1
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Prevo B, Earnshaw WC. DNA packaging by molecular motors: from bacteriophage to human chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00740-y. [PMID: 38886215 DOI: 10.1038/s41576-024-00740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Dense packaging of genomic DNA is crucial for organismal survival, as DNA length always far exceeds the dimensions of the cells that contain it. Organisms, therefore, use sophisticated machineries to package their genomes. These systems range across kingdoms from a single ultra-powerful rotary motor that spools the DNA into a bacteriophage head, to hundreds of thousands of relatively weak molecular motors that coordinate the compaction of mitotic chromosomes in eukaryotic cells. Recent technological advances, such as DNA proximity-based sequencing approaches, polymer modelling and in vitro reconstitution of DNA loop extrusion, have shed light on the biological mechanisms driving DNA organization in different systems. Here, we discuss DNA packaging in bacteriophage, bacteria and eukaryotic cells, which, despite their extreme variation in size, structure and genomic content, all rely on the action of molecular motors to package their genomes.
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Affiliation(s)
- Bram Prevo
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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2
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Martínez‐García B, Dyson S, Segura J, Ayats A, Cutts EE, Gutierrez‐Escribano P, Aragón L, Roca J. Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage. EMBO J 2023; 42:e111913. [PMID: 36533296 PMCID: PMC9890231 DOI: 10.15252/embj.2022111913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain positive DNA supercoils. However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of -0.4. This ∆Lk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. We propose that this loop is the feeding segment of DNA that is subsequently merged to enlarge an extruding loop. Such a "pinch and merge" mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop.
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Affiliation(s)
| | - Sílvia Dyson
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Joana Segura
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Alba Ayats
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Erin E Cutts
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | | | - Luís Aragón
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | - Joaquim Roca
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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3
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Regulation of the mitotic chromosome folding machines. Biochem J 2022; 479:2153-2173. [PMID: 36268993 DOI: 10.1042/bcj20210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
Abstract
Over the last several years enormous progress has been made in identifying the molecular machines, including condensins and topoisomerases that fold mitotic chromosomes. The discovery that condensins generate chromatin loops through loop extrusion has revolutionized, and energized, the field of chromosome folding. To understand how these machines fold chromosomes with the appropriate dimensions, while disentangling sister chromatids, it needs to be determined how they are regulated and deployed. Here, we outline the current understanding of how these machines and factors are regulated through cell cycle dependent expression, chromatin localization, activation and inactivation through post-translational modifications, and through associations with each other, with other factors and with the chromatin template itself. There are still many open questions about how condensins and topoisomerases are regulated but given the pace of progress in the chromosome folding field, it seems likely that many of these will be answered in the years ahead.
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4
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Ward JR, Khan A, Torres S, Crawford B, Nock S, Frisbie T, Moran J, Longworth M. Condensin I and condensin II proteins form a LINE-1 dependent super condensin complex and cooperate to repress LINE-1. Nucleic Acids Res 2022; 50:10680-10694. [PMID: 36169232 PMCID: PMC9561375 DOI: 10.1093/nar/gkac802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Condensin I and condensin II are multi-subunit complexes that are known for their individual roles in genome organization and preventing genomic instability. However, interactions between condensin I and condensin II subunits and cooperative roles for condensin I and condensin II, outside of their genome organizing functions, have not been reported. We previously discovered that condensin II cooperates with Gamma Interferon Activated Inhibitor of Translation (GAIT) proteins to associate with Long INterspersed Element-1 (LINE-1 or L1) RNA and repress L1 protein expression and the retrotransposition of engineered L1 retrotransposition in cultured human cells. Here, we report that the L1 3'UTR is required for condensin II and GAIT association with L1 RNA, and deletion of the L1 RNA 3'UTR results in increased L1 protein expression and retrotransposition. Interestingly, like condensin II, we report that condensin I also binds GAIT proteins, associates with the L1 RNA 3'UTR, and represses L1 retrotransposition. We provide evidence that the condensin I protein, NCAPD2, is required for condensin II and GAIT protein association with L1 RNA. Furthermore, condensin I and condensin II subunits interact to form a L1-dependent super condensin complex (SCC) which is located primarily within the cytoplasm of both transformed and primary epithelial cells. These data suggest that increases in L1 expression in epithelial cells promote cytoplasmic condensin protein associations that facilitate a feedback loop in which condensins may cooperate to mediate L1 repression.
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Affiliation(s)
- Jacqueline R Ward
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Afshin Khan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bert Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sarah Nock
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Trenton Frisbie
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, USA
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5
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Zhou M. DNA sliding and loop formation by E. coli SMC complex: MukBEF. Biochem Biophys Rep 2022; 31:101297. [PMID: 35770038 PMCID: PMC9234588 DOI: 10.1016/j.bbrep.2022.101297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/08/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022] Open
Abstract
SMC (structural maintenance of chromosomes) complexes share conserved architectures and function in chromosome maintenance via an unknown mechanism. Here we have used single-molecule techniques to study MukBEF, the SMC complex in Escherichia coli. Real-time movies show MukB alone can compact DNA and ATP inhibits DNA compaction by MukB. We observed that DNA unidirectionally slides through MukB, potentially by a ratchet mechanism, and the sliding speed depends on the elastic energy stored in the DNA. MukE, MukF and ATP binding stabilize MukB and DNA interaction, and ATP hydrolysis regulates the loading/unloading of MukBEF from DNA. Our data suggests a new model for how MukBEF organizes the bacterial chromosome in vivo; and this model will be relevant for other SMC proteins. ATP-independent DNA compaction by MukB. DNA unidirectionally slides through MukB, potentially by a ratchet mechanism. MukE, MukF and ATP binding stabilize MukB and DNA interaction. DNA sliding via ratchet driven by entropic force model for chromosome organization by SMC complex.
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6
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Reeling it in: how DNA topology drives loop extrusion by condensin. Nat Struct Mol Biol 2022; 29:623-625. [PMID: 35835869 PMCID: PMC9871954 DOI: 10.1038/s41594-022-00805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes such as condensin regulate chromosome organization by extruding loops. A new study uses single-molecule imaging of condensin on supercoiled DNA to understand how condensins navigate the under- and overwound DNA states common throughout the genome.
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7
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Condensin-driven loop extrusion on supercoiled DNA. Nat Struct Mol Biol 2022; 29:719-727. [PMID: 35835864 DOI: 10.1038/s41594-022-00802-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping are stimulated by positively supercoiled DNA, and condensin preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.
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8
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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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9
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Xiang JF, Corces VG. Regulation of 3D chromatin organization by CTCF. Curr Opin Genet Dev 2021; 67:33-40. [PMID: 33259986 PMCID: PMC8084898 DOI: 10.1016/j.gde.2020.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 01/12/2023]
Abstract
Studies of nuclear architecture using chromosome conformation capture methods have provided a detailed view of how chromatin folds in the 3D nuclear space. New variants of this technology now afford unprecedented resolution and allow the identification of ever smaller folding domains that offer new insights into the mechanisms by which this organization is established and maintained. Here we review recent results in this rapidly evolving field with an emphasis on CTCF function, with the goal of gaining a mechanistic understanding of the principles by which chromatin is folded in the eukaryotic nucleus.
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Affiliation(s)
- Jian-Feng Xiang
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA
| | - Victor G Corces
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA.
