1
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Liu Y, Min Y, Liu Y, Watanabe Y. Phosphorylation of Rec8 cohesin complexes regulates mono-orientation of kinetochores in meiosis I. Life Sci Alliance 2024; 7:e202302556. [PMID: 38448160 PMCID: PMC10917647 DOI: 10.26508/lsa.202302556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
In meiosis I, unlike in mitosis, sister kinetochores are captured by microtubules emanating from the same spindle pole (mono-orientation) and centromeric cohesion mediated by cohesin is protected in the following anaphase I. The conserved meiosis-specific kinetochore protein meikin (Moa1 in fission yeast) associates with polo-like kinase: Plo1 and regulates both mono-orientation and cohesion protection. Although the phosphorylation of Rec8-S450 by Plo1 associated with Moa1 plays a key role in cohesion protection, how Moa1-Plo1 regulates mono-orientation remains elusive. Here, we identify Plo1 phosphorylation sites in the cohesin subunits, Rec8 and Psm3. The non-phosphorylatable mutations at these sites showed specific defects in mono-orientation. These results enabled the genetic dissection of meikin functions at the centromeres.
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Affiliation(s)
- Yu Liu
- https://ror.org/04mkzax54 School of Bioengineering, Jiangnan University, Wuxi, China
- https://ror.org/04mkzax54 Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yu Min
- https://ror.org/04mkzax54 School of Bioengineering, Jiangnan University, Wuxi, China
- https://ror.org/04mkzax54 Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yongxin Liu
- https://ror.org/04mkzax54 School of Bioengineering, Jiangnan University, Wuxi, China
- https://ror.org/04mkzax54 Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yoshinori Watanabe
- https://ror.org/04mkzax54 Science Center for Future Foods, Jiangnan University, Wuxi, China
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2
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Nagasaka K, Davidson IF, Stocsits RR, Tang W, Wutz G, Batty P, Panarotto M, Litos G, Schleiffer A, Gerlich DW, Peters JM. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms. Mol Cell 2023; 83:3049-3063.e6. [PMID: 37591243 DOI: 10.1016/j.molcel.2023.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/28/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.
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Affiliation(s)
- Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Melanie Panarotto
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.
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3
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Corsi F, Rusch E, Goloborodko A. Loop extrusion rules: the next generation. Curr Opin Genet Dev 2023; 81:102061. [PMID: 37354885 DOI: 10.1016/j.gde.2023.102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/26/2023]
Abstract
The interphase genome of vertebrates contains roughly 100 000 dynamic loops formed by cohesins. These loops are thought to play important roles in many functions, but their exact contribution in each case remains hotly disputed. The key challenge in studying these loops is the lack of a single experimental technique that could reliably and comprehensively visualize their locations and dynamics. Yet, we can infer them using theoretical models that integrate complementary experimental observations. Modeling proved instrumental in showing that cohesins form loops via extrusion. The loop extrusion model made numerous successful qualitative and quantitative predictions and inspired many experiments. However, it also demonstrated limited accuracy in predicting contact maps. Recent research suggests that the original model did not fully account for the intricate details of the mechanism of loop extrusion and its complex regulation. Here, we review the progress in visualizing extrusion and characterizing the cohesin cofactors. These discoveries can be summarized as 'rules' of cohesin movement along chromosomes and incorporated into the next generation of models. Such improved models will enable more accurate inferences of positions and dynamics of cohesin loops and generate better predictions for designing experiments.
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Affiliation(s)
- Flavia Corsi
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@flavia_corsi
| | - Emma Rusch
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@emma__rush
| | - Anton Goloborodko
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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4
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Minamino M, Bouchoux C, Canal B, Diffley JFX, Uhlmann F. A replication fork determinant for the establishment of sister chromatid cohesion. Cell 2023; 186:837-849.e11. [PMID: 36693376 DOI: 10.1016/j.cell.2022.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/08/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023]
Abstract
Concomitant with DNA replication, the chromosomal cohesin complex establishes cohesion between newly replicated sister chromatids. Cohesion establishment requires acetylation of conserved cohesin lysine residues by Eco1 acetyltransferase. Here, we explore how cohesin acetylation is linked to DNA replication. Biochemical reconstitution of replication-coupled cohesin acetylation reveals that transient DNA structures, which form during DNA replication, control the acetylation reaction. As polymerases complete lagging strand replication, strand displacement synthesis produces DNA flaps that are trimmed to result in nicked double-stranded DNA. Both flaps and nicks stimulate cohesin acetylation, while subsequent nick ligation to complete Okazaki fragment maturation terminates the acetylation reaction. A flapped or nicked DNA substrate constitutes a transient molecular clue that directs cohesin acetylation to a window behind the replication fork, next to where cohesin likely entraps both sister chromatids. Our results provide an explanation for how DNA replication is linked to sister chromatid cohesion establishment.
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Affiliation(s)
- Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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5
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Guo Y, Wang GG. Modulation of the high-order chromatin structure by Polycomb complexes. Front Cell Dev Biol 2022; 10:1021658. [PMID: 36274840 PMCID: PMC9579376 DOI: 10.3389/fcell.2022.1021658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The multi-subunit Polycomb Repressive Complex (PRC) 1 and 2 act, either independently or synergistically, to maintain and enforce a repressive state of the target chromatin, thereby regulating the processes of cell lineage specification and organismal development. In recent years, deep sequencing-based and imaging-based technologies, especially those tailored for mapping three-dimensional (3D) chromatin organization and structure, have allowed a better understanding of the PRC complex-mediated long-range chromatin contacts and DNA looping. In this review, we review current advances as for how Polycomb complexes function to modulate and help define the high-order chromatin structure and topology, highlighting the multi-faceted roles of Polycomb proteins in gene and genome regulation.
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Affiliation(s)
- Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Yiran Guo, ; Gang Greg Wang,
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
- *Correspondence: Yiran Guo, ; Gang Greg Wang,
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6
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Choudhary K, Itzkovich Z, Alonso-Perez E, Bishara H, Dunn B, Sherlock G, Kupiec M. S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit. mBio 2022; 13:e0142022. [PMID: 35708277 PMCID: PMC9426526 DOI: 10.1128/mbio.01420-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/11/2022] Open
Abstract
During DNA replication, the newly created sister chromatids are held together until their separation at anaphase. The cohesin complex is in charge of creating and maintaining sister chromatid cohesion (SCC) in all eukaryotes. In Saccharomyces cerevisiae cells, cohesin is composed of two elongated proteins, Smc1 and Smc3, bridged by the kleisin Mcd1/Scc1. The latter also acts as a scaffold for three additional proteins, Scc3/Irr1, Wpl1/Rad61, and Pds5. Although the HEAT-repeat protein Pds5 is essential for cohesion, its precise function is still debated. Deletion of the ELG1 gene, encoding a PCNA unloader, can partially suppress the temperature-sensitive pds5-1 allele, but not a complete deletion of PDS5. We carried out a genetic screen for high-copy-number suppressors and another for spontaneously arising mutants, allowing the survival of a pds5Δ elg1Δ strain. Our results show that cells remain viable in the absence of Pds5 provided that there is both an elevation in the level of Mcd1 (which can be due to mutations in the CLN2 gene, encoding a G1 cyclin), and an increase in the level of SUMO-modified PCNA on chromatin (caused by lack of PCNA unloading in elg1Δ mutants). The elevated SUMO-PCNA levels increase the recruitment of the Srs2 helicase, which evicts Rad51 molecules from the moving fork, creating single-stranded DNA (ssDNA) regions that serve as sites for increased cohesin loading and SCC establishment. Thus, our results delineate a double role for Pds5 in protecting the cohesin ring and interacting with the DNA replication machinery. IMPORTANCE Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage. In this study, we explore the function of the essential cohesin subunit Pds5 in the regulation of sister chromatid cohesion. We performed two independent genetic screens to bypass the function of the Pds5 protein. We observe that Pds5 protein is a cohesin stabilizer, and elevating the levels of Mcd1 protein along with SUMO-PCNA accumulation on chromatin can compensate for the loss of the PDS5 gene. In addition, Pds5 plays a role in coordinating the DNA replication and sister chromatid cohesion establishment. This work elucidates the function of cohesin subunit Pds5, the G1 cyclin Cln2, and replication factors PCNA, Elg1, and Srs2 in the proper regulation of sister chromatid cohesion.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Ziv Itzkovich
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Elisa Alonso-Perez
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Hend Bishara
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Barbara Dunn
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Gavin Sherlock
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
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7
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Arruda NL, Bryan AF, Dowen JM. PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome. Epigenetics Chromatin 2022; 15:30. [PMID: 35986423 PMCID: PMC9392266 DOI: 10.1186/s13072-022-00463-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/28/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Cohesin is an important structural regulator of the genome, regulating both three-dimensional genome organization and gene expression. The core cohesin trimer interacts with various HEAT repeat accessory subunits, yielding cohesin complexes of distinct compositions and potentially distinct functions. The roles of the two mutually exclusive HEAT repeat subunits PDS5A and PDS5B are not well understood. RESULTS Here, we determine that PDS5A and PDS5B have highly similar localization patterns across the mouse embryonic stem cell (mESC) genome and they show a strong overlap with other cohesin HEAT repeat accessory subunits, STAG1 and STAG2. Using CRISPR/Cas9 genome editing to generate individual stable knockout lines for PDS5A and PDS5B, we find that loss of one PDS5 subunit does not alter the distribution of the other PDS5 subunit, nor the core cohesin complex. Both PDS5A and PDS5B are required for proper gene expression, yet they display only partially overlapping effects on gene targets. Remarkably, gene expression following dual depletion of the PDS5 HEAT repeat proteins does not completely overlap the gene expression changes caused by dual depletion of the STAG HEAT repeat proteins, despite the overlapping genomic distribution of all four proteins. Furthermore, dual loss of PDS5A and PDS5B decreases cohesin association with NIPBL and WAPL, reduces SMC3 acetylation, and does not alter overall levels of cohesin on the genome. CONCLUSIONS This work reveals the importance of PDS5A and PDS5B for proper cohesin function. Loss of either subunit has little effect on cohesin localization across the genome yet PDS5A and PDS5B are differentially required for gene expression.
