1
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Borando F, Tiana G. Effective model of protein-mediated interactions in chromatin. Phys Rev E 2024; 109:064406. [PMID: 39021027 DOI: 10.1103/physreve.109.064406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/30/2024] [Indexed: 07/20/2024]
Abstract
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular-dynamics simulations of a polymer surrounded by binders that the strength of the binder-polymer interaction separates an equilibrium from a nonequilibrium regime. In the equilibrium regime, the system can be efficiently described by an effective model in which the binders are traced out. Even in this case, the polymers display features that are different from those of a standard homopolymer interacting with two-body interactions. We then extend the effective model to deal with the case where binders cannot be regarded as in equilibrium and a new phenomenology appears, including local blobs in the polymer. An effective description of this system can be useful in elucidating the fundamental mechanisms that govern chromatin structuring in particular and indirect interactions in general.
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2
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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3
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Pati D. Role of chromosomal cohesion and separation in aneuploidy and tumorigenesis. Cell Mol Life Sci 2024; 81:100. [PMID: 38388697 PMCID: PMC10884101 DOI: 10.1007/s00018-024-05122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Cell division is a crucial process, and one of its essential steps involves copying the genetic material, which is organized into structures called chromosomes. Before a cell can divide into two, it needs to ensure that each newly copied chromosome is paired tightly with its identical twin. This pairing is maintained by a protein complex known as cohesin, which is conserved in various organisms, from single-celled ones to humans. Cohesin essentially encircles the DNA, creating a ring-like structure to handcuff, to keep the newly synthesized sister chromosomes together in pairs. Therefore, chromosomal cohesion and separation are fundamental processes governing the attachment and segregation of sister chromatids during cell division. Metaphase-to-anaphase transition requires dissolution of cohesins by the enzyme Separase. The tight regulation of these processes is vital for safeguarding genomic stability. Dysregulation in chromosomal cohesion and separation resulting in aneuploidy, a condition characterized by an abnormal chromosome count in a cell, is strongly associated with cancer. Aneuploidy is a recurring hallmark in many cancer types, and abnormalities in chromosomal cohesion and separation have been identified as significant contributors to various cancers, such as acute myeloid leukemia, myelodysplastic syndrome, colorectal, bladder, and other solid cancers. Mutations within the cohesin complex have been associated with these cancers, as they interfere with chromosomal segregation, genome organization, and gene expression, promoting aneuploidy and contributing to the initiation of malignancy. In summary, chromosomal cohesion and separation processes play a pivotal role in preserving genomic stability, and aberrations in these mechanisms can lead to aneuploidy and cancer. Gaining a deeper understanding of the molecular intricacies of chromosomal cohesion and separation offers promising prospects for the development of innovative therapeutic approaches in the battle against cancer.
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Affiliation(s)
- Debananda Pati
- Texas Children's Cancer Center, Department of Pediatrics Hematology/Oncology, Molecular and Cellular Biology, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA.
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4
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Batty P, Langer CCH, Takács Z, Tang W, Blaukopf C, Peters J, Gerlich DW. Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase. EMBO J 2023; 42:e113475. [PMID: 37357575 PMCID: PMC10425840 DOI: 10.15252/embj.2023113475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.
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Affiliation(s)
- Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Christoph CH Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Zsuzsanna Takács
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Jan‐Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
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5
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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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6
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Choudhary K, Kupiec M. The cohesin complex of yeasts: sister chromatid cohesion and beyond. FEMS Microbiol Rev 2023; 47:6825453. [PMID: 36370456 DOI: 10.1093/femsre/fuac045] [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: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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7
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Attou A, Zülske T, Wedemann G. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions. Biophys J 2022; 121:4788-4799. [PMID: 36325618 PMCID: PMC9811664 DOI: 10.1016/j.bpj.2022.10.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.
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Affiliation(s)
- Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
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8
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Pradhan B, Barth R, Kim E, Davidson IF, Bauer B, van Laar T, Yang W, Ryu JK, van der Torre J, Peters JM, Dekker C. SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Rep 2022; 41:111491. [PMID: 36261017 DOI: 10.1101/2021.07.15.452501] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 05/17/2023] Open
Abstract
Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.
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Affiliation(s)
- Biswajit Pradhan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Benedikt Bauer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands; Nynke Dekker Lab, Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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9
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Matityahu A, Onn I. It's all in the numbers: Cohesin stoichiometry. Front Mol Biosci 2022; 9:1010894. [PMID: 36330215 PMCID: PMC9623059 DOI: 10.3389/fmolb.2022.1010894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/05/2022] [Indexed: 01/09/2024] Open
Abstract
Cohesin, a structural maintenance of chromosome (SMC) complex, organizes chromatin into three-dimensional structures by threading chromatin into loops and stabilizing long-range chromatin interactions. Four subunits in a 1:1:1:1 ratio compose the cohesin core, which is regulated by auxiliary factors that interact with or modify the core subunits. An ongoing debate about cohesin's mechanism of action regards its stoichiometry. Namely, is cohesin activity mediated by a single complex or cooperation between several complexes that organize into dimers or oligomers? Several investigations that used various experimental approaches have tried to resolve this dispute. Some have convincingly demonstrated that the cohesin monomer is the active unit. However, others have revealed the formation of cohesin dimers and higher-order clusters on and off chromosomes. Elucidating the biological function of cohesin clusters and determining what regulates their formation are just two of the many new questions raised by these findings. We briefly review the history of the argument about cohesin stoichiometry and the central evidence for cohesin activity as a monomer vs. an oligomer. Finally, we discuss the possible biological significance of cohesin oligomerization and present open questions that remain to be answered.
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Affiliation(s)
| | - Itay Onn
- The Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Safed, Israel
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10
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SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Rep 2022; 41:111491. [DOI: 10.1016/j.celrep.2022.111491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
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11
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Cohesin ATPase activities regulate DNA binding and coiled-coil configuration. Proc Natl Acad Sci U S A 2022; 119:e2208004119. [PMID: 35939705 PMCID: PMC9388089 DOI: 10.1073/pnas.2208004119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cohesin is a heteropentameric protein complex consisting of two structural maintenance of chromosomes (SMC) subunits and three non-SMC subunits. The two SMC subunits form a heterodimer with an ATPase head and hinge that are connected by long coiled coils. Isolation of ATPase mutants followed by comprehensive identification of suppressor mutations in SMC subunits that can bypass ATPase defects was performed. Locations and properties of mutant alleles reflect how ATPase activities could be compromised by structural adaptation. ATP-driven conformational changes may enhance DNA anchoring by the head, alter interactions of coiled coils at the head with other subunits for DNA to go through, and fold/extend coiled coils near break sites around midpoint to bring together DNA elements far from each other. The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs.