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10
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Loop extrusion: theory meets single-molecule experiments. Curr Opin Cell Biol 2020; 64:124-138. [PMID: 32534241 DOI: 10.1016/j.ceb.2020.04.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/20/2022]
Abstract
Chromosomes are organized as chromatin loops that promote segregation, enhancer-promoter interactions, and other genomic functions. Loops were hypothesized to form by 'loop extrusion,' by which structural maintenance of chromosomes (SMC) complexes, such as condensin and cohesin, bind to chromatin, reel it in, and extrude it as a loop. However, such exotic motor activity had never been observed. Following an explosion of indirect evidence, recent single-molecule experiments directly imaged DNA loop extrusion by condensin and cohesin in vitro. These experiments observe rapid (kb/s) extrusion that requires ATP hydrolysis and stalls under pN forces. Surprisingly, condensin extrudes loops asymmetrically, challenging previous models. Extrusion by cohesin is symmetric but requires the protein Nipbl. We discuss how SMC complexes may perform their functions on chromatin in vivo.
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12
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Cui F, Hu J, Xu Z, Tan J, Tang H. Overexpression of NCAPH is upregulated and predicts a poor prognosis in prostate cancer. Oncol Lett 2019; 17:5768-5776. [PMID: 31186803 DOI: 10.3892/ol.2019.10260] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/18/2019] [Indexed: 01/07/2023] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed types of cancer worldwide. However, there remains a lack of accurate biomarkers to predict the outcome of PCa. Non-SMC condensin I complex subunit H (NCAPH) encodes a regulatory subunit of the non-structural maintenance of chromosomes condensin I complex. The present study aimed to investigate whether NCAPH may be a novel diagnostic marker for PCa by analyzing public datasets, including GSE17951, GSE55945 and a dataset from The Cancer Genome Atlas. The current results, to the best of our knowledge, demonstrated for the first time that NCAPH is significantly upregulated in PCa. Furthermore, it was identified that NCAPH expression is higher in stage T3/T4 and N1 PCa samples compared with stage T2 and N0 PCa samples, respectively. Kaplan-Meier analysis demonstrated that overexpression of NCAPH is associated with poor survival of patients with PCa. Bioinformatics analysis revealed that NCAPH is involved in regulating the PCa cell cycle by interacting with a number of proteins, including non-SMC condensin I complex subunit D2, non-SMC condensin I complex subunit G, structural maintenance of chromosomes 4, structural maintenance of chromosomes 2, Aurora kinase A, Aurora kinase B, cyclin-dependent kinase 1, H2A histone family member Z, POC1 centriolar protein A and histone cluster 2 H2A family member C. In summary, the present results suggest NCAPH may be a novel and beneficial diagnostic and therapeutic target in PCa.
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Affiliation(s)
- Feilun Cui
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Jianpeng Hu
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Zhipeng Xu
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Jian Tan
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
| | - Huaming Tang
- Department of Urology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, P.R. China
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13
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Bizard AH, Allemand JF, Hassenkam T, Paramasivam M, Sarlós K, Singh MI, Hickson ID. PICH and TOP3A cooperate to induce positive DNA supercoiling. Nat Struct Mol Biol 2019; 26:267-274. [PMID: 30936532 DOI: 10.1038/s41594-019-0201-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
All known eukaryotic topoisomerases are only able to relieve torsional stress in DNA. Nevertheless, it has been proposed that the introduction of positive DNA supercoiling is required for efficient sister-chromatid disjunction by Topoisomerase 2a during mitosis. Here we identify a eukaryotic enzymatic activity that introduces torsional stress into DNA. We show that the human Plk1-interacting checkpoint helicase (PICH) and Topoisomerase 3a proteins combine to create an extraordinarily high density of positive DNA supercoiling. This activity, which is analogous to that of a reverse-gyrase, is apparently driven by the ability of PICH to progressively extrude hypernegatively supercoiled DNA loops that are relaxed by Topoisomerase 3a. We propose that this positive supercoiling provides an optimal substrate for the rapid disjunction of sister centromeres by Topoisomerase 2a at the onset of anaphase in eukaryotic cells.
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Affiliation(s)
- Anna H Bizard
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jean-Francois Allemand
- Laboratoire de Physique de l'Ecole Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Tue Hassenkam
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Manikandan Paramasivam
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kata Sarlós
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Manika Indrajit Singh
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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14
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Ramos F, Leonard J, Clemente-Blanco A, Aragón L. Cdc14 and Chromosome Condensation: Evaluation of the Recruitment of Condensin to Genomic Regions. Methods Mol Biol 2018; 1505:229-243. [PMID: 27826868 DOI: 10.1007/978-1-4939-6502-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Chromosome condensation is an essential morphological event required for successful DNA segregation during mitosis. The high level of genome compaction achieved during this process is attained by the evolutionary conserved condensin complex. Recently, several lines of evidences have demonstrated that the mitotic phosphatase Cdc14 is required to ensure condensin loading onto chromosomes. To date several approaches have been used in order to characterize condensin activity and regulation, however these techniques are time-consuming and require complex equipment. In this chapter we described an easy and reliable protocol to analyze Cdc14-dependent condensin loading onto specific genomic DNA regions by using a chromatin immunoprecipitation (ChIP) technique.
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Affiliation(s)
- Facundo Ramos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González 2, Salamanca, 37007, Spain
| | - Joanne Leonard
- Cell Cycle Group, Medical Research Council, Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González 2, Salamanca, 37007, Spain
| | - Luis Aragón
- Cell Cycle Group, Medical Research Council, Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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15
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Eeftens JM, Bisht S, Kerssemakers J, Kschonsak M, Haering CH, Dekker C. Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism. EMBO J 2017; 36:3448-3457. [PMID: 29118001 PMCID: PMC5709735 DOI: 10.15252/embj.201797596] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 11/09/2022] Open
Abstract
Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual DNA molecules by the budding yeast condensin complex. We show that compaction can proceed in large steps, driving DNA molecules into a fully condensed state against forces of up to 2 pN. Compaction can be reversed by applying high forces or adding buffer of high ionic strength. While condensin can stably bind DNA in the absence of ATP, ATP hydrolysis by the SMC subunits is required for rendering the association salt insensitive and for the subsequent compaction process. Our results indicate that the condensin reaction cycle involves two distinct steps, where condensin first binds DNA through electrostatic interactions before using ATP hydrolysis to encircle the DNA topologically within its ring structure, which initiates DNA compaction. The finding that both binding modes are essential for its DNA compaction activity has important implications for understanding the mechanism of chromosome compaction.
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Affiliation(s)
- Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
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16
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Eeftens J, Dekker C. Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins. Nat Struct Mol Biol 2017; 24:1012-1020. [DOI: 10.1038/nsmb.3507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
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17
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Oligomerization and ATP stimulate condensin-mediated DNA compaction. Sci Rep 2017; 7:14279. [PMID: 29079757 PMCID: PMC5660149 DOI: 10.1038/s41598-017-14701-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/16/2017] [Indexed: 11/09/2022] Open
Abstract
Large-scale chromatin remodeling during mitosis is catalyzed by a heteropentameric enzyme known as condensin. The DNA-organizing mechanism of condensin depends on the energy of ATP hydrolysis but how this activity specifically promotes proper compaction and segregation of chromosomes during mitosis remains poorly understood. Purification of budding yeast condensin reveals that it occurs not only in the classical heteropentameric "monomer" form, but that it also adopts much larger configurations consistent with oligomerization. We use a single-DNA magnetic tweezers assay to study compaction of DNA by yeast condensin, with the result that only the multimer shows ATP-enhanced DNA-compaction. The compaction reaction involves step-like events of 200 nm (600 bp) size and is strongly suppressed by forces above 1 pN, consistent with a loop-capture mechanism for initial binding and compaction. The compaction reactions are largely insensitive to DNA torsional stress. Our results suggest a physiological role for oligomerized condensin in driving gradual chromatin compaction by step-like and slow "creeping" dynamics consistent with a loop-extrusion mechanism.