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Affiliation(s)
- Nicole L Arruda
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Audra F Bryan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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8
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A walk through the SMC cycle: From catching DNAs to shaping the genome. Mol Cell 2022; 82:1616-1630. [PMID: 35477004 DOI: 10.1016/j.molcel.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes such as transcription, recombination, repair, and mitosis.
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9
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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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10
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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.
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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.
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11
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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.
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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
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12
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Fresán U, Rodríguez-Sánchez MA, Reina O, Corces VG, Espinàs ML. Haspin kinase modulates nuclear architecture and Polycomb-dependent gene silencing. PLoS Genet 2020; 16:e1008962. [PMID: 32750047 PMCID: PMC7428214 DOI: 10.1371/journal.pgen.1008962] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 08/14/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Haspin, a highly conserved kinase in eukaryotes, has been shown to be responsible for phosphorylation of histone H3 at threonine 3 (H3T3ph) during mitosis, in mammals and yeast. Here we report that haspin is the kinase that phosphorylates H3T3 in Drosophila melanogaster and it is involved in sister chromatid cohesion during mitosis. Our data reveal that haspin also phosphorylates H3T3 in interphase. H3T3ph localizes in broad silenced domains at heterochromatin and lamin-enriched euchromatic regions. Loss of haspin compromises insulator activity in enhancer-blocking assays and triggers a decrease in nuclear size that is accompanied by changes in nuclear envelope morphology. We show that haspin is a suppressor of position-effect variegation involved in heterochromatin organization. Our results also demonstrate that haspin is necessary for pairing-sensitive silencing and it is required for robust Polycomb-dependent homeotic gene silencing. Haspin associates with the cohesin complex in interphase, mediates Pds5 binding to chromatin and cooperates with Pds5-cohesin to modify Polycomb-dependent homeotic transformations. Therefore, this study uncovers an unanticipated role for haspin kinase in genome organization of interphase cells and demonstrates that haspin is required for homeotic gene regulation.
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Affiliation(s)
- Ujué Fresán
- Institut de Biologia Molecular de Barcelona, IBMB-CSIC, Barcelona, Spain
- Institute for Research in Biomedicine IRB, Barcelona, Spain
| | | | - Oscar Reina
- Bioinformatics and Biostatistics Unit, Institute for Research in Biomedicine IRB, Barcelona, Spain
| | - Victor G. Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - M. Lluisa Espinàs
- Institut de Biologia Molecular de Barcelona, IBMB-CSIC, Barcelona, Spain
- Institute for Research in Biomedicine IRB, Barcelona, Spain
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13
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Dauban L, Montagne R, Thierry A, Lazar-Stefanita L, Bastié N, Gadal O, Cournac A, Koszul R, Beckouët F. Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners. Mol Cell 2020; 77:1279-1293.e4. [PMID: 32032532 DOI: 10.1016/j.molcel.2020.01.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/24/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Cohesin, a member of the SMC complex family, holds sister chromatids together but also shapes chromosomes by promoting the formation of long-range intra-chromatid loops, a process proposed to be mediated by DNA loop extrusion. Here we describe the roles of three cohesin partners, Pds5, Wpl1, and Eco1, in loop formation along either unreplicated or mitotic Saccharomyces cerevisiae chromosomes. Pds5 limits the size of DNA loops via two different pathways: the canonical Wpl1-mediated releasing activity and an Eco1-dependent mechanism. In the absence of Pds5, the main barrier to DNA loop expansion appears to be the centromere. Our data also show that Eco1 acetyl-transferase inhibits the translocase activity that powers loop formation and contributes to the positioning of loops through a mechanism that is distinguishable from its role in cohesion establishment. This study reveals that the mechanisms regulating cohesin-dependent chromatin loops are conserved among eukaryotes while promoting different functions.
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Affiliation(s)
- Lise Dauban
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Rémi Montagne
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Nathalie Bastié
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris 75015, France.
| | - Frédéric Beckouët
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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14
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Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM. ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin STAG1 from WAPL. eLife 2020; 9:e52091. [PMID: 32065581 PMCID: PMC7054000 DOI: 10.7554/elife.52091] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin's chromatin residence time to minutes, it has been reported that some loops exist for hours. How these loops can persist is unknown. We show that during G1-phase, mammalian cells contain acetylated cohesinSTAG1 which binds chromatin for hours, whereas cohesinSTAG2 binds chromatin for minutes. Our results indicate that CTCF and the acetyltransferase ESCO1 protect a subset of cohesinSTAG1 complexes from WAPL, thereby enable formation of long and presumably long-lived loops, and that ESCO1, like CTCF, contributes to boundary formation in chromatin looping. Our data are consistent with a model of nested loop extrusion, in which acetylated cohesinSTAG1 forms stable loops between CTCF sites, demarcating the boundaries of more transient cohesinSTAG2 extrusion activity.