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12
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Zuilkoski CM, Skibbens RV. Integrating Sister Chromatid Cohesion Establishment to DNA Replication. Genes (Basel) 2022; 13:genes13040625. [PMID: 35456431 PMCID: PMC9032331 DOI: 10.3390/genes13040625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
The intersection through which two fundamental processes meet provides a unique vantage point from which to view cellular regulation. On the one hand, DNA replication is at the heart of cell division, generating duplicate chromosomes that allow each daughter cell to inherit a complete copy of the parental genome. Among other factors, the PCNA (proliferating cell nuclear antigen) sliding clamp ensures processive DNA replication during S phase and is essential for cell viability. On the other hand, the process of chromosome segregation during M phase—an act that occurs long after DNA replication—is equally fundamental to a successful cell division. Eco1/Ctf7 ensures that chromosomes faithfully segregate during mitosis, but functions during DNA replication to activate cohesins and thereby establish cohesion between sister chromatids. To achieve this, Eco1 binds PCNA and numerous other DNA replication fork factors that include MCM helicase, Chl1 helicase, and the Rtt101-Mms1-Mms22 E3 ubiquitin ligase. Here, we review the multi-faceted coordination between cohesion establishment and DNA replication. SUMMARY STATEMENT: New findings provide important insights into the mechanisms through which DNA replication and the establishment of sister chromatid cohesion are coupled.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47401, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Correspondence: ; Tel.: +610-758-6162
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13
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Bürmann F, Funke LFH, Chin JW, Löwe J. Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites. Mol Cell 2021; 81:4891-4906.e8. [PMID: 34739874 PMCID: PMC8669397 DOI: 10.1016/j.molcel.2021.10.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
| | - Louise F H Funke
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jason W Chin
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
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14
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Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
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Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
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15
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Mfarej MG, Skibbens RV. An ever-changing landscape in Roberts syndrome biology: Implications for macromolecular damage. PLoS Genet 2020; 16:e1009219. [PMID: 33382686 PMCID: PMC7774850 DOI: 10.1371/journal.pgen.1009219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Roberts syndrome (RBS) is a rare developmental disorder that can include craniofacial abnormalities, limb malformations, missing digits, intellectual disabilities, stillbirth, and early mortality. The genetic basis for RBS is linked to autosomal recessive loss-of-function mutation of the establishment of cohesion (ESCO) 2 acetyltransferase. ESCO2 is an essential gene that targets the DNA-binding cohesin complex. ESCO2 acetylates alternate subunits of cohesin to orchestrate vital cellular processes that include sister chromatid cohesion, chromosome condensation, transcription, and DNA repair. Although significant advances were made over the last 20 years in our understanding of ESCO2 and cohesin biology, the molecular etiology of RBS remains ambiguous. In this review, we highlight current models of RBS and reflect on data that suggests a novel role for macromolecular damage in the molecular etiology of RBS.
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Affiliation(s)
- Michael G. Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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16
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A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions. Genes (Basel) 2020; 11:genes11090985. [PMID: 32847102 PMCID: PMC7563616 DOI: 10.3390/genes11090985] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
The role of three-dimensional genome organization as a critical regulator of gene expression has become increasingly clear over the last decade. Most of our understanding of this association comes from the study of long range chromatin interaction maps provided by Chromatin Conformation Capture-based techniques, which have greatly improved in recent years. Since these procedures are experimentally laborious and expensive, in silico prediction has emerged as an alternative strategy to generate virtual maps in cell types and conditions for which experimental data of chromatin interactions is not available. Several methods have been based on predictive models trained on one-dimensional (1D) sequencing features, yielding promising results. However, different approaches vary both in the way they model chromatin interactions and in the machine learning-based strategy they rely on, making it challenging to carry out performance comparison of existing methods. In this study, we use publicly available 1D sequencing signals to model cohesin-mediated chromatin interactions in two human cell lines and evaluate the prediction performance of six popular machine learning algorithms: decision trees, random forests, gradient boosting, support vector machines, multi-layer perceptron and deep learning. Our approach accurately predicts long-range interactions and reveals that gradient boosting significantly outperforms the other five methods, yielding accuracies of about 95%. We show that chromatin features in close genomic proximity to the anchors cover most of the predictive information, as has been previously reported. Moreover, we demonstrate that gradient boosting models trained with different subsets of chromatin features, unlike the other methods tested, are able to produce accurate predictions. In this regard, and besides architectural proteins, transcription factors are shown to be highly informative. Our study provides a framework for the systematic prediction of long-range chromatin interactions, identifies gradient boosting as the best suited algorithm for this task and highlights cell-type specific binding of transcription factors at the anchors as important determinants of chromatin wiring mediated by cohesin.
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17
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Wang Z, Wang W, Wang L. Epigenetic regulation of covalently closed circular DNA minichromosome in hepatitis B virus infection. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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18
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Shi D, Zhao S, Zuo MQ, Zhang J, Hou W, Dong MQ, Cao Q, Lou H. The acetyltransferase Eco1 elicits cohesin dimerization during S phase. J Biol Chem 2020; 295:7554-7565. [PMID: 32312753 PMCID: PMC7261783 DOI: 10.1074/jbc.ra120.013102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin is a DNA-associated protein complex that forms a tripartite ring controlling sister chromatid cohesion, chromosome segregation and organization, DNA replication, and gene expression. Sister chromatid cohesion is established by the protein acetyltransferase Eco1, which acetylates two conserved lysine residues on the cohesin subunit Smc3 and thereby ensures correct chromatid separation in yeast (Saccharomyces cerevisiae) and other eukaryotes. However, the consequence of Eco1-catalyzed cohesin acetylation is unknown, and the exact nature of the cohesive state of chromatids remains controversial. Here, we show that self-interactions of the cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication-coupled manner in both yeast and human cells. Using cross-linking MS-based and in vivo disulfide cross-linking analyses of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, upon temperature-sensitive and auxin-induced degron-mediated Eco1 depletion, the cohesin-cohesin interactions became significantly compromised, whereas deleting either the deacetylase Hos1 or the Eco1 antagonist Wpl1/Rad61 increased cohesin dimer levels by ∼20%. These results indicate that cohesin dimerizes in the S phase and monomerizes in mitosis, processes that are controlled by Eco1, Wpl1, and Hos1 in the sister chromatid cohesion-dissolution cycle. These findings suggest that cohesin dimerization is controlled by the cohesion cycle and support the notion that a double-ring cohesin model operates in sister chromatid cohesion.