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18
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Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PLoS Genet 2017; 13:e1007051. [PMID: 29028794 PMCID: PMC5656329 DOI: 10.1371/journal.pgen.1007051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/25/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1). GAIT has been shown to inhibit translation of mRNAs encoding inflammatory proteins in myeloid cells by preventing the binding of the translation initiation complex, in response to Interferon gamma (IFN-γ). Excitingly, our data show that Condensin II promotes complexation of GAIT subunits. Furthermore, RNA-Immunoprecipitation experiments in epithelial cells demonstrate that Condensin II and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-γ. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells.
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Sen N, Leonard J, Torres R, Garcia-Luis J, Palou-Marin G, Aragón L. Physical Proximity of Sister Chromatids Promotes Top2-Dependent Intertwining. Mol Cell 2016; 64:134-147. [PMID: 27716481 PMCID: PMC5065527 DOI: 10.1016/j.molcel.2016.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 04/01/2016] [Accepted: 09/06/2016] [Indexed: 01/06/2023]
Abstract
Sister chromatid intertwines (SCIs), or catenanes, are topological links between replicated chromatids that interfere with chromosome segregation. The formation of SCIs is thought to be a consequence of fork swiveling during DNA replication, and their removal is thought to occur because of the intrinsic feature of type II topoisomerases (Top2) to simplify DNA topology. Here, we report that SCIs are also formed independently of DNA replication during G2/M by Top2-dependent concatenation of cohesed chromatids due to their physical proximity. We demonstrate that, in contrast to G2/M, Top2 removes SCIs from cohesed chromatids at the anaphase onset. Importantly, SCI removal in anaphase requires condensin and coincides with the hyperactivation of condensin DNA supercoiling activity. This is consistent with the longstanding proposal that condensin provides a bias in Top2 function toward decatenation. A comprehensive model for the formation and resolution of toxic SCI entanglements on eukaryotic genomes is proposed.
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Affiliation(s)
- Nicholas Sen
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Joanne Leonard
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Raul Torres
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Jonay Garcia-Luis
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Gloria Palou-Marin
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Luis Aragón
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
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20
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Klebanow LR, Peshel EC, Schuster AT, De K, Sarvepalli K, Lemieux ME, Lenoir JJ, Moore AW, McDonald JA, Longworth MS. Drosophila Condensin II subunit Chromosome-associated protein D3 regulates cell fate determination through non-cell-autonomous signaling. Development 2016; 143:2791-802. [PMID: 27317808 PMCID: PMC5004906 DOI: 10.1242/dev.133686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/03/2016] [Indexed: 12/19/2022]
Abstract
The pattern of the Drosophila melanogaster adult wing is heavily influenced by the expression of proteins that dictate cell fate decisions between intervein and vein during development. dSRF (Blistered) expression in specific regions of the larval wing disc promotes intervein cell fate, whereas EGFR activity promotes vein cell fate. Here, we report that the chromatin-organizing protein CAP-D3 acts to dampen dSRF levels at the anterior/posterior boundary in the larval wing disc, promoting differentiation of cells into the anterior crossvein. CAP-D3 represses KNOT expression in cells immediately adjacent to the anterior/posterior boundary, thus blocking KNOT-mediated repression of EGFR activity and preventing cell death. Maintenance of EGFR activity in these cells depresses dSRF levels in the neighboring anterior crossvein progenitor cells, allowing them to differentiate into vein cells. These findings uncover a novel transcriptional regulatory network influencing Drosophila wing vein development, and are the first to identify a Condensin II subunit as an important regulator of EGFR activity and cell fate determination in vivo.
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Affiliation(s)
- Lindsey R Klebanow
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Emanuela C Peshel
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Andrew T Schuster
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Kuntal De
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Kavitha Sarvepalli
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | | | - Jessica J Lenoir
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Adrian W Moore
- Disease Mechanism Research Core, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | | | - Michelle S Longworth
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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21
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Kim H, Loparo JJ. Multistep assembly of DNA condensation clusters by SMC. Nat Commun 2016; 7:10200. [PMID: 26725510 PMCID: PMC4725763 DOI: 10.1038/ncomms10200] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022] Open
Abstract
SMC (structural maintenance of chromosomes) family members play essential roles in chromosome condensation, sister chromatid cohesion and DNA repair. It remains unclear how SMCs structure chromosomes and how their mechanochemical cycle regulates their interactions with DNA. Here we used single-molecule fluorescence microscopy to visualize how Bacillus subtilis SMC (BsSMC) interacts with flow-stretched DNAs. We report that BsSMC can slide on DNA, switching between static binding and diffusion. At higher concentrations, BsSMCs form clusters that condense DNA in a weakly ATP-dependent manner. ATP increases the apparent cooperativity of DNA condensation, demonstrating that BsSMC can interact cooperatively through their ATPase head domains. Consistent with these results, ATPase mutants compact DNA more slowly than wild-type BsSMC in the presence of ATP. Our results suggest that transiently static BsSMC molecules can nucleate the formation of clusters that act to locally condense the chromosome while forming long-range DNA bridges. The Structural Maintenance of Chromosomes (SMC) proteins are essential for chromosome condensation, cohesion and DNA repair. Here the authors use single molecule imaging to visualise how Bacillus subtilis SMC interacts with and condenses DNA.
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Affiliation(s)
- HyeongJun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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22
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Leonard J, Sen N, Torres R, Sutani T, Jarmuz A, Shirahige K, Aragón L. Condensin Relocalization from Centromeres to Chromosome Arms Promotes Top2 Recruitment during Anaphase. Cell Rep 2015; 13:2336-2344. [PMID: 26686624 PMCID: PMC4695335 DOI: 10.1016/j.celrep.2015.11.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/08/2015] [Accepted: 11/11/2015] [Indexed: 11/29/2022] Open
Abstract
Condensin is a conserved chromosomal complex necessary to promote mitotic chromosome condensation and sister chromatid resolution during anaphase. Here, we report that yeast condensin binds to replicated centromere regions. We show that centromeric condensin relocalizes to chromosome arms as cells undergo anaphase segregation. We find that condensin relocalization is initiated immediately after the bipolar attachment of sister kinetochores to spindles and requires Polo kinase activity. Moreover, condensin localization during anaphase involves a higher binding rate on DNA and temporally overlaps with condensin’s DNA overwinding activity. Finally, we demonstrate that topoisomerase 2 (Top2) is also recruited to chromosome arms during anaphase in a condensin-dependent manner. Our results uncover a functional relation between condensin and Top2 during anaphase to mediate chromosome segregation. Condensin recruitment to centromeric regions requires DNA replication Centromeric condensin spreads to chromosome arms during anaphase Condensin promotes recruitment of Top2 during anaphase Condensin localization requires Polo kinase and correlates with DNA overwinding
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Affiliation(s)
- Joanne Leonard
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Nicholas Sen
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Raul Torres
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Takashi Sutani
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Adam Jarmuz
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Luis Aragón
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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The Smc5/6 Complex Is an ATP-Dependent Intermolecular DNA Linker. Cell Rep 2015; 12:1471-82. [PMID: 26299966 DOI: 10.1016/j.celrep.2015.07.048] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/30/2015] [Accepted: 07/23/2015] [Indexed: 12/13/2022] Open
Abstract
The structural maintenance of chromosome (SMC) protein complexes cohesin and condensin and the Smc5/6 complex (Smc5/6) are crucial for chromosome dynamics and stability. All contain essential ATPase domains, and cohesin and condensin interact with chromosomes through topological entrapment of DNA. However, how Smc5/6 binds DNA and chromosomes has remained largely unknown. Here, we show that purified Smc5/6 binds DNA through a mechanism that requires ATP hydrolysis by the complex and circular DNA to be established. This also promotes topoisomerase 2-dependent catenation of plasmids, suggesting that Smc5/6 interconnects two DNA molecules using ATP-regulated topological entrapment of DNA, similar to cohesin. We also show that a complex containing an Smc6 mutant that is defective in ATP binding fails to interact with DNA and chromosomes and leads to cell death with concomitant accumulation of DNA damage when overexpressed. Taken together, these results indicate that Smc5/6 executes its cellular functions through ATP-regulated intermolecular DNA linking.