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Affiliation(s)
- Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Benoit Pignard
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Adrian Sanborn
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Miroslav P Ivanov
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
| | - Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Genome Sciences, University of WashingtonSeattleUnited States
| | - Gerhard Dürnberger
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | | | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Department of Biological Science, Florida State UniversityTallahasseeUnited States
| | - Erez Lieberman-Aiden
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech UniversityShanghaiChina
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
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15
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Davidson IF, Bauer B, Goetz D, Tang W, Wutz G, Peters JM. DNA loop extrusion by human cohesin. Science 2019; 366:1338-1345. [PMID: 31753851 DOI: 10.1126/science.aaz3418] [Citation(s) in RCA: 436] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/06/2019] [Indexed: 01/03/2023]
Abstract
Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo-base pairs per second. Loop formation and maintenance depend on cohesin's ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Benedikt Bauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniela Goetz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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16
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Folco HD, McCue A, Balachandran V, Grewal SIS. Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5. Genetics 2019; 213:127-141. [PMID: 31278118 PMCID: PMC6727797 DOI: 10.1534/genetics.119.302256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/24/2019] [Indexed: 01/05/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a powerful genetic model system for uncovering fundamental principles of heterochromatin assembly and epigenetic inheritance of chromatin states. Heterochromatin defined by histone H3 lysine 9 methylation and HP1 proteins coats large chromosomal domains at centromeres, telomeres, and the mating-type (mat) locus. Although genetic and biochemical studies have provided valuable insights into heterochromatin assembly, many key mechanistic details remain unclear. Here, we use a sensitized reporter system at the mat locus to screen for factors affecting heterochromatic silencing. In addition to known components of heterochromatin assembly pathways, our screen identified eight new factors including the cohesin-associated protein Pds5. We find that Pds5 enriched throughout heterochromatin domains is required for proper maintenance of heterochromatin. This function of Pds5 requires its associated Eso1 acetyltransferase, which is implicated in the acetylation of cohesin. Indeed, introducing an acetylation-mimicking mutation in a cohesin subunit suppresses defects in heterochromatin assembly in pds5∆ and eso1∆ cells. Our results show that in cells lacking Pds5, cohesin interferes with heterochromatin assembly. Supporting this, eliminating cohesin from the mat locus in the pds5∆ mutant restores both heterochromatin assembly and gene silencing. These analyses highlight an unexpected requirement for Pds5 in ensuring proper coordination between cohesin and heterochromatin factors to effectively maintain gene silencing.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrea McCue
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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17
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Yang C, Hamamura Y, Sofroni K, Böwer F, Stolze SC, Nakagami H, Schnittger A. SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis. Nat Commun 2019; 10:1755. [PMID: 30988453 PMCID: PMC6465247 DOI: 10.1038/s41467-019-09759-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/25/2019] [Indexed: 02/06/2023] Open
Abstract
Mitosis and meiosis both rely on cohesin, which embraces the sister chromatids and plays a crucial role for the faithful distribution of chromosomes to daughter cells. Prior to the cleavage by Separase at anaphase onset, cohesin is largely removed from chromosomes by the non-proteolytic action of WINGS APART-LIKE (WAPL), a mechanism referred to as the prophase pathway. To prevent the premature loss of sister chromatid cohesion, WAPL is inhibited in early mitosis by Sororin. However, Sororin homologs have only been found to function as WAPL inhibitors during mitosis in vertebrates and Drosophila. Here we show that SWITCH 1/DYAD defines a WAPL antagonist that acts in meiosis of Arabidopsis. Crucially, SWI1 becomes dispensable for sister chromatid cohesion in the absence of WAPL. Despite the lack of any sequence similarities, we found that SWI1 is regulated and functions in a similar manner as Sororin hence likely representing a case of convergent molecular evolution across the eukaryotic kingdom.
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Affiliation(s)
- Chao Yang
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Yuki Hamamura
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Kostika Sofroni
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Franziska Böwer
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | | | - Hirofumi Nakagami
- Max-Planck-Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany.
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18
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Lin SJ, O'Connell MJ. DNA Topoisomerase II modulates acetyl-regulation of cohesin-mediated chromosome dynamics. Curr Genet 2017; 63:923-930. [PMID: 28382430 PMCID: PMC5628089 DOI: 10.1007/s00294-017-0691-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
Cohesin is one of three multi-protein structural maintenance of chromosome (SMC) complexes that regulate eukaryotic chromosome dynamics. It forms a ring-shaped structure that embraces sister chromatids through interphase to promote their pairing. In preparation for mitosis, most cohesin is stripped from the chromosome arms in prophase by a poorly defined process that is associated with cohesin phosphorylation. In the fission yeast Schizosaccharomyces pombe this prophase pathway is dependent on the cohesin-related Smc5/6 complex, and this requirement is heightened in Smc5/6 hypomorphs by DNA damage, replication stress and Topoisomerase II (Top2) dysfunction. Cohesin interacts with chromosomes immediately upon mitotic exit and becomes cohesive coincident with DNA replication. Cohesiveness is promoted by acetylation of the Smc3 subunit by an acetyltransferase, known as Eso1 in the S. pombe, which counteracts the anti-cohesive function(s) of the cohesin regulators Pds5 and Wpl1. We recently showed that Eso1 and Smc5/6 antagonize each other, and concurrent inactivation restores sister chromatid separation following genotoxic stress. Here, we have investigated the relationship between Top2 and Eso1 in successful completion of mitosis. We observe that partial inactivation of both results in a synthetic lethal mitotic block, but this is not overcome by deleting pds5 or wpl1. However, analysis of both acetyl-blocking and mimetic mutations in Smc3 indicates that the cycling of cohesin acetyl-regulation is more important than acetyl-status per se, highlighting the non-linear nature of the cohesin cycle.
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Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Birot A, Eguienta K, Vazquez S, Claverol S, Bonneu M, Ekwall K, Javerzat JP, Vaur S. A second Wpl1 anti-cohesion pathway requires dephosphorylation of fission yeast kleisin Rad21 by PP4. EMBO J 2017; 36:1364-1378. [PMID: 28438891 PMCID: PMC5430217 DOI: 10.15252/embj.201696050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/10/2017] [Accepted: 03/27/2017] [Indexed: 01/06/2023] Open
Abstract
Cohesin mediates sister chromatid cohesion which is essential for chromosome segregation and repair. Sister chromatid cohesion requires an acetyl-transferase (Eso1 in fission yeast) counteracting Wpl1, promoting cohesin release from DNA We report here that Wpl1 anti-cohesion function includes an additional mechanism. A genetic screen uncovered that Protein Phosphatase 4 (PP4) mutants allowed cell survival in the complete absence of Eso1. PP4 co-immunoprecipitated Wpl1 and cohesin and Wpl1 triggered Rad21 de-phosphorylation in a PP4-dependent manner. Relevant residues were identified and mapped within the central domain of Rad21. Phospho-mimicking alleles dampened Wpl1 anti-cohesion activity, while alanine mutants were neutral indicating that Rad21 phosphorylation would shelter cohesin from Wpl1 unless erased by PP4. Experiments in post-replicative cells lacking Eso1 revealed two cohesin populations. Type 1 was released from DNA by Wpl1 in a PP4-independent manner. Type 2 cohesin, however, remained DNA-bound and lost its cohesiveness in a manner depending on Wpl1- and PP4-mediated Rad21 de-phosphorylation. These results reveal that Wpl1 antagonizes sister chromatid cohesion by a novel pathway regulated by the phosphorylation status of the cohesin kleisin subunit.
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Affiliation(s)
- Adrien Birot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Karen Eguienta
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Stéphanie Vazquez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Stéphane Claverol
- Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Marc Bonneu
- Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jean-Paul Javerzat
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Sabine Vaur
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
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20
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Goto Y, Yamagishi Y, Shintomi-Kawamura M, Abe M, Tanno Y, Watanabe Y. Pds5 Regulates Sister-Chromatid Cohesion and Chromosome Bi-orientation through a Conserved Protein Interaction Module. Curr Biol 2017; 27:1005-1012. [PMID: 28343969 DOI: 10.1016/j.cub.2017.02.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/06/2017] [Accepted: 02/28/2017] [Indexed: 11/24/2022]
Abstract
Sister-chromatid cohesion is established by the cohesin complex in S phase and persists until metaphase, when sister chromatids are captured by microtubules emanating from opposite poles [1]. The Aurora-B-containing chromosome passenger complex (CPC) plays a crucial role in achieving chromosome bi-orientation by correcting erroneous microtubule attachment [2]. The centromeric localization of the CPC relies largely on histone H3-T3 phosphorylation (H3-pT3), which is mediated by the mitotic histone kinase Haspin/Hrk1 [3-5]. Hrk1 localization to centromeres depends largely on the cohesin subunit Pds5 in fission yeast [5]; however, it is unknown how Pds5 regulates Hrk1 localization. Here we identify a conserved Hrk1-interacting motif (HIM) in Pds5 and a Pds5-interacting motif (PIM) in Hrk1 in fission yeast. Mutations in either motif result in the displacement of Hrk1 from centromeres. We also show that the mechanism of Pds5-dependent Hrk1 recruitment is conserved in human cells. Notably, the PIM in Haspin/Hrk1 is reminiscent of the YSR motif found in the mammalian cohesin destabilizer Wapl and stabilizer Sororin, both of which bind PDS5 [6-12]. Similarly, and through the same motifs, fission yeast Pds5 binds to Wpl1/Wapl and acetyltransferase Eso1/Eco1, in addition to Hrk1. Thus, we have identified a protein-protein interaction module in Pds5 that serves as a chromatin platform for regulating sister-chromatid cohesion and chromosome bi-orientation.