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Affiliation(s)
- Di Shi
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Shuaijun Zhao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Wenya Hou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
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19
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Birot A, Tormos-Pérez M, Vaur S, Feytout A, Jaegy J, Alonso Gil D, Vazquez S, Ekwall K, Javerzat JP. The CDK Pef1 and protein phosphatase 4 oppose each other for regulating cohesin binding to fission yeast chromosomes. eLife 2020; 9:e50556. [PMID: 31895039 PMCID: PMC6954021 DOI: 10.7554/elife.50556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Cohesin has essential roles in chromosome structure, segregation and repair. Cohesin binding to chromosomes is catalyzed by the cohesin loader, Mis4 in fission yeast. How cells fine tune cohesin deposition is largely unknown. Here, we provide evidence that Mis4 activity is regulated by phosphorylation of its cohesin substrate. A genetic screen for negative regulators of Mis4 yielded a CDK called Pef1, whose closest human homologue is CDK5. Inhibition of Pef1 kinase activity rescued cohesin loader deficiencies. In an otherwise wild-type background, Pef1 ablation stimulated cohesin binding to its regular sites along chromosomes while ablating Protein Phosphatase 4 had the opposite effect. Pef1 and PP4 control the phosphorylation state of the cohesin kleisin Rad21. The CDK phosphorylates Rad21 on Threonine 262. Pef1 ablation, non-phosphorylatable Rad21-T262 or mutations within a Rad21 binding domain of Mis4 alleviated the effect of PP4 deficiency. Such a CDK/PP4-based regulation of cohesin loader activity could provide an efficient mechanism for translating cellular cues into a fast and accurate cohesin response.
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Affiliation(s)
- Adrien Birot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Marta Tormos-Pérez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Sabine Vaur
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Amélie Feytout
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Julien Jaegy
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Dácil Alonso Gil
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Stéphanie Vazquez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Karl Ekwall
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Jean-Paul Javerzat
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
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20
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Abstract
Protein complexes built of structural maintenance of chromosomes (SMC) and kleisin subunits, including cohesin, condensin and the Smc5/6 complex, are master organizers of genome architecture in all kingdoms of life. How these large ring-shaped molecular machines use the energy of ATP hydrolysis to change the topology of chromatin fibers has remained a central unresolved question of chromosome biology. A currently emerging concept suggests that the common principle that underlies the essential functions of SMC protein complexes in the control of gene expression, chromosome segregation or DNA damage repair is their ability to expand DNA into large loop structures. Here, we review the current knowledge about the biochemical and structural properties of SMC protein complexes that might enable them to extrude DNA loops and compare their action to other motor proteins and nucleic acid translocases. We evaluate the currently predominant models of active loop extrusion and propose a detailed version of a 'scrunching' model, which reconciles much of the available mechanistic data and provides an elegant explanation for how SMC protein complexes fulfill an array of seemingly diverse tasks during the organization of genomes.
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21
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Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Extrusion without a motor: a new take on the loop extrusion model of genome organization. Nucleus 2019; 9:95-103. [PMID: 29300120 PMCID: PMC5973195 DOI: 10.1080/19491034.2017.1421825] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo “Non-equilibrium chromosome looping via molecular slip-links”, Physical Review Letters 119 138101 (2017)
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Affiliation(s)
- C A Brackley
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - J Johnson
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - D Michieletto
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - A N Morozov
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - M Nicodemi
- b Dipartimento di Fisica , Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo , Naples , Italy
| | - P R Cook
- c Sir William Dunn School of Pathology , University of Oxford , South Parks Road, Oxford , OX1 3RE , UK
| | - D Marenduzzo
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
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22
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Manalastas-Cantos K, Kschonsak M, Haering CH, Svergun DI. Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1. J Biol Chem 2019; 294:13822-13829. [PMID: 31350339 DOI: 10.1074/jbc.ra119.008661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/24/2019] [Indexed: 02/03/2023] Open
Abstract
High-resolution structural analysis of flexible proteins is frequently challenging and requires the synergistic application of different experimental techniques. For these proteins, small-angle X-ray scattering (SAXS) allows for a quantitative assessment and modeling of potentially flexible and heterogeneous structural states. Here, we report SAXS characterization of the condensin HEAT-repeat subunit Ycg1Cnd3 in solution, complementing currently available high-resolution crystallographic models. We show that the free Ycg1 subunit is flexible in solution but becomes considerably more rigid when bound to its kleisin-binding partner protein Brn1Cnd2 The analysis of SAXS and dynamic and static multiangle light scattering data furthermore reveals that Ycg1 tends to oligomerize with increasing concentrations in the absence of Brn1. Based on these data, we present a model of the free Ycg1 protein constructed by normal mode analysis, as well as tentative models of Ycg1 dimers and tetramers. These models enable visualization of the conformational transitions that Ycg1 has to undergo to adopt a closed rigid shape and thereby create a DNA-binding surface in the condensin complex.
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Affiliation(s)
| | - Marc Kschonsak
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
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23
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Nishiyama T. Compartments in the Ring. Mol Cell 2019; 75:201-203. [PMID: 31348876 DOI: 10.1016/j.molcel.2019.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sister chromatid cohesion has been thought to be mediated by DNA entrapment within the large cohesin ring. Vazquez Nunez et al. and Chapard et al. now show that the ring is divided up into two sub-compartments, with implications for how these chromosomal organizers entrap DNA.
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Affiliation(s)
- Tomoko Nishiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
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24
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Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM. Absolute quantification of cohesin, CTCF and their regulators in human cells. eLife 2019; 8:e46269. [PMID: 31204999 PMCID: PMC6606026 DOI: 10.7554/elife.46269] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022] Open
Abstract
The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are ~250,000 nuclear cohesin complexes, of which ~ 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.