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Abstract
How eukaryotic genomes are packaged into compact cylindrical chromosomes in preparation for cell divisions has remained one of the major unsolved questions of cell biology. Novel approaches to study the topology of DNA helices inside the nuclei of intact cells, paired with computational modeling and precise biomechanical measurements of isolated chromosomes, have advanced our understanding of mitotic chromosome architecture. In this Review Essay, we discuss - in light of these recent insights - the role of chromatin architecture and the functions and possible mechanisms of SMC protein complexes and other molecular machines in the formation of mitotic chromosomes. Based on the information available, we propose a stepwise model of mitotic chromosome condensation that envisions the sequential generation of intra-chromosomal linkages by condensin complexes in the context of cohesin-mediated inter-chromosomal linkages, assisted by topoisomerase II. The described scenario results in rod-shaped metaphase chromosomes ready for their segregation to the cell poles.
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Affiliation(s)
- Marc Kschonsak
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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25
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Kleine Borgmann LAK, Graumann PL. Structural maintenance of chromosome complex in bacteria. J Mol Microbiol Biotechnol 2015; 24:384-95. [PMID: 25732340 DOI: 10.1159/000368931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In all organisms, from eukaryotes to prokaryotes, the chromosome is highly compacted and organized. Chromosome condensation is essential in all cells and ranges from 1,000- to more than 10,000-fold between bacterial and eukaryotic cells. Replication and transcription occur in parallel with chromosome segregation in bacteria. Structural maintenance of chromosome proteins play a key role in chromosome compaction and segregation, their coordination with the cell cycle, and in various other chromosome dynamics, including DNA repair. In spite of their essential nature in almost all organisms, their function at a molecular level is only slowly beginning to emerge.
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Affiliation(s)
- Luise A K Kleine Borgmann
- Division of Biological Sciences and Section of Molecular Biology, University of California, San Diego, La Jolla, Calif., USA
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Condensin II subunit dCAP-D3 restricts retrotransposon mobilization in Drosophila somatic cells. PLoS Genet 2013; 9:e1003879. [PMID: 24204294 PMCID: PMC3814330 DOI: 10.1371/journal.pgen.1003879] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Retrotransposon sequences are positioned throughout the genome of almost every eukaryote that has been sequenced. As mobilization of these elements can have detrimental effects on the transcriptional regulation and stability of an organism's genome, most organisms have evolved mechanisms to repress their movement. Here, we identify a novel role for the Drosophila melanogaster Condensin II subunit, dCAP-D3 in preventing the mobilization of retrotransposons located in somatic cell euchromatin. dCAP-D3 regulates transcription of euchromatic gene clusters which contain or are proximal to retrotransposon sequence. ChIP experiments demonstrate that dCAP-D3 binds to these loci and is important for maintaining a repressed chromatin structure within the boundaries of the retrotransposon and for repressing retrotransposon transcription. We show that dCAP-D3 prevents accumulation of double stranded DNA breaks within retrotransposon sequence, and decreased dCAP-D3 levels leads to a precise loss of retrotransposon sequence at some dCAP-D3 regulated gene clusters and a gain of sequence elsewhere in the genome. Homologous chromosomes exhibit high levels of pairing in Drosophila somatic cells, and our FISH analyses demonstrate that retrotransposon-containing euchromatic loci are regions which are actually less paired than euchromatic regions devoid of retrotransposon sequences. Decreased dCAP-D3 expression increases pairing of homologous retrotransposon-containing loci in tissue culture cells. We propose that the combined effects of dCAP-D3 deficiency on double strand break levels, chromatin structure, transcription and pairing at retrotransposon-containing loci may lead to 1) higher levels of homologous recombination between repeats flanking retrotransposons in dCAP-D3 deficient cells and 2) increased retrotransposition. These findings identify a novel role for the anti-pairing activities of dCAP-D3/Condensin II and uncover a new way in which dCAP-D3/Condensin II influences local chromatin structure to help maintain genome stability. Condensins are conserved complexes that are well known for their roles in promoting the efficient condensation of chromosomes during early mitosis. Previously, we have shown that the Drosophila Condensin II subunit, dCAP-D3, also functions to regulate transcription in somatic cells during the later stages of development. A significant number of dCAP-D3 regulated genes were found to be positioned very close to one another in clusters. In this study, we report that some of the most strongly regulated dCAP-D3 gene clusters are positioned near retrotransposons. Unexpectedly, we find that decreased dCAP-D3 expression results in a precise loss of retrotransposon sequence at these loci. Additionally, dCAP-D3 knockdown causes increased levels of double strand breaks within retrotransposon sequence, an opening of the chromatin in the region, increased retrotransposon transcription and a very significant increase in homologous pairing at the locus. Taken together, these results suggest that dCAP-D3/Condensin II functions to prevent recombination of retrotransposons between homologous chromosomes and possibly retrotransposition as well. This report identifies a novel function for Condensin II that may contribute to its role in genome organization.
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A shared role for RBF1 and dCAP-D3 in the regulation of transcription with consequences for innate immunity. PLoS Genet 2012; 8:e1002618. [PMID: 22496667 PMCID: PMC3320600 DOI: 10.1371/journal.pgen.1002618] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 02/08/2012] [Indexed: 12/27/2022] Open
Abstract
Previously, we discovered a conserved interaction between RB proteins and the Condensin II protein CAP-D3 that is important for ensuring uniform chromatin condensation during mitotic prophase. The Drosophila melanogaster homologs RBF1 and dCAP-D3 co-localize on non-dividing polytene chromatin, suggesting the existence of a shared, non-mitotic role for these two proteins. Here, we show that the absence of RBF1 and dCAP-D3 alters the expression of many of the same genes in larvae and adult flies. Strikingly, most of the genes affected by the loss of RBF1 and dCAP-D3 are not classic cell cycle genes but are developmentally regulated genes with tissue-specific functions and these genes tend to be located in gene clusters. Our data reveal that RBF1 and dCAP-D3 are needed in fat body cells to activate transcription of clusters of antimicrobial peptide (AMP) genes. AMPs are important for innate immunity, and loss of either dCAP-D3 or RBF1 regulation results in a decrease in the ability to clear bacteria. Interestingly, in the adult fat body, RBF1 and dCAP-D3 bind to regions flanking an AMP gene cluster both prior to and following bacterial infection. These results describe a novel, non-mitotic role for the RBF1 and dCAP-D3 proteins in activation of the Drosophila immune system and suggest dCAP-D3 has an important role at specific subsets of RBF1-dependent genes. The retinoblastoma protein (pRB) is a tumor suppressor protein known for its ability to repress transcription of E2F-dependent genes and induce cell cycle arrest. We have previously shown that RB proteins in Drosophila and human cells interact with the Condensin II subunit, CAP-D3, in an E2F-independent manner. Condensins promote condensation of chomosomes in mitosis. Our previous studies suggested that the Drosophila pRB and CAP-D3 homologs, RBF1 and dCAP-D3, co-localize on DNA and may share a function in cells that never undergo mitosis. In this study, we show that one non-mitotic function shared between RBF1 and dCAP-D3 is the regulation of many non-cell-cycle-related, clustered, and cell-type-specific transcripts including a conserved family of genes that are important for the immune response in the fly. In fact, results show that normal levels of dCAP-D3 and RBF1 expression are necessary for the ability of the fly to clear infection with human bacterial pathogens. This work demonstrates that dCAP-D3 proteins can regulate a unique subset of RBF1-dependent transcripts in vivo and identifies a novel role for both RBF1 and dCAP-D3 protein in activation of innate immune genes, which may be conserved in human cells.