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Affiliation(s)
- Yuhei Goto
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yuya Yamagishi
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Miyuki Shintomi-Kawamura
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Mayumi Abe
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yuji Tanno
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yoshinori Watanabe
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan.
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21
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Reichman R, Alleva B, Smolikove S. Prophase I: Preparing Chromosomes for Segregation in the Developing Oocyte. Results Probl Cell Differ 2017; 59:125-173. [PMID: 28247048 DOI: 10.1007/978-3-319-44820-6_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Formation of an oocyte involves a specialized cell division termed meiosis. In meiotic prophase I (the initial stage of meiosis), chromosomes undergo elaborate events to ensure the proper segregation of their chromosomes into gametes. These events include processes leading to the formation of a crossover that, along with sister chromatid cohesion, forms the physical link between homologous chromosomes. Crossovers are formed as an outcome of recombination. This process initiates with programmed double-strand breaks that are repaired through the use of homologous chromosomes as a repair template. The accurate repair to form crossovers takes place in the context of the synaptonemal complex, a protein complex that links homologous chromosomes in meiotic prophase I. To allow proper execution of meiotic prophase I events, signaling processes connect different steps in recombination and synapsis. The events occurring in meiotic prophase I are a prerequisite for proper chromosome segregation in the meiotic divisions. When these processes go awry, chromosomes missegregate. These meiotic errors are thought to increase with aging and may contribute to the increase in aneuploidy observed in advanced maternal age female oocytes.
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Affiliation(s)
- Rachel Reichman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Benjamin Alleva
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.
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22
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Bolaños-Villegas P, De K, Pradillo M, Liu D, Makaroff CA. In Favor of Establishment: Regulation of Chromatid Cohesion in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:846. [PMID: 28588601 PMCID: PMC5440745 DOI: 10.3389/fpls.2017.00846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/05/2017] [Indexed: 05/07/2023]
Abstract
In eukaryotic organisms, the correct regulation of sister chromatid cohesion, whereby sister chromatids are paired and held together, is essential for accurate segregation of the sister chromatids and homologous chromosomes into daughter cells during mitosis and meiosis, respectively. Sister chromatid cohesion requires a cohesin complex comprised of structural maintenance of chromosome adenosine triphosphatases and accessory proteins that regulate the association of the complex with chromosomes or that are involved in the establishment or release of cohesion. The cohesin complex also plays important roles in the repair of DNA double-strand breaks, regulation of gene expression and chromosome condensation. In this review, we summarize progress in understanding cohesion dynamics in plants, with the aim of uncovering differences at specific stages. We also highlight dissimilarities between plants and other eukaryotes with respect to the key players involved in the achievement of cohesion, pointing out areas that require further study.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Laboratory of Molecular and Cell Biology, Fabio Baudrit Agricultural Research Station, University of Costa RicaAlajuela, Costa Rica
- *Correspondence: Christopher A. Makaroff, Pablo Bolaños-Villegas,
| | - Kuntal De
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University Wexner School of Medicine, ColumbusOH, United States
| | - Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad Complutense de MadridMadrid, Spain
| | - Desheng Liu
- Hughes Laboratories, Department of Chemistry and Biochemistry, Miami University, OxfordOH, United States
| | - Christopher A. Makaroff
- Hughes Laboratories, Department of Chemistry and Biochemistry, Miami University, OxfordOH, United States
- *Correspondence: Christopher A. Makaroff, Pablo Bolaños-Villegas,
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23
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Lin SJ, Tapia-Alveal C, Jabado OJ, Germain D, O'Connell MJ. An acetyltransferase-independent function of Eso1 regulates centromere cohesion. Mol Biol Cell 2016; 27:4002-4010. [PMID: 27798241 PMCID: PMC5156541 DOI: 10.1091/mbc.e16-08-0596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Eukaryotes contain three essential Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin, and Smc5/6. Cohesin forms a ring-shaped structure that embraces sister chromatids to promote their cohesion. The cohesiveness of cohesin is promoted by acetylation of N-terminal lysines of the Smc3 subunit by the acetyltransferases Eco1 in Saccharomyces cerevisiae and the homologue, Eso1, in Schizosaccharomyces pombe. In both yeasts, these acetyltransferases are essential for cell viability. However, whereas nonacetylatable Smc3 mutants are lethal in S. cerevisiae, they are not in S. pombe We show that the lethality of a temperature-sensitive allele of eso1 (eso1-H17) is due to activation of the spindle assembly checkpoint (SAC) and is associated with premature centromere separation. The lack of cohesion at the centromeres does not correlate with Psm3 acetylation or cohesin levels at the centromeres, but is associated ith significantly reduced recruitment of the cohesin regulator Pds5. The SAC activation in this context is dependent on Smc5/6 function, which is required to remove cohesin from chromosome arms but not centromeres. The mitotic defects caused by Smc5/6 and Eso1 dysfunction are cosuppressed in double mutants. This identifies a novel function (or functions) for Eso1 and Smc5/6 at centromeres and extends the functional relationships between these SMC complexes.
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Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Omar J Jabado
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Doris Germain
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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24
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Abstract
Cohesin is a large ring-shaped protein complex, conserved from yeast to human, which participates in most DNA transactions that take place in the nucleus. It mediates sister chromatid cohesion, which is essential for chromosome segregation and homologous recombination (HR)-mediated DNA repair. Together with architectural proteins and transcriptional regulators, such as CTCF and Mediator, respectively, it contributes to genome organization at different scales and thereby affects transcription, DNA replication, and locus rearrangement. Although cohesin is essential for cell viability, partial loss of function can affect these processes differently in distinct cell types. Mutations in genes encoding cohesin subunits and regulators of the complex have been identified in several cancers. Understanding the functional significance of these alterations may have relevant implications for patient classification, risk prediction, and choice of treatment. Moreover, identification of vulnerabilities in cancer cells harboring cohesin mutations may provide new therapeutic opportunities and guide the design of personalized treatments.
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Affiliation(s)
- Magali De Koninck
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
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25
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Gligoris T, Löwe J. Structural Insights into Ring Formation of Cohesin and Related Smc Complexes. Trends Cell Biol 2016; 26:680-693. [PMID: 27134029 PMCID: PMC4989898 DOI: 10.1016/j.tcb.2016.04.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022]
Abstract
Cohesin facilitates sister chromatid cohesion through the formation of a large ring structure that encircles DNA. Its function relies on two structural maintenance of chromosomes (Smc) proteins, which are found in almost all organisms tested, from bacteria to humans. In accordance with their ubiquity, Smc complexes, such as cohesin, condensin, Smc5-6, and the dosage compensation complex, affect almost all processes of DNA homeostasis. Although their precise molecular mechanism remains enigmatic, here we provide an overview of the architecture of eukaryotic Smc complexes with a particular focus on cohesin, which has seen the most progress recently. Given the evident conservation of many structural features between Smc complexes, it is expected that architecture and topology will have a significant role when deciphering their precise molecular mechanisms.