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Affiliation(s)
- Johann Holzmann
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Antonio Z Politi
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | | | - Nike Walther
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Birgit Koch
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Johannes Fuchs
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Georg A Busslinger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Béla Novák
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Medical University of ViennaViennaAustria
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25
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Mirkovic M, Oliveira RA. Centromeric Cohesin: Molecular Glue and Much More. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:485-513. [PMID: 28840250 DOI: 10.1007/978-3-319-58592-5_20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sister chromatid cohesion, mediated by the cohesin complex, is a prerequisite for faithful chromosome segregation during mitosis. Premature release of sister chromatid cohesion leads to random segregation of the genetic material and consequent aneuploidy. Multiple regulatory mechanisms ensure proper timing for cohesion establishment, concomitant with DNA replication, and cohesion release during the subsequent mitosis. Here we summarize the most important phases of the cohesin cycle and the coordination of cohesion release with the progression through mitosis. We further discuss recent evidence that has revealed additional functions for centromeric localization of cohesin in the fidelity of mitosis in metazoans. Beyond its well-established role as "molecular glue", centromeric cohesin complexes are now emerging as a scaffold for multiple fundamental processes during mitosis, including the formation of correct chromosome and kinetochore architecture, force balance with the mitotic spindle, and the association with key molecules that regulate mitotic fidelity, particularly at the chromosomal inner centromere. Centromeric chromatin may be thus seen as a dynamic place where cohesin ensures mitotic fidelity by multiple means.
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Affiliation(s)
- Mihailo Mirkovic
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal.
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26
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Howard-Till R, Tian M, Loidl J. A specialized condensin complex participates in somatic nuclear maturation in Tetrahymena thermophila. Mol Biol Cell 2019; 30:1326-1338. [PMID: 30893010 PMCID: PMC6724606 DOI: 10.1091/mbc.e18-08-0487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Condensins are highly conserved proteins that are important for chromosome maintenance in nearly all forms of life. Although many organisms employ two forms of the condensin complex, the condensin genes in Tetrahymena have expanded even further. Here we report a form of condensin that is specifically active during sexual reproduction. This complex, condensin D, is composed of the core condensin proteins, Smc2 and Smc4, and two unique subunits, the kleisin Cph5 and Cpd2. Cpd2 is also found in somatic nuclei in vegetative cells, but is dispensable for growth and nuclear division. Immunoprecipitation experiments show that condensin D interacts with a putative member of a chromatin-remodeling complex during development. Condensin D is required for sexual reproduction and for endoreplication and genome reduction of the progeny’s somatic nuclei. Altogether, Tetrahymena possesses at least four forms of condensin to fulfill the needs of maintaining chromosomes in two different nuclei containing the somatic and germline genomes.
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Affiliation(s)
- Rachel Howard-Till
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Miao Tian
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
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27
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Hara K, Kinoshita K, Migita T, Murakami K, Shimizu K, Takeuchi K, Hirano T, Hashimoto H. Structural basis of HEAT-kleisin interactions in the human condensin I subcomplex. EMBO Rep 2019; 20:embr.201847183. [PMID: 30858338 PMCID: PMC6501013 DOI: 10.15252/embr.201847183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 12/30/2022] Open
Abstract
Condensin I is a multi‐protein complex that plays an essential role in mitotic chromosome assembly and segregation in eukaryotes. It is composed of five subunits: two SMC (SMC2 and SMC4), a kleisin (CAP‐H), and two HEAT‐repeat (CAP‐D2 and CAP‐G) subunits. Although balancing acts of the two HEAT‐repeat subunits have been demonstrated to enable this complex to support the dynamic assembly of chromosomal axes in vertebrate cells, its underlying mechanisms remain poorly understood. Here, we report the crystal structure of a human condensin I subcomplex comprising hCAP‐G and hCAP‐H. hCAP‐H binds to the concave surfaces of a harp‐shaped HEAT‐repeat domain of hCAP‐G. Physical interaction between hCAP‐G and hCAP‐H is indeed essential for mitotic chromosome assembly recapitulated in Xenopus egg cell‐free extracts. Furthermore, this study reveals that the human CAP‐G‐H subcomplex has the ability to interact with not only double‐stranded DNA, but also single‐stranded DNA, suggesting functional divergence of the vertebrate condensin I complex in proper mitotic chromosome assembly.
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Affiliation(s)
- Kodai Hara
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | | | - Tomoko Migita
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kei Murakami
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kenichiro Shimizu
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kozo Takeuchi
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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28
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Abstract
Condensins and cohesins are highly conserved complexes that tether together DNA loci within a single DNA molecule to produce DNA loops. Condensin and cohesin structures, however, are different, and the DNA loops produced by each underlie distinct cell processes. Condensin rods compact chromosomes during mitosis, with condensin I and II complexes producing spatially defined and nested looping in metazoan cells. Structurally adaptive cohesin rings produce loops, which organize the genome during interphase. Cohesin-mediated loops, termed topologically associating domains or TADs, antagonize the formation of epigenetically defined but untethered DNA volumes, termed compartments. While condensin complexes formed through cis-interactions must maintain chromatin compaction throughout mitosis, cohesins remain highly dynamic during interphase to allow for transcription-mediated responses to external cues and the execution of developmental programs. Here, I review differences in condensin and cohesin structures, and highlight recent advances regarding the intramolecular or cis-based tetherings through which condensins compact DNA during mitosis and cohesins organize the genome during interphase.
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Affiliation(s)
- Robert V Skibbens
- Department of Biological Sciences, 111 Research Drive, Lehigh University, Bethlehem, PA 18015, USA
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29
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Mirkovic M, Guilgur LG, Tavares A, Passagem-Santos D, Oliveira RA. Induced aneuploidy in neural stem cells triggers a delayed stress response and impairs adult life span in flies. PLoS Biol 2019; 17:e3000016. [PMID: 30794535 PMCID: PMC6402706 DOI: 10.1371/journal.pbio.3000016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/06/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023] Open
Abstract
Studying aneuploidy during organism development has strong limitations because chronic mitotic perturbations used to generate aneuploidy usually result in lethality. We developed a genetic tool to induce aneuploidy in an acute and time-controlled manner during Drosophila development. This is achieved by reversible depletion of cohesin, a key molecule controlling mitotic fidelity. Larvae challenged with aneuploidy hatch into adults with severe motor defects shortening their life span. Neural stem cells, despite being aneuploid, display a delayed stress response and continue proliferating, resulting in the rapid appearance of chromosomal instability, a complex array of karyotypes, and cellular abnormalities. Notably, when other brain-cell lineages are forced to self-renew, aneuploidy-associated stress response is significantly delayed. Protecting only the developing brain from induced aneuploidy is sufficient to rescue motor defects and adult life span, suggesting that neural tissue is the most ill-equipped to deal with developmental aneuploidy.