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Abstract
Topology is the study of geometric properties that are preserved during bending, twisting and stretching of objects. In the context of the genome, topology is discussed at two interconnected and overlapping levels. The first focuses the DNA double helix itself, and includes alterations such as those triggered by DNA interacting proteins, processes which require the separation of the two DNA strands and DNA knotting. The second level is centered on the higher order organization of DNA into chromosomes, as well as dynamic conformational changes that occur on a chromosomal scale. Here, we refer to the first level as "DNA topology", the second as "chromosome topology". Since their identification, evidences suggesting that the so called structural maintenance of chromosomes (SMC) protein complexes are central to the interplay between DNA and chromosome topology have accumulated. The SMC complexes regulate replication, segregation, repair and transcription, all processes which influence, and are influenced by, DNA and chromosome topology. This review focuses on the details of the relationship between the SMC complexes and topology. It also discusses the possibility that the SMC complexes are united by a capability to sense the geometrical chirality of DNA crossings.
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Affiliation(s)
- Sidney D Carter
- Karolinska Institute, Department of Cell and Molecular Biology, Stockholm, Sweden
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29
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Cuylen S, Haering CH. Deciphering condensin action during chromosome segregation. Trends Cell Biol 2011; 21:552-9. [PMID: 21763138 DOI: 10.1016/j.tcb.2011.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 12/24/2022]
Abstract
The correct segregation of eukaryotic genomes requires the resolution of sister DNA molecules and their movement into opposite halves of the cell before cell division. The dynamic changes chromosomes need to undergo during these events depend on the action of a multi-subunit SMC (structural maintenance of chromosomes) protein complex named condensin, but its molecular function in chromosome segregation is still poorly understood. Recent studies suggest that condensin has a role in the removal of sister chromatid cohesin, in sister chromatid decatenation by topoisomerases, and in the structural reconfiguration of mitotic chromosomes. In this review we discuss possible mechanisms that could explain the variety of condensin actions during chromosome segregation.
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Affiliation(s)
- Sara Cuylen
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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30
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Condensin structures chromosomal DNA through topological links. Nat Struct Mol Biol 2011; 18:894-901. [PMID: 21765419 DOI: 10.1038/nsmb.2087] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/10/2011] [Indexed: 12/28/2022]
Abstract
The multisubunit condensin complex is essential for the structural organization of eukaryotic chromosomes during their segregation by the mitotic spindle, but the mechanistic basis for its function is not understood. To address how condensin binds to and structures chromosomes, we have isolated from Saccharomyces cerevisiae cells circular minichromosomes linked to condensin. We find that either linearization of minichromosome DNA or proteolytic opening of the ring-like structure formed through the connection of the two ATPase heads of condensin's structural maintenance of chromosomes (SMC) heterodimer by its kleisin subunit eliminates their association. This suggests that condensin rings encircle chromosomal DNA. We further show that release of condensin from chromosomes by ring opening in dividing cells compromises the partitioning of chromosome regions distal to centromeres. Condensin hence forms topological links within chromatid arms that provide the arms with the structural rigidity necessary for their segregation.
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31
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Abstract
Recent data show that cells from many cancers exhibit massive chromosome instability. The traditional view is that the gradual accumulation of mutations in genes involved in transcriptional regulation and cell cycle controls results in tumor development. This, however, does not exclude the possibility that some mutations could be more potent than others in destabilizing the genome by targeting both chromosomal integrity and corresponding checkpoint mechanisms simultaneously. Three such examples of "single-hit" lesions potentially leading to heritable genome destabilization are discussed. They include: failure to release sister chromatid cohesion due to the incomplete proteolytic cleavage of cohesin; massive merotelic kinetochore misattachments upon condensin depletion; and chromosome under-replication. In all three cases, cells fail to detect potential chromosomal bridges before anaphase entry, indicating that there is a basic cell cycle requirement to maintain a degree of sister chromatid bridging that is not recognizable as chromosomal damage.
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Affiliation(s)
- Alexander V Strunnikov
- Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5640 Fishers Lane, Room 1524, Rockville, MD 20852, USA.
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32
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Wang M, Wang K, Tang D, Wei C, Li M, Shen Y, Chi Z, Gu M, Cheng Z. The central element protein ZEP1 of the synaptonemal complex regulates the number of crossovers during meiosis in rice. THE PLANT CELL 2010; 22:417-30. [PMID: 20154151 PMCID: PMC2845403 DOI: 10.1105/tpc.109.070789] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 01/18/2009] [Accepted: 01/27/2010] [Indexed: 05/18/2023]
Abstract
ZEP1, a transverse filament (TF) protein, is the rice (Oryza sativa) homolog of Arabidopsis thaliana ZYP1. In the Tos17-insertional zep1 mutants, homologous chromosomes align along the entire length of the chromosome, but the synaptonemal complex is not assembled in early prophase I. Crossovers are well formed, and 12 bivalents could be detected from diakinesis to metaphase I, which leads to equal chromosomal segregation in anaphase I. Moreover, the number of crossovers has a tendency to be increased compared with that in the wild type. These phenomena are different from the TF mutants identified so far in other organisms. Chiasma terminalization of the bivalent, which occurs frequently in the wild type, seldom occurred in zep1. Transmission electron micrographs and immunodetection using an antibody against ZEP1 showed that ZEP1 is the central element of the synaptonemal complex. Although PAIR2 and MER3 were loaded normally in zep1, their dissociation was delayed severely compared with the wild type. In addition, ZEP1 is reloaded onto chromosomes in early microspores as the chromosome decondense, suggesting that ZEP1 might have other biological functions during this process.
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Affiliation(s)
- Mo Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kejian Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cunxu Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ming Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengchang Chi
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Address correspondence to
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Abstract
Dosage compensation in the nematode Caenorhabditis elegans is achieved by the binding of a condensin-like dosage compensation complex (DCC) to both X chromosomes in hermaphrodites to downregulate gene expression two-fold. Condensin I(DC), a sub-part of the DCC, differs from the mitotic condensin I complex by a single subunit, strengthening the connection between dosage compensation and mitotic chromosome condensation. The DCC is targeted to X chromosomes by initial binding to a number of recruiting elements, followed by dispersal or spreading to secondary sites. While the complex is greatly enriched on the X chromosomes, many sites on autosomes also bind the complex. DCC binding does not correlate with DCC-mediated repression, suggesting that the complex acts in a chromosome-wide manner, rather than on a gene-by-gene basis. Worm dosage compensation represents an excellent model system to study how condensin-mediated changes in higher order chromatin organization affect gene expression.
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34
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Abstract
Condensin is a highly conserved pentameric complex consisting of two structural maintenance of chromosome (SMC) ATPase subunits and three auxiliary components. While initially regarded as a key driver of mitotic chromosome condensation, condensin is increasingly viewed as having a more subtle influence on chromosome architecture. The two condensin complexes are required to direct the correct folding and organization of chromosomes prior to anaphase and for keeping the chromosomes compact as they separate to the poles. This ancient complex is essential in mitosis and meiosis and has additional roles in gene regulation and DNA repair. The wide variety of biochemical and genetic tools available are gradually unravelling the numerous roles condensin plays during the cell cycle and shedding light on its mechanism of action.