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Affiliation(s)
- Thomas Gligoris
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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26
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Hons MT, Huis in ‘t Veld PJ, Kaesler J, Rombaut P, Schleiffer A, Herzog F, Stark H, Peters JM. Topology and structure of an engineered human cohesin complex bound to Pds5B. Nat Commun 2016; 7:12523. [PMID: 27549742 PMCID: PMC4996973 DOI: 10.1038/ncomms12523] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/12/2016] [Indexed: 12/19/2022] Open
Abstract
The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1/2 and Pds5A/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.
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Affiliation(s)
- Michael T. Hons
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | | | - Jan Kaesler
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Pascaline Rombaut
- Department of Biochemistry, Gene Center, Ludwig-Maximilian University, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, Vienna 1030, Austria
| | - Franz Herzog
- Department of Biochemistry, Gene Center, Ludwig-Maximilian University, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, Vienna 1030, Austria
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27
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Bhardwaj S, Schlackow M, Rabajdova M, Gullerova M. Transcription facilitates sister chromatid cohesion on chromosomal arms. Nucleic Acids Res 2016; 44:6676-92. [PMID: 27084937 PMCID: PMC5001582 DOI: 10.1093/nar/gkw252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cohesin is a multi-subunit protein complex essential for sister chromatid cohesion, gene expression and DNA damage repair. Although structurally well studied, the underlying determinant of cohesion establishment on chromosomal arms remains enigmatic. Here, we show two populations of functionally distinct cohesin on chromosomal arms using a combination of genomics and single-locus specific DNA-FISH analysis. Chromatin bound cohesin at the loading sites co-localizes with Pds5 and Eso1 resulting in stable cohesion. In contrast, cohesin independent of its loader is unable to maintain cohesion and associates with chromatin in a dynamic manner. Cohesive sites coincide with highly expressed genes and transcription inhibition leads to destabilization of cohesin on chromatin. Furthermore, induction of transcription results in de novo recruitment of cohesive cohesin. Our data suggest that transcription facilitates cohesin loading onto chromosomal arms and is a key determinant of cohesive sites in fission yeast.
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Affiliation(s)
- Shweta Bhardwaj
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | | | | | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
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28
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Ouyang Z, Zheng G, Tomchick DR, Luo X, Yu H. Structural Basis and IP6 Requirement for Pds5-Dependent Cohesin Dynamics. Mol Cell 2016; 62:248-259. [PMID: 26971492 PMCID: PMC5560056 DOI: 10.1016/j.molcel.2016.02.033] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/25/2016] [Accepted: 02/26/2016] [Indexed: 11/24/2022]
Abstract
The ring-shaped cohesin complex regulates transcription, DNA repair, and chromosome segregation by dynamically entrapping chromosomes to promote chromosome compaction and sister-chromatid cohesion. The cohesin ring needs to open and close to allow its loading to and release from chromosomes. Cohesin dynamics are controlled by the releasing factors Pds5 and Wapl and the cohesin stabilizer Sororin. Here, we report the crystal structure of human Pds5B bound to a conserved peptide motif found in both Wapl and Sororin. Our structure establishes the basis for how Wapl and Sororin antagonistically influence cohesin dynamics. The structure further reveals that Pds5 can bind inositol hexakisphosphate (IP6). The IP6-binding segment of Pds5B is shaped like the jaw of a plier lever and inhibits the binding of Scc1 to Smc3. We propose that Pds5 stabilizes a transient, open state of cohesin to promote its release from chromosomes.
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Affiliation(s)
- Zhuqing Ouyang
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Ge Zheng
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Xuelian Luo
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
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29
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Muir KW, Kschonsak M, Li Y, Metz J, Haering CH, Panne D. Structure of the Pds5-Scc1 Complex and Implications for Cohesin Function. Cell Rep 2016; 14:2116-2126. [PMID: 26923589 DOI: 10.1016/j.celrep.2016.01.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/28/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Sister chromatid cohesion is a fundamental prerequisite to faithful genome segregation. Cohesion is precisely regulated by accessory factors that modulate the stability with which the cohesin complex embraces chromosomes. One of these factors, Pds5, engages cohesin through Scc1 and is both a facilitator of cohesion, and, conversely also mediates the release of cohesin from chromatin. We present here the crystal structure of a complex between budding yeast Pds5 and Scc1, thus elucidating the molecular basis of Pds5 function. Pds5 forms an elongated HEAT repeat that binds to Scc1 via a conserved surface patch. We demonstrate that the integrity of the Pds5-Scc1 interface is indispensable for the recruitment of Pds5 to cohesin, and that its abrogation results in loss of sister chromatid cohesion and cell viability.
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Affiliation(s)
- Kyle W Muir
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Marc Kschonsak
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit and Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Yan Li
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Jutta Metz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit and Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian H Haering
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit and Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel Panne
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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30
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Lee BG, Roig MB, Jansma M, Petela N, Metson J, Nasmyth K, Löwe J. Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1. Cell Rep 2016; 14:2108-2115. [PMID: 26923598 PMCID: PMC4793087 DOI: 10.1016/j.celrep.2016.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Sister chromatid cohesion is mediated by cohesin, whose Smc1, Smc3, and kleisin (Scc1) subunits form a ring structure that entraps sister DNAs. The ring is opened either by separase, which cleaves Scc1 during anaphase, or by a releasing activity involving Wapl, Scc3, and Pds5, which bind to Scc1 and open its interface with Smc3. We present crystal structures of Pds5 from the yeast L. thermotolerans in the presence and absence of the conserved Scc1 region that interacts with Pds5. Scc1 binds along the spine of the Pds5 HEAT repeat fold and is wedged between the spine and C-terminal hook of Pds5. We have isolated mutants that confirm the observed binding mode of Scc1 and verified their effect on cohesin by immunoprecipitation and calibrated ChIP-seq. The Pds5 structure also reveals architectural similarities to Scc3, the other large HEAT repeat protein of cohesin and, most likely, Scc2. The crystal structure of the cohesin subunit Pds5 was determined The crystal structure of Pds5 in complex with Scc1 binding region was determined Structure-based mutants in Pds5 and Scc1 were analyzed by coIP and ChIP-seq Pds5 shows some similarity to Scc3, the other large HEAT repeat cohesin subunit
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Affiliation(s)
- Byung-Gil Lee
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Maurici B Roig
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Marijke Jansma
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Naomi Petela
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jean Metson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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31
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Pradillo M, Knoll A, Oliver C, Varas J, Corredor E, Puchta H, Santos JL. Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:1034. [PMID: 26648949 PMCID: PMC4664637 DOI: 10.3389/fpls.2015.01034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/06/2015] [Indexed: 05/23/2023]
Abstract
Maintenance and precise regulation of sister chromatid cohesion is essential for faithful chromosome segregation during mitosis and meiosis. Cohesin cofactors contribute to cohesin dynamics and interact with cohesin complexes during cell cycle. One of these, PDS5, also known as SPO76, is essential during mitosis and meiosis in several organisms and also plays a role in DNA repair. In yeast, the complex Wapl-Pds5 controls cohesion maintenance and colocalizes with cohesin complexes into chromosomes. In Arabidopsis, AtWAPL proteins are essential during meiosis, however, the role of AtPDS5 remains to be ascertained. Here we have isolated mutants for each of the five AtPDS5 genes (A-E) and obtained, after different crosses between them, double, triple, and even quadruple mutants (Atpds5a Atpds5b Atpds5c Atpds5e). Depletion of AtPDS5 proteins has a weak impact on meiosis, but leads to severe effects on development, fertility, somatic homologous recombination (HR) and DNA repair. Furthermore, this cohesin cofactor could be important for the function of the AtSMC5/AtSMC6 complex. Contrarily to its function in other species, our results suggest that AtPDS5 is dispensable during the meiotic division of Arabidopsis, although it plays an important role in DNA repair by HR.