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Stormo BM, Fox DT. Interphase cohesin regulation ensures mitotic fidelity after genome reduplication. Mol Biol Cell 2019; 30:219-227. [PMID: 30462577 PMCID: PMC6589556 DOI: 10.1091/mbc.e17-10-0582] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/17/2018] [Accepted: 11/15/2018] [Indexed: 12/24/2022] Open
Abstract
To ensure faithful genome propagation, mitotic cells alternate one round of chromosome duplication with one round of chromosome separation. Chromosome separation failure thus causes genome reduplication, which alters mitotic chromosome structure. Such structural alterations are well documented to impair mitotic fidelity following aberrant genome reduplication, including in diseased states. In contrast, we recently showed that naturally occurring genome reduplication does not alter mitotic chromosome structure in Drosophila papillar cells. Our discovery raised the question of how a cell undergoing genome reduplication might regulate chromosome structure to prevent mitotic errors. Here, we show that papillar cells ensure mitotic fidelity through interphase cohesin regulation. We demonstrate a requirement for cohesins during programmed rounds of papillar genome reduplication known as endocycles. This interphase cohesin regulation relies on cohesin release but not cohesin cleavage and depends on the conserved cohesin regulator Pds5 . Our data suggest that a distinct form of interphase cohesin regulation ensures mitotic fidelity after genome reduplication.
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Affiliation(s)
- Benjamin M. Stormo
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Donald T. Fox
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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31
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Palecek JJ. SMC5/6: Multifunctional Player in Replication. Genes (Basel) 2018; 10:genes10010007. [PMID: 30583551 PMCID: PMC6356406 DOI: 10.3390/genes10010007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
The genome replication process is challenged at many levels. Replication must proceed through different problematic sites and obstacles, some of which can pause or even reverse the replication fork (RF). In addition, replication of DNA within chromosomes must deal with their topological constraints and spatial organization. One of the most important factors organizing DNA into higher-order structures are Structural Maintenance of Chromosome (SMC) complexes. In prokaryotes, SMC complexes ensure proper chromosomal partitioning during replication. In eukaryotes, cohesin and SMC5/6 complexes assist in replication. Interestingly, the SMC5/6 complexes seem to be involved in replication in many ways. They stabilize stalled RFs, restrain RF regression, participate in the restart of collapsed RFs, and buffer topological constraints during RF progression. In this (mini) review, I present an overview of these replication-related functions of SMC5/6.
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Affiliation(s)
- Jan J Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
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32
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Tran NT, Laub MT, Le TBK. SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription. Cell Rep 2018; 20:2057-2071. [PMID: 28854358 PMCID: PMC5583512 DOI: 10.1016/j.celrep.2017.08.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/07/2017] [Accepted: 08/03/2017] [Indexed: 11/16/2022] Open
Abstract
The structural maintenance of chromosomes (SMC) complex plays an important role in chromosome organization and segregation in most living organisms. In Caulobacter crescentus, SMC is required to align the left and the right arms of the chromosome that run in parallel down the long axis of the cell. However, the mechanism of SMC-mediated alignment of chromosomal arms remains elusive. Here, using genome-wide methods and microscopy of single cells, we show that Caulobacter SMC is recruited to the centromeric parS site and that SMC-mediated arm alignment depends on the chromosome-partitioning protein ParB. We provide evidence that SMC likely tethers the parS-proximal regions of the chromosomal arms together, promoting arm alignment. Furthermore, we show that highly transcribed genes near parS that are oriented against SMC translocation disrupt arm alignment, suggesting that head-on transcription interferes with SMC translocation. Our results demonstrate a tight interdependence of bacterial chromosome organization and global patterns of transcription. Caulobacter SMC aligns the two chromosomal arms progressively from ori to ter SMC is loaded at parS, and ParB is essential for SMC-mediated arm alignment SMC likely functions as a tether to cohese parS-proximal DNA together Head-on transcription interferes with SMC translocation from parS
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Affiliation(s)
- Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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33
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Countryman P, Fan Y, Gorthi A, Pan H, Strickland E, Kaur P, Wang X, Lin J, Lei X, White C, You C, Wirth N, Tessmer I, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem 2018; 293:1054-1069. [PMID: 29175904 PMCID: PMC5777247 DOI: 10.1074/jbc.m117.806406] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA. We observed that SA2 can switch between the 1D diffusing (search) mode on dsDNA and stable binding (recognition) mode at ssDNA gaps. Although SA2 does not specifically bind to centromeric or telomeric sequences, it does recognize DNA structures often associated with DNA replication and double-strand break repair, such as a double-stranded end, single-stranded overhang, flap, fork, and ssDNA gap. SA2 loss leads to a defect in homologous recombination-mediated DNA double-strand break repair. These results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways. These findings have important implications for understanding the function of cohesin in these pathways.
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Affiliation(s)
| | - Yanlin Fan
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Aparna Gorthi
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | | | | | | | | | - Jiangguo Lin
- From the Physics Department
- the Institute of Biomechanics, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaoying Lei
- the Department of BioSciences, Rice University, Houston, Texas 77251
- the School of Public Health, Shandong University, Jinan 250012, China
| | | | - Changjiang You
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | - Nicolas Wirth
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jacob Piehler
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | | | - Alexander J R Bishop
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | - Yizhi Jane Tao
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Hong Wang
- From the Physics Department,
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
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34
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Hansen AS, Cattoglio C, Darzacq X, Tjian R. Recent evidence that TADs and chromatin loops are dynamic structures. Nucleus 2018; 9:20-32. [PMID: 29077530 PMCID: PMC5990973 DOI: 10.1080/19491034.2017.1389365] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 11/15/2022] Open
Abstract
Mammalian genomes are folded into spatial domains, which regulate gene expression by modulating enhancer-promoter contacts. Here, we review recent studies on the structure and function of Topologically Associating Domains (TADs) and chromatin loops. We discuss how loop extrusion models can explain TAD formation and evidence that TADs are formed by the ring-shaped protein complex, cohesin, and that TAD boundaries are established by the DNA-binding protein, CTCF. We discuss our recent genomic, biochemical and single-molecule imaging studies on CTCF and cohesin, which suggest that TADs and chromatin loops are dynamic structures. We highlight complementary polymer simulation studies and Hi-C studies employing acute depletion of CTCF and cohesin, which also support such a dynamic model. We discuss the limitations of each approach and conclude that in aggregate the available evidence argues against stable loops and supports a model where TADs are dynamic structures that continually form and break throughout the cell cycle.