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Affiliation(s)
- Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia.
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35
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Mitotic catastrophe is the predominant response to histone acetyltransferase depletion. Cell Death Differ 2008; 16:483-97. [PMID: 19096391 DOI: 10.1038/cdd.2008.182] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation induces chromatin opening by perturbing higher-order chromatin compaction and folding, suggesting that histone acetylation and deacetylation dynamics are central to chromosome condensation or decondensation. The condensation of chromosomes during mitosis is an essential prerequisite for successful chromosome segregation. In this study, we depleted three representative histone acetyltransferases (HATs; p300, CBP, and P/CAF) using shRNAs to explore their role in regulating mitotic progression and chromosome segregation. We showed that HAT depletion severely interfered with the normal timing of mitotic progression, and it reduced condensin subunit levels. The predominant response to HAT depletion, in both human primary and cancer cells, was a mitotic catastrophe following aberrant mitotic arrest. Alternatively, adaptation to HAT depletion, particularly in cancer cells, led to multinucleation and aneuploidy. Interestingly, mitotic catastrophe induced by HAT depletion appeared to be coupled to the signaling process of H2AX phosphorylation and foci formation, independently of DNA double-strand breaks and DNA damage. Taken together, our results provide novel molecular evidence that HAT proteins maintain mitotic chromatin assembly and integrity as a cellular determinant of mitotic cell death.
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36
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D’Ambrosio C, Schmidt CK, Katou Y, Kelly G, Itoh T, Shirahige K, Uhlmann F. Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Genes Dev 2008; 22:2215-27. [PMID: 18708580 PMCID: PMC2518811 DOI: 10.1101/gad.1675708] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 06/25/2008] [Indexed: 01/06/2023]
Abstract
Eukaryotic chromosomes reach their stable rod-shaped appearance in mitosis in a reaction dependent on the evolutionarily conserved condensin complex. Little is known about how and where condensin associates with chromosomes. Here, we analyze condensin binding to budding yeast chromosomes using high-resolution oligonucleotide tiling arrays. Condensin-binding sites coincide with those of the loading factor Scc2/4 of the related cohesin complex. The sites map to tRNA and other genes bound by the RNA polymerase III transcription factor TFIIIC, and ribosomal protein and SNR genes. An ectopic B-box element, recognized by TFIIIC, constitutes a minimal condensin-binding site, and TFIIIC and the Scc2/4 complex promote functional condensin association with chromosomes. A similar pattern of condensin binding is conserved along fission yeast chromosomes. This reveals that TFIIIC-binding sites, including tRNA genes, constitute a hitherto unknown chromosomal feature with important implications for chromosome architecture during both interphase and mitosis.
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Affiliation(s)
- Claudio D’Ambrosio
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London WC2A 3PX, United Kingdom
| | - Christine Katrin Schmidt
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London WC2A 3PX, United Kingdom
| | - Yuki Katou
- Laboratory of Chromosome Structure and Function, Department of Biological Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Gavin Kelly
- Bioinformatics & Biostatistics Service, Cancer Research UK London Research Institute, London WC2A 3PX, United Kingdom
| | - Takehiko Itoh
- Research Center for Advanced Science and Technology, Mitsubishi Research Institute Inc., Chiyoda-ku, Tokyo 100-8141, Japan
| | - Katsuhiko Shirahige
- Laboratory of Chromosome Structure and Function, Department of Biological Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London WC2A 3PX, United Kingdom
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37
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Bazett-Jones DP, Li R, Fussner E, Nisman R, Dehghani H. Elucidating chromatin and nuclear domain architecture with electron spectroscopic imaging. Chromosome Res 2008; 16:397-412. [PMID: 18461480 DOI: 10.1007/s10577-008-1237-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electron microscopy has been the 'gold standard' of spatial resolution for studying the structure of the cell nucleus. Electron spectroscopic imaging (ESI) offers advantages over conventional transmission electron microscopy by eliminating the need for heavy-atom contrast agents. ESI also provides mass-dependent and element-specific information at high resolution, permitting the distinguishing of structures that are primarily composed of protein, DNA, or RNA. The technique can be applied to understand the structural consequences of epigenetic modifications, such as modified histones, on chromatin fiber morphology. ESI can also be applied to elucidate the multifunctional behavior of subnuclear 'organelles' such as the nucleolus and promyelocytic leukemia nuclear bodies.
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Affiliation(s)
- David P Bazett-Jones
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Research Institute, 101 College Street, East Tower, 15th Floor, 15-401T, Toronto, ON M5G 1L7, Canada.
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38
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Abstract
Rb mutants exhibit aneuploidy and aberrant chromosome structure during mitosis. In this issue of Genes & Development, a new paper from Longworth and colleagues (1011-1024) describes both physical and functional interactions between Drosophila Rbf1 and the dCAP-D3 subunit of condensin II. This work directly implicates the Rb family proteins in mitotic chromosome condensation and suggests that a failure in targeting condensin II to chromatin underlies the aneuploidy in rbf1 mutants.
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Affiliation(s)
- Brigitte D Lavoie
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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39
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Hudson DF, Ohta S, Freisinger T, MacIsaac F, Sennels L, Alves F, Lai F, Kerr A, Rappsilber J, Earnshaw WC. Molecular and genetic analysis of condensin function in vertebrate cells. Mol Biol Cell 2008; 19:3070-9. [PMID: 18480406 PMCID: PMC2441691 DOI: 10.1091/mbc.e08-01-0057] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 04/14/2008] [Accepted: 05/01/2008] [Indexed: 01/02/2023] Open
Abstract
We engineered mutants into residues of SMC2 to dissect the role of ATPase function in the condensin complex. These residues are predicted to be involved in ATP binding or hydrolysis and in the Q-loop, which is thought to act as a mediator of conformational changes induced by substrate binding. All the engineered ATPase mutations resulted in lethality when introduced into SMC2 null cells. We found that ATP binding, but not hydrolysis, is essential to allow stable condensin association with chromosomes. How SMC proteins bind and interact with DNA is still a major question. Cohesin may form a ring structure that topologically encircles DNA. We examined whether condensin behaves in an analogous way to its cohesin counterpart, and we have generated a cleavable form of biologically active condensin with PreScission protease sites engineered into the SMC2 protein. This has allowed us to demonstrate that topological integrity of the SMC2-SMC4 heterodimer is not necessary for the stability of the condensin complex in vitro or for its stable association with mitotic chromosomes. Thus, despite their similar molecular organization, condensin and cohesin exhibit fundamental differences in their structure and function.