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Affiliation(s)
- Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad ComplutenseMadrid, Spain
| | - Alexander Knoll
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad ComplutenseMadrid, Spain
| | - Javier Varas
- Departamento de Genética, Facultad de Biología, Universidad ComplutenseMadrid, Spain
| | - Eduardo Corredor
- Departamento de Genética, Facultad de Biología, Universidad ComplutenseMadrid, Spain
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Juan L. Santos
- Departamento de Genética, Facultad de Biología, Universidad ComplutenseMadrid, Spain
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32
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Mizuguchi T, Barrowman J, Grewal SIS. Chromosome domain architecture and dynamic organization of the fission yeast genome. FEBS Lett 2015; 589:2975-86. [PMID: 26096785 PMCID: PMC4598268 DOI: 10.1016/j.febslet.2015.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 12/20/2022]
Abstract
Advanced techniques including the chromosome conformation capture (3C) methodology and its derivatives are complementing microscopy approaches to study genome organization, and are revealing new details of three-dimensional (3D) genome architecture at increasing resolution. The fission yeast Schizosaccharomyces pombe (S. pombe) comprises a small genome featuring organizational elements of more complex eukaryotic systems, including conserved heterochromatin assembly machinery. Here we review key insights into genome organization revealed in this model system through a variety of techniques. We discuss the predominant role of Rabl-like configuration for interphase chromosome organization and the dynamic changes that occur during mitosis and meiosis. High resolution Hi-C studies have also revealed the presence of locally crumpled chromatin regions called "globules" along chromosome arms, and implicated a critical role for pericentromeric heterochromatin in imposing fundamental constraints on the genome to maintain chromosome territoriality and stability. These findings have shed new light on the connections between genome organization and function. It is likely that insights gained from the S. pombe system will also broadly apply to higher eukaryotes.
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Affiliation(s)
- Takeshi Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jemima Barrowman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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33
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Rahman S, Jones MJK, Jallepalli PV. Cohesin recruits the Esco1 acetyltransferase genome wide to repress transcription and promote cohesion in somatic cells. Proc Natl Acad Sci U S A 2015; 112:11270-5. [PMID: 26305936 PMCID: PMC4568707 DOI: 10.1073/pnas.1505323112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The cohesin complex links DNA molecules and plays key roles in the organization, expression, repair, and segregation of eukaryotic genomes. In vertebrates the Esco1 and Esco2 acetyltransferases both modify cohesin's Smc3 subunit to establish sister chromatid cohesion during S phase, but differ in their N-terminal domains and expression during development and across the cell cycle. Here we show that Esco1 and Esco2 also differ dramatically in their interaction with chromatin, as Esco1 is recruited by cohesin to over 11,000 sites, whereas Esco2 is infrequently enriched at REST/NRSF target genes. Esco1's colocalization with cohesin occurs throughout the cell cycle and depends on two short motifs (the A-box and B-box) present in and unique to all Esco1 orthologs. Deleting either motif led to the derepression of Esco1-proximal genes and functional uncoupling of cohesion from Smc3 acetylation. In contrast, other mutations that preserved Esco1's recruitment separated its roles in cohesion establishment and gene silencing. We conclude that Esco1 uses cohesin as both a substrate and a scaffold for coordinating multiple chromatin-based transactions in somatic cells.
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Affiliation(s)
- Sadia Rahman
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Mathew J K Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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34
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Rankin S. Complex elaboration: making sense of meiotic cohesin dynamics. FEBS J 2015; 282:2426-43. [PMID: 25895170 PMCID: PMC4490075 DOI: 10.1111/febs.13301] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/02/2015] [Accepted: 04/15/2015] [Indexed: 11/30/2022]
Abstract
In mitotically dividing cells, the cohesin complex tethers sister chromatids, the products of DNA replication, together from the time they are generated during S phase until anaphase. Cohesion between sister chromatids ensures accurate chromosome segregation, and promotes normal gene regulation and certain kinds of DNA repair. In somatic cells, the core cohesin complex is composed of four subunits: Smc1, Smc3, Rad21 and an SA subunit. During meiotic cell divisions meiosis-specific isoforms of several of the cohesin subunits are also expressed and incorporated into distinct meiotic cohesin complexes. The relative contributions of these meiosis-specific forms of cohesin to chromosome dynamics during meiotic progression have not been fully worked out. However, the localization of these proteins during chromosome pairing and synapsis, and their unique loss-of-function phenotypes, suggest non-overlapping roles in controlling meiotic chromosome behavior. Many of the proteins that regulate cohesin function during mitosis also appear to regulate cohesin during meiosis. Here we review how cohesin contributes to meiotic chromosome dynamics, and explore similarities and differences between cohesin regulation during the mitotic cell cycle and meiotic progression. A deeper understanding of the regulation and function of cohesin in meiosis will provide important new insights into how the cohesin complex is able to promote distinct kinds of chromosome interactions under diverse conditions.
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Affiliation(s)
- Susannah Rankin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, OK, USA
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35
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Minamino M, Ishibashi M, Nakato R, Akiyama K, Tanaka H, Kato Y, Negishi L, Hirota T, Sutani T, Bando M, Shirahige K. Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2. Curr Biol 2015; 25:1694-706. [PMID: 26051894 DOI: 10.1016/j.cub.2015.05.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Sister chromatid cohesion is mediated by cohesin and is essential for accurate chromosome segregation. The cohesin subunits SMC1, SMC3, and Rad21 form a tripartite ring within which sister chromatids are thought to be entrapped. This event requires the acetylation of SMC3 and the association of sororin with cohesin by the acetyltransferases Esco1 and Esco2 in humans, but the functional mechanisms of these acetyltransferases remain elusive. Here, we showed that Esco1 requires Pds5, a cohesin regulatory subunit bound to Rad21, to form cohesion via SMC3 acetylation and the stabilization of the chromatin association of sororin, whereas Esco2 function was not affected by Pds5 depletion. Consistent with the functional link between Esco1 and Pds5, Pds5 interacted exclusively with Esco1, and this interaction was dependent on a unique and conserved Esco1 domain. Crucially, this interaction was essential for SMC3 acetylation and sister chromatid cohesion. Esco1 localized to cohesin localization sites on chromosomes throughout interphase in a manner that required the Esco1-Pds5 interaction, and it could acetylate SMC3 before and after DNA replication. These results indicate that Esco1 acetylates SMC3 via a mechanism different from that of Esco2. We propose that, by interacting with a unique domain of Esco1, Pds5 recruits Esco1 to chromatin-bound cohesin complexes to form cohesion. Furthermore, Esco1 acetylates SMC3 independently of DNA replication.
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Affiliation(s)
- Masashi Minamino
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Mai Ishibashi
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Kazuhiro Akiyama
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Hiroshi Tanaka
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Yuki Kato
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Lumi Negishi
- Laboratory of Cancer Stem Cell Biology, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Toru Hirota
- Cancer Institute of the Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake Koto-Ku, Tokyo 135-8550, Japan
| | - Takashi Sutani
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Masashige Bando
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan.
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi Bunkyo-Ku, Tokyo 113-0032, Japan; CREST, JST, K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.
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36
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Guacci V, Stricklin J, Bloom MS, Guō X, Bhatter M, Koshland D. A novel mechanism for the establishment of sister chromatid cohesion by the ECO1 acetyltransferase. Mol Biol Cell 2015; 26:117-33. [PMID: 25378582 PMCID: PMC4279223 DOI: 10.1091/mbc.e14-08-1268] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/06/2014] [Accepted: 10/27/2014] [Indexed: 11/30/2022] Open
Abstract
Cohesin complex mediates cohesion between sister chromatids, which promotes high-fidelity chromosome segregation. Eco1p acetylates the cohesin subunit Smc3p during S phase to establish cohesion. The current model posits that this Eco1p-mediated acetylation promotes establishment by abrogating the ability of Wpl1p to destabilize cohesin binding to chromosomes. Here we present data from budding yeast that is incompatible with this Wpl1p-centric model. Two independent in vivo assays show that a wpl1∆ fails to suppress cohesion defects of eco1∆ cells. Moreover, a wpl1∆ also fails to suppress cohesion defects engendered by blocking just the essential Eco1p acetylation sites on Smc3p (K112, K113). Thus removing WPL1 inhibition is insufficient for generating cohesion without ECO1 activity. To elucidate how ECO1 promotes cohesion, we conducted a genetic screen and identified a cohesion activator mutation in the SMC3 head domain (D1189H). Smc3-D1189H partially restores cohesion in eco1∆ wpl1∆ or eco1 mutant cells but robustly restores cohesion in cells blocked for Smc3p K112 K113 acetylation. These data support two important conclusions. First, acetylation of the K112 K113 region by Eco1p promotes cohesion establishment by altering Smc3p head function independent of its ability to antagonize Wpl1p. Second, Eco1p targets other than Smc3p K112 K113 are necessary for efficient establishment.