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Affiliation(s)
- Anders S. Hansen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
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35
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Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V, Hassler M, Haering CH. Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes. Cell 2017; 171:588-600.e24. [PMID: 28988770 PMCID: PMC5651216 DOI: 10.1016/j.cell.2017.09.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022]
Abstract
Condensin protein complexes coordinate the formation of mitotic chromosomes and thereby ensure the successful segregation of replicated genomes. Insights into how condensin complexes bind to chromosomes and alter their topology are essential for understanding the molecular principles behind the large-scale chromatin rearrangements that take place during cell divisions. Here, we identify a direct DNA-binding site in the eukaryotic condensin complex, which is formed by its Ycg1Cnd3 HEAT-repeat and Brn1Cnd2 kleisin subunits. DNA co-crystal structures reveal a conserved, positively charged groove that accommodates the DNA double helix. A peptide loop of the kleisin subunit encircles the bound DNA and, like a safety belt, prevents its dissociation. Firm closure of the kleisin loop around DNA is essential for the association of condensin complexes with chromosomes and their DNA-stimulated ATPase activity. Our data suggest a sophisticated molecular basis for anchoring condensin complexes to chromosomes that enables the formation of large-sized chromatin loops.
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Affiliation(s)
- Marc Kschonsak
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fabian Merkel
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jutta Metz
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Rybin
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
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36
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Rohban S, Cerutti A, Morelli MJ, d'Adda di Fagagna F, Campaner S. The cohesin complex prevents Myc-induced replication stress. Cell Death Dis 2017; 8:e2956. [PMID: 28749464 PMCID: PMC5550886 DOI: 10.1038/cddis.2017.345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022]
Abstract
The cohesin complex is mutated in cancer and in a number of rare syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells rescued Myc-dependent transcription and promoted S-phase entry but failed to sustain S-phase progression due to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc-dependent transcription but essential to prevent Myc-induced replicative stress. This suggests the presence of a feed-forward regulatory loop where cohesins by regulating Myc level control S-phase entry and prevent replicative stress.
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Affiliation(s)
- Sara Rohban
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Aurora Cerutti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
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37
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Rizvi SMA, Prajapati HK, Ghosh SK. The 2 micron plasmid: a selfish genetic element with an optimized survival strategy within Saccharomyces cerevisiae. Curr Genet 2017; 64:25-42. [PMID: 28597305 DOI: 10.1007/s00294-017-0719-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 11/27/2022]
Abstract
Since its discovery in the early 70s, the 2 micron plasmid of Saccharomyces cerevisiae continues to intrigue researchers with its high protein-coding capacity and a selfish nature yet high stability, earning it the title of a 'miniaturized selfish genetic element'. It codes for four proteins (Rep1, Rep2, Raf1, and Flp) vital for its own survival and recruits several host factors (RSC2, Cohesin, Cse4, Kip1, Bik1, Bim1, and microtubules) for its faithful segregation during cell division. The plasmid maintains a high-copy number with the help of Flp-mediated recombination. The plasmids organize in the form of clusters that hitch-hike the host chromosomes presumably with the help of the plasmid-encoded Rep proteins and host factors such as microtubules, Kip1 motor, and microtubule-associated proteins Bik1 and Bim1. Although there is no known yeast cell phenotype associated with the 2 micron plasmid, excessive copies of the plasmid are lethal for the cells, warranting a tight control over the plasmid copy number. This control is achieved through a combination of feedback loops involving the 2 micron encoded proteins. Thus, faithful segregation and a concomitant tightly controlled plasmid copy number ensure an optimized benign parasitism of the 2 micron plasmid within budding yeast.
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Affiliation(s)
- Syed Meraj Azhar Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Hemant Kumar Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India.
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38
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Chavda AP, Ang K, Ivanov D. The torments of the cohesin ring. Nucleus 2017; 8:261-267. [PMID: 28453390 PMCID: PMC5499920 DOI: 10.1080/19491034.2017.1295200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 10/20/2022] Open
Abstract
Cohesin is a ring-shaped protein complex which comprises the Smc1, Smc3 and Scc1 subunits. It topologically embraces chromosomal DNA to connect sister chromatids and stabilize chromatin loops. It is required for proper chromosomal segregation, DNA repair and transcriptional regulation. We have recently reported that cohesin rings can adopt a "collapsed" rod-like conformation which is driven by the interaction between the Smc1 and Smc3 coiled coil arms and is regulated by post-translational modifications. The "collapsed" conformation plays a role in cohesin ring assembly and its loading on the DNA. Here we speculate about the mechanism of cohesin's conformational transitions in relation to its loading on the DNA and draw parallels with other Smc-like complexes.
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Affiliation(s)
| | - Keven Ang
- Bioinformatics Institute, A*STAR, Singapore
| | - Dmitri Ivanov
- Bioinformatics Institute, A*STAR, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany
- Department of Physics, National University of Singapore, Singapore
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39
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Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife 2017; 6:e25776. [PMID: 28467304 PMCID: PMC5446243 DOI: 10.7554/elife.25776] [Citation(s) in RCA: 368] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/30/2017] [Indexed: 12/13/2022] Open
Abstract
Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1-2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging 'dynamic complex' rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and frequently break and reform throughout the cell cycle.
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Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
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40
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Abstract
While chromatin characteristics in interphase are widely studied, characteristics of mitotic chromatin and their inheritance through mitosis are still poorly understood. During mitosis, chromatin undergoes dramatic changes: transcription stalls, chromatin-binding factors leave the chromatin, histone modifications change and chromatin becomes highly condensed. Many key insights into mitotic chromosome state and conformation have come from extensive microscopy studies over the last century. Over the last decade, the development of 3C-based techniques has enabled the study of higher order chromosome organization during mitosis in a genome-wide manner. During mitosis, chromosomes lose their cell type-specific and locus-dependent chromatin organization that characterizes interphase chromatin and fold into randomly positioned loop arrays. Upon exit of mitosis, cells are capable of quickly rearranging the chromosome conformation to form the cell type-specific interphase organization again. The information that enables this rearrangement after mitotic exit is thought to be encoded at least in part in mitotic bookmarks, e.g. histone modifications and variants, histone remodelers, chromatin factors, and non-coding RNA. Here we give an overview of the chromosomal organization and epigenetic characteristics of interphase and mitotic chromatin in vertebrates. Second, we describe different ways in which mitotic bookmarking enables epigenetic memory of the features of interphase chromatin through mitosis. And third, we explore the role of epigenetic modifications and mitotic bookmarking in cell differentiation.