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Affiliation(s)
- Damien F. Hudson
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Shinya Ohta
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Tina Freisinger
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
- Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Fiona MacIsaac
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Lau Sennels
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Flavia Alves
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Fan Lai
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
- Centre for Genomic Regulation, E-08003 Barcelona, Spain
| | - Alastair Kerr
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Juri Rappsilber
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - William C. Earnshaw
- *Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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40
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Surcel A, Koshland D, Ma H, Simpson RT. Cohesin interaction with centromeric minichromosomes shows a multi-complex rod-shaped structure. PLoS One 2008; 3:e2453. [PMID: 18545699 PMCID: PMC2408725 DOI: 10.1371/journal.pone.0002453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/08/2008] [Indexed: 12/30/2022] Open
Abstract
Cohesin is the protein complex responsible for maintaining sister chromatid cohesion. Cohesin interacts with centromeres and specific loci along chromosome arms known as Chromosome Attachment Regions (CARs). The cohesin holocomplex contains four subunits. Two of them, Smc1p (Structural maintenance of chromosome 1 protein) and Smc3p, are long coiled-coil proteins, which heterodimerize with each other at one end. They are joined together at the other end by a third subunit, Scc1p, which also binds to the fourth subunit, Scc3p. How cohesin interacts with chromosomes is not known, although several models have been proposed, in part on the basis of in vitro assembly of purified cohesin proteins. To be able to observe in vivo cohesin-chromatin interactions, we have modified a Minichromosome Affinity Purification (MAP) method to isolate a CAR-containing centromeric minichromosome attached to in vivo assembled cohesin. Transmission Electron Microscopy (TEM) analysis of these minichromosomes suggests that cohesin assumes a rod shape and interacts with replicated minichromosome at one end of that rod. Additionally, our data implies that more than one cohesin molecule interacts with each pair of replicated minichromsomes. These molecules seem to be packed into a single thick rod, suggesting that the Smc1p and Smc3p subunits may interact extensively.
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Affiliation(s)
- Alexandra Surcel
- The Intercollege Graduate Program in Cell and Developmental Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Douglas Koshland
- Howard Hughes Medical Institute, Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland, United States of America
| | - Hong Ma
- The Intercollege Graduate Program in Cell and Developmental Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Robert T. Simpson
- The Intercollege Graduate Program in Cell and Developmental Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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41
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Longworth MS, Herr A, Ji JY, Dyson NJ. RBF1 promotes chromatin condensation through a conserved interaction with the Condensin II protein dCAP-D3. Genes Dev 2008; 22:1011-24. [PMID: 18367646 DOI: 10.1101/gad.1631508] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Drosophila retinoblastoma family of proteins (RBF1 and RBF2) and their mammalian homologs (pRB, p130, and p107) are best known for their regulation of the G1/S transition via the repression of E2F-dependent transcription. However, RB family members also possess additional functions. Here, we report that rbf1 mutant larvae have extensive defects in chromatin condensation during mitosis. We describe a novel interaction between RBF1 and dCAP-D3, a non-SMC component of the Condensin II complex that links RBF1 to the regulation of chromosome structure. RBF1 physically interacts with dCAP-D3, RBF1 and dCAP-D3 partially colocalize on polytene chromosomes, and RBF1 is required for efficient association of dCAP-D3 with chromatin. dCap-D3 mutants also exhibit chromatin condensation defects, and mutant alleles of dCap-D3 suppress cellular and developmental phenotypes induced by the overexpression of RBF1. Interestingly, this interaction is conserved between flies and humans. The re-expression of pRB into a pRB-deficient human tumor cell line promotes chromatin association of hCAP-D3 in a manner that depends on the LXCXE-binding cleft of pRB. These results uncover an unexpected link between pRB/RBF1 and chromatin condensation, providing a mechanism by which the functional inactivation of RB family members in human tumor cells may contribute to genome instability.
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Affiliation(s)
- Michelle S Longworth
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129, USA
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42
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König P, Braunfeld MB, Sedat JW, Agard DA. The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography. Chromosoma 2007; 116:349-72. [PMID: 17333236 DOI: 10.1007/s00412-007-0101-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2006] [Revised: 01/16/2007] [Accepted: 01/17/2007] [Indexed: 01/27/2023]
Abstract
We have studied the in vitro reconstitution of sperm nuclei and small DNA templates to mitotic chromatin in Xenopus laevis egg extracts by three-dimensional (3D) electron microscopy (EM) tomography. Using specifically developed software, the reconstituted chromatin was interpreted in terms of nucleosomal patterns and the overall chromatin connectivity. The condensed chromatin formed from small DNA templates was characterized by aligned arrays of packed nucleosomal clusters having a typical 10-nm spacing between nucleosomes within the same cluster and a 30-nm spacing between nucleosomes in different clusters. A similar short-range nucleosomal clustering was also observed in condensed chromosomes; however, the clusters were smaller, and they were organized in 30- to 40-nm large domains. An analysis of the overall chromatin connectivity in condensed chromosomes showed that the 30-40-nm domains are themselves organized into a regularly spaced and interconnected 3D chromatin network that extends uniformly throughout the chromosomal volume, providing little indication of a systematic large-scale organization. Based on their topology and high degree of interconnectedness, it is unlikely that 30-40-nm domains arise from the folding of local stretches of nucleosomal fibers. Instead, they appear to be formed by the close apposition of more distant chromatin segments. By combining 3D immunolabeling and EM tomography, we found topoisomerase II to be randomly distributed within this network, while the stable maintenance of chromosomes head domain of condensin was preferentially associated with the 30-40-nm chromatin domains. These observations suggest that 30-40-nm domains are essential for establishing long-range chromatin associations that are central for chromosome condensation.
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Affiliation(s)
- Peter König
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
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43
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Takemoto A, Kimura K, Yanagisawa J, Yokoyama S, Hanaoka F. Negative regulation of condensin I by CK2-mediated phosphorylation. EMBO J 2006; 25:5339-48. [PMID: 17066080 PMCID: PMC1636611 DOI: 10.1038/sj.emboj.7601394] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 09/27/2006] [Indexed: 01/17/2023] Open
Abstract
Condensin I, which plays an essential role in mitotic chromosome assembly and segregation in vivo, constrains positive supercoils into DNA in the presence of adenosine triphosphate in vitro. Condensin I is constitutively present in a phosphorylated form throughout the HeLa cell cycle, but the sites at which it is phosphorylated in interphase cells differ from those recognized by Cdc2 during mitosis. Immunodepletion, in vitro phosphorylation, and immunoblot analysis using a phospho-specific antibody suggested that the CK2 kinase is likely to be responsible for phosphorylation of condensin I during interphase. In contrast to the slight stimulatory effect of Cdc2-induced phosphorylation of condensin I on supercoiling, phosphorylation by CK2 reduced the supercoiling activity of condensin I. CK2-mediated phosphorylation of condensin I is spatially and temporally regulated in a manner different to that of Cdc2-mediated phosphorylation: CK2-dependent phosphorylation increases during interphase and decreases on chromosomes during mitosis. These findings are the first to demonstrate a negative regulatory mode for condensin I, a process that may influence chromatin structure during interphase and mitosis.
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Affiliation(s)
- Ai Takemoto
- Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- These authors contributed equally to this work
| | - Keiji Kimura
- Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki, Japan
- Solution Oriented Research for Science and Technology (SORST) from the Japan Science and Technology Agency, Wako, Saitama, Japan
- These authors contributed equally to this work
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8572, Japan. Tel.: +81 29 853 6632; Fax: +81 29 853 4605; E-mail:
| | - Junn Yanagisawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki, Japan
| | - Shigeyuki Yokoyama
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RIKEN Genomic Sciences Center, Suehiro-cho, Tsurumi, Yokohama, Japan
| | - Fumio Hanaoka
- Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
- Solution Oriented Research for Science and Technology (SORST) from the Japan Science and Technology Agency, Wako, Saitama, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita, Osaka 565-0871, Japan. Tel.: +81 6 6879 7975; Fax: +81 6 6877 9382. E-mail:
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44
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Structure and Function of Rad50/SMC Protein Complexes in Chromosome Biology. Genome Integr 2006. [DOI: 10.1007/7050_006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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45
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Wang BD, Butylin P, Strunnikov A. Condensin function in mitotic nucleolar segregation is regulated by rDNA transcription. Cell Cycle 2006; 5:2260-7. [PMID: 16969110 PMCID: PMC3225123 DOI: 10.4161/cc.5.19.3292] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromosome condensation is established and maintained by the condensin complex. The mechanisms governing loading of condensin onto specific chromosomal sites remain unknown. To elucidate the molecular pathways that determine condensin binding to the nucleolar organizer, a key condensin binding site, we analyzed the properties of condensin-bound sites within the rDNA repeat in budding yeast and demonstrated that the bulk of mitotic condensin binding to rDNA is reduced or eliminated when Pol I transcription is elevated. Conversely, when Pol I transcription is repressed either by rapamycin treatment or by promoter shut-off, condensin binding to rDNA is increased. This novel potential role for constitutive and/or periodic repression of Pol I transcription in rDNA condensin loading is an important factor in determining the segregation proficiency of NOR-containing chromosomes.