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Affiliation(s)
- Vincent Guacci
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Jeremiah Stricklin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Michelle S. Bloom
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Xuánzōng Guō
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Meghna Bhatter
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Douglas Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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37
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Abstract
The X shape of chromosomes is one of the iconic images in biology. Cohesin actually connects the sister chromatids along their entire length, from S phase until mitosis. Then, cohesin's antagonist Wapl allows the separation of chromosome arms by opening a DNA exit gate in cohesin rings. Centromeres are protected against this removal activity, resulting in the X shape of mitotic chromosomes. The destruction of the remaining centromeric cohesin by Separase triggers chromosome segregation. We review the two-phase regulation of cohesin removal and discuss how this affects chromosome alignment and decatenation in mitosis and cohesin reloading in the next cell cycle.
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Affiliation(s)
- Judith H I Haarhuis
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ahmed M O Elbatsh
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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38
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Tapia-Alveal C, Lin SJ, O’Connell MJ. Functional interplay between cohesin and Smc5/6 complexes. Chromosoma 2014; 123:437-45. [PMID: 24981336 PMCID: PMC4169997 DOI: 10.1007/s00412-014-0474-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 12/14/2022]
Abstract
Chromosomes are subjected to massive reengineering as they are replicated, transcribed, repaired, condensed, and segregated into daughter cells. Among the engineers are three large protein complexes collectively known as the structural maintenance of chromosome (SMC) complexes: cohesin, condensin, and Smc5/6. As their names suggest, cohesin controls sister chromatid cohesion, condensin controls chromosome condensation, and while precise functions for Smc5/6 have remained somewhat elusive, most reports have focused on the control of recombinational DNA repair. Here, we focus on cohesin and Smc5/6 function. It is becoming increasingly clear that the functional repertoires of these complexes are greater than sister chromatid cohesion and recombination. These SMC complexes are emerging as interrelated and cooperating factors that control chromosome dynamics throughout interphase. However, they also release their embrace of sister chromatids to enable their segregation at anaphase, resetting the dynamic cycle of SMC-chromosome interactions.
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Affiliation(s)
- Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew J. O’Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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39
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Tong K, Skibbens RV. Cohesin without cohesion: a novel role for Pds5 in Saccharomyces cerevisiae. PLoS One 2014; 9:e100470. [PMID: 24963665 PMCID: PMC4070927 DOI: 10.1371/journal.pone.0100470] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/18/2014] [Indexed: 11/18/2022] Open
Abstract
High fidelity chromosome segregation during mitosis requires that cells identify the products of DNA replication during S-phase and then maintain that identity until anaphase onset. Sister chromatid identity is achieved through cohesin complexes (Smc1, Smc3, and Mcd1 and Irr1/Scc3), but the structure through which cohesins perform this task remains enigmatic. In the absence of unambiguous data, a popular model is that a subset of cohesin subunits form a huge ring-like structure that embraces both sister chromatids. This 'one-ring two-sister chromatid embrace' model makes clear predictions--including that premature cohesion loss in mitotic cells must occur through a substantial reduction in cohesin-DNA associations. We used chromatin immunoprecipitation to directly test for cohesin dissociation from well-established cohesin binding sites in mitotic cells inactivated for Pds5--a key cohesin regulatory protein. The results reveal little if any chromatin dissociation from cohesins, despite a regimen that produces both massive loss of sister chromatid tethering and cell inviability. We further excluded models that cohesion loss in mitotic cells inactivated for Pds5 arises through either cohesin subunit degradation, premature Hos1-dependent Smc3 de-acetylation or Rad61/WAPL-dependent regulation of cohesin dynamics. In combination, our findings support a model that cohesin complexes associate with each sister and that sister chromatid cohesion likely results from cohesin-cohesin interactions. We further assessed the role that Pds5 plays in cohesion establishment during S-phase. The results show that Pds5 inactivation can result in establishment defects despite normal cohesion loading and Smc3 acetylation, revealing a novel establishment role for Pds5 that is independent of these processes. The combination of findings provides important new insights that significantly impact current models of both cohesion establishment reactions and maintenance.
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Affiliation(s)
- Kevin Tong
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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40
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D'Ambrosio LM, Lavoie BD. Pds5 prevents the PolySUMO-dependent separation of sister chromatids. Curr Biol 2014; 24:361-71. [PMID: 24485833 DOI: 10.1016/j.cub.2013.12.038] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/24/2013] [Accepted: 12/17/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND The establishment, maintenance, and dissolution of sister chromatid cohesion are sequentially coordinated during the cell cycle to ensure faithful chromosome transmission. This cell-cycle-dependent regulation of cohesion is mediated, in part, by distinct posttranslational modifications of cohesin, a protein complex consisting of the Smc1-Smc3 ATPase, the Mcd1/Scc1 α-kleisin, and Scc3. Although cohesion is established in S phase, cohesins are not sufficient to maintain cohesion as cells progress from G2 to the metaphase-to-anaphase transition. Rather, the cohesin-associated factor Pds5 is also required to keep sisters paired until anaphase onset. How Pds5 maintains cohesion at the molecular level and whether this maintenance involves the regulation of cohesin modifications remains to be defined. RESULTS In pds5 mutants, we find that Mcd1 is extensively SUMOylated and that premature sister separation requires Siz2-dependent polySUMOylation. Moreover, abrogation of Pds5 function promotes the proteasome-dependent degradation of Mcd1 and a significant loss of cohesin from chromatin independently of anaphase onset. We further demonstrate that inactivation of the Slx5-Slx8 SUMO-targeted ubiquitin ligase, required for targeting polySUMOylated factors for proteasome-mediated destruction, limits Mcd1 turnover and restores both cell growth and cohesion in metaphase cells defective for Pds5 function. CONCLUSIONS We propose that Pds5 maintains cohesion, at least in part, by antagonizing the polySUMO-dependent degradation of cohesin.
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Affiliation(s)
- Lisa M D'Ambrosio
- Department of Molecular Genetics, University of Toronto, Medical Sciences Building, Room 4278, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Brigitte D Lavoie
- Department of Molecular Genetics, University of Toronto, Medical Sciences Building, Room 4278, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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41
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Carretero M, Ruiz-Torres M, Rodríguez-Corsino M, Barthelemy I, Losada A. Pds5B is required for cohesion establishment and Aurora B accumulation at centromeres. EMBO J 2013; 32:2938-49. [PMID: 24141881 PMCID: PMC3831313 DOI: 10.1038/emboj.2013.230] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/02/2013] [Indexed: 12/23/2022] Open
Abstract
Cohesin mediates sister chromatid cohesion and contributes to the organization of interphase chromatin through DNA looping. In vertebrate somatic cells, cohesin consists of Smc1, Smc3, Rad21, and either SA1 or SA2. Three additional factors Pds5, Wapl, and Sororin bind to cohesin and modulate its dynamic association with chromatin. There are two Pds5 proteins in vertebrates, Pds5A and Pds5B, but their functional specificity remains unclear. Here, we demonstrate that Pds5 proteins are essential for cohesion establishment by allowing Smc3 acetylation by the cohesin acetyl transferases (CoATs) Esco1/2 and binding of Sororin. While both proteins contribute to telomere and arm cohesion, Pds5B is specifically required for centromeric cohesion. Furthermore, reduced accumulation of Aurora B at the inner centromere region in cells lacking Pds5B impairs its error correction function, promoting chromosome mis-segregation and aneuploidy. Our work supports a model in which the composition and function of cohesin complexes differs between different chromosomal regions.