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Affiliation(s)
- Marlies E. Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
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41
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Tuned SMC Arms Drive Chromosomal Loading of Prokaryotic Condensin. Mol Cell 2017; 65:861-872.e9. [PMID: 28238653 PMCID: PMC5344682 DOI: 10.1016/j.molcel.2017.01.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/23/2016] [Accepted: 01/18/2017] [Indexed: 11/24/2022]
Abstract
SMC proteins support vital cellular processes in all domains of life by organizing chromosomal DNA. They are composed of ATPase “head” and “hinge“ dimerization domains and a connecting coiled-coil “arm.” Binding to a kleisin subunit creates a closed tripartite ring, whose ∼47-nm-long SMC arms act as barrier for DNA entrapment. Here, we uncover another, more active function of the bacterial Smc arm. Using high-throughput genetic engineering, we resized the arm in the range of 6–60 nm and found that it was functional only in specific length regimes following a periodic pattern. Natural SMC sequences reflect these length constraints. Mutants with improper arm length or peptide insertions in the arm efficiently target chromosomal loading sites and hydrolyze ATP but fail to use ATP hydrolysis for relocation onto flanking DNA. We propose that SMC arms implement force transmission upon nucleotide hydrolysis to mediate DNA capture or loop extrusion. Short and long but not intermediate-length Smc coiled-coil arms are functional Smc complexes with improper arms accumulate at chromosomal loading sites Smc arms are functional units linking ATP hydrolysis to an essential DNA transaction Pro- and eukaryotic SMC sequences reflect similar periodic length constraints
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Abstract
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor.This chapter summarizes our current knowledge on kollerin function and the recent studies on the genomic localization of Scc2, highlighting and critically discussing controversial data.
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Affiliation(s)
- Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Faculty Building, Room Ee1020, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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43
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Davidson IF, Goetz D, Zaczek MP, Molodtsov MI, Huis In 't Veld PJ, Weissmann F, Litos G, Cisneros DA, Ocampo-Hafalla M, Ladurner R, Uhlmann F, Vaziri A, Peters JM. Rapid movement and transcriptional re-localization of human cohesin on DNA. EMBO J 2016; 35:2671-2685. [PMID: 27799150 PMCID: PMC5167347 DOI: 10.15252/embj.201695402] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/08/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA-bound proteins and nucleosomes but is constrained in its movement by transcription and DNA-bound CCCTC-binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Daniela Goetz
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Maciej P Zaczek
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Maxim I Molodtsov
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | | | | | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - David A Cisneros
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Alipasha Vaziri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- The Rockefeller University, New York, NY, USA
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44
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Bhardwaj S, Schlackow M, Rabajdova M, Gullerova M. Transcription facilitates sister chromatid cohesion on chromosomal arms. Nucleic Acids Res 2016; 44:6676-92. [PMID: 27084937 PMCID: PMC5001582 DOI: 10.1093/nar/gkw252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cohesin is a multi-subunit protein complex essential for sister chromatid cohesion, gene expression and DNA damage repair. Although structurally well studied, the underlying determinant of cohesion establishment on chromosomal arms remains enigmatic. Here, we show two populations of functionally distinct cohesin on chromosomal arms using a combination of genomics and single-locus specific DNA-FISH analysis. Chromatin bound cohesin at the loading sites co-localizes with Pds5 and Eso1 resulting in stable cohesion. In contrast, cohesin independent of its loader is unable to maintain cohesion and associates with chromatin in a dynamic manner. Cohesive sites coincide with highly expressed genes and transcription inhibition leads to destabilization of cohesin on chromatin. Furthermore, induction of transcription results in de novo recruitment of cohesive cohesin. Our data suggest that transcription facilitates cohesin loading onto chromosomal arms and is a key determinant of cohesive sites in fission yeast.
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Affiliation(s)
- Shweta Bhardwaj
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | | | | | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
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45
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Stigler J, Çamdere GÖ, Koshland DE, Greene EC. Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin. Cell Rep 2016; 15:988-998. [PMID: 27117417 PMCID: PMC4856582 DOI: 10.1016/j.celrep.2016.04.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/05/2016] [Accepted: 03/28/2016] [Indexed: 11/30/2022] Open
Abstract
Cohesin is essential for the hierarchical organization of the eukaryotic genome and plays key roles in many aspects of chromosome biology. The conformation of cohesin bound to DNA remains poorly defined, leaving crucial gaps in our understanding of how cohesin fulfills its biological functions. Here, we use single-molecule microscopy to directly observe the dynamic and functional characteristics of cohesin bound to DNA. We show that cohesin can undergo rapid one-dimensional (1D) diffusion along DNA, but individual nucleosomes, nucleosome arrays, and other protein obstacles significantly restrict its mobility. Furthermore, we demonstrate that DNA motor proteins can readily push cohesin along DNA, but they cannot pass through the interior of the cohesin ring. Together, our results reveal that DNA-bound cohesin has a central pore that is substantially smaller than anticipated. These findings have direct implications for understanding how cohesin and other SMC proteins interact with and distribute along chromatin.
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Affiliation(s)
- Johannes Stigler
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gamze Ö Çamdere
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas E Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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46
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Zabrady K, Adamus M, Vondrova L, Liao C, Skoupilova H, Novakova M, Jurcisinova L, Alt A, Oliver AW, Lehmann AR, Palecek JJ. Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Res 2016; 44:1064-79. [PMID: 26446992 PMCID: PMC4756808 DOI: 10.1093/nar/gkv1021] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 11/13/2022] Open
Abstract
SMC5/6 is a highly conserved protein complex related to cohesin and condensin, which are the key components of higher-order chromatin structures. The SMC5/6 complex is essential for proliferation in yeast and is involved in replication fork stability and processing. However, the precise mechanism of action of SMC5/6 is not known. Here we present evidence that the NSE1/NSE3/NSE4 sub-complex of SMC5/6 binds to double-stranded DNA without any preference for DNA-replication/recombination intermediates. Mutations of key basic residues within the NSE1/NSE3/NSE4 DNA-binding surface reduce binding to DNA in vitro. Their introduction into the Schizosaccharomyces pombe genome results in cell death or hypersensitivity to DNA damaging agents. Chromatin immunoprecipitation analysis of the hypomorphic nse3 DNA-binding mutant shows a reduced association of fission yeast SMC5/6 with chromatin. Based on our results, we propose a model for loading of the SMC5/6 complex onto the chromatin.
