesin is symmetric but requires the protein Nipbl. We discuss how SMC complexes may perform their functions on chromatin in vivo.
Collapse
|
17
|
Allyn BM, Lee KD, Bassing CH. Genome Topology Control of Antigen Receptor Gene Assembly. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:2617-2626. [PMID: 32366683 PMCID: PMC7440635 DOI: 10.4049/jimmunol.1901356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/22/2020] [Indexed: 02/02/2023]
Abstract
The past decade has increased our understanding of how genome topology controls RAG endonuclease-mediated assembly of lymphocyte AgR genes. New technologies have illuminated how the large IgH, Igκ, TCRα/δ, and TCRβ loci fold into compact structures that place their numerous V gene segments in similar three-dimensional proximity to their distal recombination center composed of RAG-bound (D)J gene segments. Many studies have shown that CTCF and cohesin protein-mediated chromosome looping have fundamental roles in lymphocyte lineage- and developmental stage-specific locus compaction as well as broad usage of V segments. CTCF/cohesin-dependent loops have also been shown to direct and restrict RAG activity within chromosome domains. We summarize recent work in elucidating molecular mechanisms that govern three-dimensional chromosome organization and in investigating how these dynamic mechanisms control V(D)J recombination. We also introduce remaining questions for how CTCF/cohesin-dependent and -independent genome architectural mechanisms might regulate compaction and recombination of AgR loci.
Collapse
Affiliation(s)
- Brittney M Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
18
|
Li Y, Haarhuis JHI, Sedeño Cacciatore Á, Oldenkamp R, van Ruiten MS, Willems L, Teunissen H, Muir KW, de Wit E, Rowland BD, Panne D. The structural basis for cohesin-CTCF-anchored loops. Nature 2020; 578:472-476. [PMID: 31905366 PMCID: PMC7035113 DOI: 10.1038/s41586-019-1910-z] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
Cohesin catalyses the folding of the genome into loops that are anchored by CTCF1. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of human cohesin. We report a crystal structure of SA2-SCC1 in complex with CTCF at a resolution of 2.7 Å, which reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF binding sites. A similar motif is present in a number of established and newly identified cohesin ligands, including the cohesin release factor WAPL2,3. Our data suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables the dynamic regulation of chromatin folding by cohesin and CTCF.
Collapse
Affiliation(s)
- Yan Li
- European Molecular Biology Laboratory, Grenoble, France
| | - Judith H I Haarhuis
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Roel Oldenkamp
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjon S van Ruiten
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Laureen Willems
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kyle W Muir
- European Molecular Biology Laboratory, Grenoble, France.
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Benjamin D Rowland
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France.
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
| |
Collapse
|
19
|
Kim Y, Shi Z, Zhang H, Finkelstein IJ, Yu H. Human cohesin compacts DNA by loop extrusion. Science 2019; 366:1345-1349. [PMID: 31780627 PMCID: PMC7387118 DOI: 10.1126/science.aaz4475] [Citation(s) in RCA: 397] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/11/2019] [Accepted: 11/16/2019] [Indexed: 12/23/2022]
Abstract
Cohesin is a chromosome-bound, multisubunit adenosine triphosphatase complex. After loading onto chromosomes, it generates loops to regulate chromosome functions. It has been suggested that cohesin organizes the genome through loop extrusion, but direct evidence is lacking. Here, we used single-molecule imaging to show that the recombinant human cohesin-NIPBL complex compacts both naked and nucleosome-bound DNA by extruding DNA loops. DNA compaction by cohesin requires adenosine triphosphate (ATP) hydrolysis and is force sensitive. This compaction is processive over tens of kilobases at an average rate of 0.5 kilobases per second. Compaction of double-tethered DNA suggests that a cohesin dimer extrudes DNA loops bidirectionally. Our results establish cohesin-NIPBL as an ATP-driven molecular machine capable of loop extrusion.
Collapse
Affiliation(s)
- Yoori Kim
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhubing Shi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongshan Zhang
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|