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Affiliation(s)
- María Carretero
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miguel Ruiz-Torres
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Barthelemy
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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42
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Rudra S, Skibbens RV. Chl1 DNA helicase regulates Scc2 deposition specifically during DNA-replication in Saccharomyces cerevisiae. PLoS One 2013; 8:e75435. [PMID: 24086532 PMCID: PMC3784445 DOI: 10.1371/journal.pone.0075435] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
The conserved family of cohesin proteins that mediate sister chromatid cohesion requires Scc2, Scc4 for chromatin-association and Eco1/Ctf7 for conversion to a tethering competent state. A popular model, based on the notion that cohesins form huge ring-like structures, is that Scc2, Scc4 function is essential only during G1 such that sister chromatid cohesion results simply from DNA replisome passage through pre-loaded cohesin rings. In such a scenario, cohesin deposition during G1 is temporally uncoupled from Eco1-dependent establishment reactions that occur during S-phase. Chl1 DNA helicase (homolog of human ChlR1/DDX11 and BACH1/BRIP1/FANCJ helicases implicated in Fanconi anemia, breast and ovarian cancer and Warsaw Breakage Syndrome) plays a critical role in sister chromatid cohesion, however, the mechanism through which Chl1 promotes cohesion remains poorly understood. Here, we report that Chl1 promotes Scc2 loading unto DNA such that both Scc2 and cohesin enrichment to chromatin are defective in chl1 mutant cells. The results further show that both Chl1 expression and chromatin-recruitment are tightly regulated through the cell cycle, peaking during S-phase. Importantly, kinetic ChIP studies reveals that Chl1 is required for Scc2 chromatin-association specifically during S-phase, but not during G1. Despite normal chromatin enrichment of both Scc2 and cohesin during G1, chl1 mutant cells exhibit severe chromosome segregation and cohesion defects--revealing that G1-loaded cohesins is insufficient to promote cohesion. Based on these findings, we propose a new model wherein S-phase cohesin loading occurs during DNA replication and in concert with both cohesion establishment and chromatin assembly reactions--challenging the notion that DNA replication fork navigates through or around pre-loaded cohesin rings.
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Affiliation(s)
- Soumya Rudra
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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43
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Chan KL, Gligoris T, Upcher W, Kato Y, Shirahige K, Nasmyth K, Beckouët F. Pds5 promotes and protects cohesin acetylation. Proc Natl Acad Sci U S A 2013; 110:13020-5. [PMID: 23878248 PMCID: PMC3740900 DOI: 10.1073/pnas.1306900110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cohesin's Smc1 and Smc3 subunits form V-shaped heterodimers, the nucleotide binding domains (NBDs) of which bind the C- and N-terminal domains, respectively, of the α-kleisin subunit, forming a large tripartite ring within in which sister DNAs are entrapped, and thereby held together (sister chromatid cohesion). During replication, establishment of stable cohesion is dependent on Eco1-mediated acetylation of Smc3's NBD, which is thought to prevent dissociation of α-kleisin from Smc3, thereby locking shut a "DNA exit gate." How Scc3 and Pds5, regulatory subunits bound to α-kleisin, regulate cohesion establishment and maintenance is poorly understood. We show here that by binding to α-kleisin adjacent to its Smc3 nucleotide binding N-terminal domain, Pds5 not only promotes cohesin's release from chromatin but also mediates de novo acetylation of Smc3 by Eco1 during S phase and subsequently prevents de-acetylation by the deacetylase Hos1/HDAC8. By first promoting cohesin's release from chromosomes and subsequently creating and guarding the chemical modification responsible for blocking release, Pds5 enables chromosomal cohesin to switch during S phase from a state of high turnover to one capable of tenaciously holding sister chromatids together for extended periods of time, a duality that has hitherto complicated analysis of this versatile cohesin subunit.
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Affiliation(s)
- Kok-Lung Chan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Thomas Gligoris
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - William Upcher
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Yuki Kato
- Department for Epigenetic Disease, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Department for Epigenetic Disease, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Frédéric Beckouët
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
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44
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Equilibrina I, Matsunaga S, Morimoto A, Hashimoto T, Uchiyama S, Fukui K. ASURA (PHB2) interacts with Scc1 through chromatin. Cytogenet Genome Res 2013; 139:225-33. [PMID: 23548868 DOI: 10.1159/000350004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2012] [Indexed: 11/19/2022] Open
Abstract
Sister chromatid cohesion mediated by the cohesin complex is essential for faithful chromosome segregation. Previously we reported that PHB2 (prohibitin2/ASURA), a multifunctional protein, has a role in sister chromatid cohesion. Nevertheless, how ASURA is involved in sister chromatid cohesion still remains unclear. The present co-immunoprecipitation analysis reveals that ASURA interacts with cohesin subunit Scc1 in vivo. We show that ASURA associates with chromatin in a similar manner as Scc1 throughout the cell cycle. Furthermore, our observation using the Fucci (fluorescent ubiquitination-based cell cycle indicator) system indicates that ASURA is important for cohesin maintenance at early mitosis. We have also identified that the conserved PHB domain is responsible for chromatin targeting of ASURA. Our results suggest that the regulation of sister chromatid cohesion is mediated by ASURA binding to chromatin, where ASURA might be involved in cohesin protection through ASURA-Scc1 interactions.
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Affiliation(s)
- I Equilibrina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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45
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Remeseiro S, Losada A. Cohesin, a chromatin engagement ring. Curr Opin Cell Biol 2013; 25:63-71. [PMID: 23219370 DOI: 10.1016/j.ceb.2012.10.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/18/2012] [Indexed: 12/15/2022]
Abstract
Cohesin is a four subunit complex, conserved from yeast to man, with the ability to hold together two DNA segments within its ring-shaped structure. When the two segments belong to sister chromatids, cohesin is mediating cohesion, which is essential for chromosome segregation in mitosis and meiosis and for homologous DNA repair. When the two DNA segments are in the same chromatid, a loop is formed. These chromatin loops are emerging as a mechanism for controlling the communication between enhancers and promoters and thereby regulate gene expression. They also facilitate DNA replication and recombination. Given all its essential functions, it is not surprising that mutations in cohesin and its interacting factors have been associated to cancer and developmental syndromes known as cohesinopathies.
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Affiliation(s)
- Silvia Remeseiro
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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46
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Horsfield JA, Print CG, Mönnich M. Diverse developmental disorders from the one ring: distinct molecular pathways underlie the cohesinopathies. Front Genet 2012; 3:171. [PMID: 22988450 PMCID: PMC3439829 DOI: 10.3389/fgene.2012.00171] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/17/2012] [Indexed: 11/13/2022] Open
Abstract
The multi-subunit protein complex, cohesin, is responsible for sister chromatid cohesion during cell division. The interaction of cohesin with DNA is controlled by a number of additional regulatory proteins. Mutations in cohesin, or its regulators, cause a spectrum of human developmental syndromes known as the “cohesinopathies.” Cohesinopathy disorders include Cornelia de Lange Syndrome and Roberts Syndrome. The discovery of novel roles for chromatid cohesion proteins in regulating gene expression led to the idea that cohesinopathies are caused by dysregulation of multiple genes downstream of mutations in cohesion proteins. Consistent with this idea, Drosophila, mouse, and zebrafish cohesinopathy models all show altered expression of developmental genes. However, there appears to be incomplete overlap among dysregulated genes downstream of mutations in different components of the cohesion apparatus. This is surprising because mutations in all cohesion proteins would be predicted to affect cohesin’s roles in cell division and gene expression in similar ways. Here we review the differences and similarities between genetic pathways downstream of components of the cohesion apparatus, and discuss how such differences might arise, and contribute to the spectrum of cohesinopathy disorders. We propose that mutations in different elements of the cohesion apparatus have distinct developmental outcomes that can be explained by sometimes subtly different molecular effects.
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Affiliation(s)
- Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago Dunedin, New Zealand
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