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Affiliation(s)
- Katerina Zabrady
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marek Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lucie Vondrova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Chunyan Liao
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Hana Skoupilova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marketa Novakova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Lenka Jurcisinova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Aaron Alt
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Jan J Palecek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
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47
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Regulation of sister chromatid cohesion during the mitotic cell cycle. SCIENCE CHINA-LIFE SCIENCES 2015; 58:1089-98. [DOI: 10.1007/s11427-015-4956-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/16/2015] [Indexed: 01/02/2023]
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48
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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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49
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Sun X, Huang L, Markowitz TE, Blitzblau HG, Chen D, Klein F, Hochwagen A. Transcription dynamically patterns the meiotic chromosome-axis interface. eLife 2015; 4. [PMID: 26258962 PMCID: PMC4530585 DOI: 10.7554/elife.07424] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/17/2015] [Indexed: 11/15/2022] Open
Abstract
Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus chromosome compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation nearby. A separate modulating mechanism that requires the conserved axial-element component Hop1 biases axis protein binding towards small chromosomes. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the axial element to promote recombination while easily adapting to changes in chromosome activity. DOI:http://dx.doi.org/10.7554/eLife.07424.001 Chromosomes are long molecules of DNA that represent the genetic material of an organism. In most animal cells, chromosomes are found in pairs; with one inherited from the mother and the other from the father. Sex cells—egg cells and sperm—contain half the normal number of chromosomes, so that when they fuse, the resulting single-celled embryo inherits the full set. When sex cells are being produced, a ring made from a protein called cohesin encircles each pair of chromosomes and holds them together until they are ready to be separated. The paired chromosomes also swap sections of DNA via a process called recombination. Structures, referred to as axial elements, compact the chromosomes in each pair and bring them in close contact so that recombination can take place. In the sexually reproducing baker's yeast, axial elements contain three main proteins: cohesin, Hop1, and Red1, but it remains unclear how the entire structure is anchored to the underlying chromosomes. Furthermore, the genes encoded within the DNA of the compacted chromosomes remain active, but it is also not clear how this is possible. This is because the compacted structure would be expected to prevent the molecular machinery that expresses genes from accessing the DNA. Sun, Huang et al. have now studied this process in budding yeast cells by using a method called ChIP-seq to determine where cohesin and the Hop1 and Red1 proteins are found along the chromosomes. The experiments showed that cohesin, Hop1, and Red1 are enriched in regions between two genes that run in the opposite directions to each other. Sun, Huang et al. also observed that cohesin recruits Red1, which in turn, recruits Hop1, and that all three proteins physically interact with one another. These findings imply that it is cohesin that anchors the axial elements to the underlying chromosomes. Further experiments showed that cohesin slides along chromosomes towards areas where genes are active. This suggests that cohesin provides a robust, but flexible, link between the axial elements and the chromosomes. This flexibility would enable recombination and gene expression to continue in compacted chromosomes. A loss of flexibility may be one of the reasons why mutations in cohesin components of the axial element cause infertility in men and condition called premature ovarian failure in women. DOI:http://dx.doi.org/10.7554/eLife.07424.002
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Affiliation(s)
- Xiaoji Sun
- Department of Biology, New York University, New York, United States
| | - Lingzhi Huang
- Max F. Perutz Laboratories, University of Vienna, Wien, Austria
| | | | | | - Doris Chen
- Max F. Perutz Laboratories, University of Vienna, Wien, Austria
| | - Franz Klein
- Max F. Perutz Laboratories, University of Vienna, Wien, Austria
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50
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Roy MA, Dhanaraman T, D'Amours D. The Smc5-Smc6 heterodimer associates with DNA through several independent binding domains. Sci Rep 2015; 5:9797. [PMID: 25984708 PMCID: PMC4434891 DOI: 10.1038/srep09797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/20/2015] [Indexed: 12/12/2022] Open
Abstract
The Smc5-6 complex is required for the maintenance of genome integrity through its
functions in DNA repair and chromosome biogenesis. However, the specific mode of
action of Smc5 and Smc6 in these processes remains largely unknown. We previously
showed that individual components of the Smc5-Smc6 complex bind strongly to DNA as
monomers, despite the absence of a canonical DNA-binding domain (DBD) in these
proteins. How heterodimerization of Smc5-6 affects its binding to DNA, and which
parts of the SMC molecules confer DNA-binding activity is not known at present. To
address this knowledge gap, we characterized the functional domains of the Smc5-6
heterodimer and identify two DBDs in each SMC molecule. The first DBD is located
within the SMC hinge region and its adjacent coiled-coil arms, while the second is
found in the conserved ATPase head domain. These DBDs can independently recapitulate
the substrate preference of the full-length Smc5 and Smc6 proteins. We also show
that heterodimerization of full-length proteins specifically increases the affinity
of the resulting complex for double-stranded DNA substrates. Collectively, our
findings provide critical insights into the structural requirements for effective
binding of the Smc5-6 complex to DNA repair substrates in vitro and in live
cells.
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Affiliation(s)
- Marc-André Roy
- Institute for Research in Immunology and Cancer, and Département de Pathologie et biologie cellulaire, Université de Montréal P.O. Box 6128, Succursale Centre-Ville Montréal, QC, H3C 3J7, Canada
| | - Thillaivillalan Dhanaraman
- Institute for Research in Immunology and Cancer, and Département de Pathologie et biologie cellulaire, Université de Montréal P.O. Box 6128, Succursale Centre-Ville Montréal, QC, H3C 3J7, Canada
| | - Damien D'Amours
- Institute for Research in Immunology and Cancer, and Département de Pathologie et biologie cellulaire, Université de Montréal P.O. Box 6128, Succursale Centre-Ville Montréal, QC, H3C 3J7, Canada
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