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Affiliation(s)
| | | | - Alexander Strunnikov
- Correspondence to: Alexander V. Strunnikov; NIH, NICHD, LGRD; 18T Library Drive, Room 106; Bethesda, Maryland 20892 USA; Tel.: 301.402.8384; Fax: 301.402.1323;
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46
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Abstract
The SMC (structural maintenance of chromosomes) proteins are a highly conserved and ubiquitous family of ATPases, found in nearly all living organisms examined, where they play crucial roles in transmission of the hereditary material. However, the extent to which efficient ATP hydrolysis is required for SMC function has been a matter of some debate. Here we investigate the potential functional significance of ATP binding and hydrolysis in different eukaryotic SMC proteins, both by comparing the conservation of conserved ATPase motifs and by exploring potential coevolution between associated domains. In this way, we have been able to account for the reduced requirement for ATPase activity in cohesin's SMC3 and demonstrate the greater apparent conservation requirements for such activity in condensin SMC proteins. Finally, we explore possible interactions between the SMC and non-SMC components of the condensin complex that are required for full condensin activity and may modulate ATPase activity in the holocomplex.
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Affiliation(s)
- Neville Cobbe
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh, United Kingdom.
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47
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Gerlich D, Hirota T, Koch B, Peters JM, Ellenberg J. Condensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells. Curr Biol 2006; 16:333-44. [PMID: 16488867 DOI: 10.1016/j.cub.2005.12.040] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 12/07/2005] [Accepted: 12/20/2005] [Indexed: 11/23/2022]
Abstract
BACKGROUND Restructuring chromatin into morphologically distinct chromosomes is essential for cell division, but the molecular mechanisms underlying this process are poorly understood. Condensin complexes have been proposed as key factors, although controversial conclusions about their contribution to chromosome structure were reached by different experimental approaches in fixed cells or cell extracts. Their function under physiological conditions still needs to be defined. RESULTS Here, we investigated the specific functions of condensin I and II in live cells by fluorescence microscopy and RNAi depletion. Photobleaching and quantitative time-lapse imaging showed that GFP-tagged condensin II bound stably to chromosomes throughout mitosis. By contrast, the canonical condensin I interacted dynamically with chromatin after completion of prophase compaction, reaching steady-state levels on chromosomes before congression. In condensin I-depleted cells, compaction was normal, but chromosomes were mechanically labile and unable to withstand spindle forces during alignment. However, normal levels of condensin II were not required for chromosome stability. CONCLUSIONS We conclude that while condensin I seems dispensable for normal chromosome compaction, its dynamic binding after nuclear envelope breakdown locks already condensed chromatin in a rigid state required for mechanically stable spindle attachment.
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Affiliation(s)
- Daniel Gerlich
- Gene Expression and Cell Biology/Biophysics Programmes, EMBL, 69117 Heidelberg, Germany
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48
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Abstract
Structural maintenance of chromosomes (SMC) proteins are ubiquitous in organisms from bacteria to humans, and function as core components of the condensin and cohesin complexes in eukaryotes. SMC proteins adopt a V-shaped structure with two long arms, each of which has an ATP-binding head domain at the distal end. It is important to understand how these uniquely designed protein machines interact with DNA strands and how such interactions are modulated by the ATP-binding and -hydrolysis cycle. An emerging idea is that SMC proteins use a diverse array of intramolecular and intermolecular protein-protein interactions to actively fold, tether and manipulate DNA strands.
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Affiliation(s)
- Tatsuya Hirano
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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49
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Siddiqui NU, Rusyniak S, Hasenkampf CA, Riggs CD. Disruption of the Arabidopsis SMC4 gene, AtCAP-C, compromises gametogenesis and embryogenesis. PLANTA 2006; 223:990-7. [PMID: 16482433 DOI: 10.1007/s00425-006-0234-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 08/31/2005] [Indexed: 05/06/2023]
Abstract
In higher eukaryotes, the condensin complex is a multisubunit apparatus that plays a pivotal role in the coordinated condensation of chromatin during mitosis. The catalytic subunits, CAP-E and CAP-C, members of the SMC family of ATPases, form a heterodimer, the activity of which is controlled by the non-SMC subunits CAP-D2, CAP-G and CAP-H. Here, we report the characterization of a T-DNA insertion mutant of the Arabidopsis CAP-C gene. Analysis of the progeny of selfed heterozygotes revealed that the homozygous null genotype is embryo lethal, with arrest occurring at or before the globular stage of development. Patterning defects associated with altered planes of cytokinesis were found in both the embryo and the suspensor. Crosses of heterozygotes with wild type plants revealed both male and female gametophytic defects. Stretched chromatin was observed between segregating mitotic chromosomes in pollen produced by selfed heterozygotes. Additionally, some plants heterozygous for the T-DNA insertion exhibited loss of apical dominance and mild fasciation, indicating a semi-dominant effect of the mutation. These results reveal a critical role for AtCAP-C during cell division and, unlike our previous studies on the AtCAP-E genes, suggest that no redundant factors for AtCAP-C exist in the Arabidopsis genome.
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Affiliation(s)
- Najeeb U Siddiqui
- Department of Botany, Division of Life Sciences, University of Toronto, 1265 Military Trail, M1C 1A4, Scarborough, ON, Canada
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50
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Maeshima K, Eltsov M, Laemmli UK. Chromosome structure: improved immunolabeling for electron microscopy. Chromosoma 2005; 114:365-75. [PMID: 16175370 DOI: 10.1007/s00412-005-0023-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 08/05/2005] [Accepted: 08/15/2005] [Indexed: 11/30/2022]
Abstract
To structurally dissect mitotic chromosomes, we aim to position along the folded chromatin fiber proteins involved in long-range order, such as topoisomerase IIalpha (topoIIalpha) and condensin. Immuno-electron microscopy (EM) of thin-sectioned chromosomes is the method of choice toward this goal. A much-improved immunoprocedure that avoids problems associated with aldehyde fixation, such as chemical translinking and networking of chromatin fibers, is reported here. We show that ultraviolet irradiation of isolated nuclei or chromosomes facilitates high-level specific immunostaining, as established by fluorescence microscopy with a variety of antibodies and especially by immuno-EM. Ultrastructural localizations of topoIIalpha and condensin I component hBarren (hBar; hCAP-H) in mitotic chromosomes were studied by immuno-EM. We show that the micrographs of thin-sectioned chromosomes map topoIIalpha and hBar to the center of the chromosomal body where the chromatin fibers generally converge. This localization is defined by many clustered gold particles with only rare individual particles in the peripheral halo. The data obtained are consistent with the view that condensin and perhaps topoIIalpha tether chromatin to loops according to a scaffolding-type model.
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Affiliation(s)
- Kazuhiro Maeshima
- Department of Biochemistry, University of Geneva, 30, Quai Ernest-Ansermet, 1211, Geneva 4, Switzerland
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