1
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Palek M, Palkova N, Kleiblova P, Kleibl Z, Macurek L. RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin. Nucleic Acids Res 2024; 52:7687-7703. [PMID: 38884202 PMCID: PMC11260465 DOI: 10.1093/nar/gkae499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
RAD18 is an E3 ubiquitin ligase that prevents replication fork collapse by promoting DNA translesion synthesis and template switching. Besides this classical role, RAD18 has been implicated in homologous recombination; however, this function is incompletely understood. Here, we show that RAD18 is recruited to DNA lesions by monoubiquitination of histone H2A at K15 and counteracts accumulation of 53BP1. Super-resolution microscopy revealed that RAD18 localizes to the proximity of DNA double strand breaks and limits the distribution of 53BP1 to the peripheral chromatin nanodomains. Whereas auto-ubiquitination of RAD18 mediated by RAD6 inhibits its recruitment to DNA breaks, interaction with SLF1 promotes RAD18 accumulation at DNA breaks in the post-replicative chromatin by recognition of histone H4K20me0. Surprisingly, suppression of 53BP1 function by RAD18 is not involved in homologous recombination and rather leads to reduction of non-homologous end joining. Instead, we provide evidence that RAD18 promotes HR repair by recruiting the SMC5/6 complex to DNA breaks. Finally, we identified several new loss-of-function mutations in RAD18 in cancer patients suggesting that RAD18 could be involved in cancer development.
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Affiliation(s)
- Matous Palek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Natalie Palkova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
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2
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Lorite NP, Apostolova S, Guasch-Vallés M, Pryer A, Unzueta F, Freire R, Solé-Soler R, Pedraza N, Dolcet X, Garí E, Agell N, Taylor EM, Colomina N, Torres-Rosell J. Crucial role of the NSE1 RING domain in Smc5/6 stability and FANCM-independent fork progression. Cell Mol Life Sci 2024; 81:251. [PMID: 38847937 PMCID: PMC11335289 DOI: 10.1007/s00018-024-05275-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 08/22/2024]
Abstract
The Smc5/6 complex is a highly conserved molecular machine involved in the maintenance of genome integrity. While its functions largely depend on restraining the fork remodeling activity of Mph1 in yeast, the presence of an analogous Smc5/6-FANCM regulation in humans remains unknown. We generated human cell lines harboring mutations in the NSE1 subunit of the Smc5/6 complex. Point mutations or truncations in the RING domain of NSE1 result in drastically reduced Smc5/6 protein levels, with differential contribution of the two zinc-coordinating centers in the RING. In addition, nse1-RING mutant cells display cell growth defects, reduced replication fork rates, and increased genomic instability. Notably, our findings uncover a synthetic sick interaction between Smc5/6 and FANCM and show that Smc5/6 controls fork progression and chromosome disjunction in a FANCM-independent manner. Overall, our study demonstrates that the NSE1 RING domain plays vital roles in Smc5/6 complex stability and fork progression through pathways that are not evolutionary conserved.
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Affiliation(s)
- Neus P Lorite
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Sonia Apostolova
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Marta Guasch-Vallés
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Aaron Pryer
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Fernando Unzueta
- Departament Biomedicina, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Universidad de La Laguna, Campus Ciencias de la Salud, Santa Cruz de Tenerife, Spain
- Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Roger Solé-Soler
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Neus Pedraza
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Xavier Dolcet
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Eloi Garí
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain
| | - Neus Agell
- Departament Biomedicina, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elaine M Taylor
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Neus Colomina
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain.
| | - Jordi Torres-Rosell
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, 25198, Spain.
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3
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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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4
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Jeppsson K, Pradhan B, Sutani T, Sakata T, Umeda Igarashi M, Berta DG, Kanno T, Nakato R, Shirahige K, Kim E, Björkegren C. Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils. Mol Cell 2024; 84:867-882.e5. [PMID: 38295804 DOI: 10.1016/j.molcel.2024.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/16/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024]
Abstract
The structural maintenance of chromosomes (SMC) protein complexes-cohesin, condensin, and the Smc5/6 complex (Smc5/6)-are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6's recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 associates with transcription-induced positively supercoiled DNA at cohesin-dependent loop boundaries on budding yeast (Saccharomyces cerevisiae) chromosomes. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes and efficiently initiate loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Biswajit Pradhan
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Takashi Sutani
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Miki Umeda Igarashi
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
| | - Davide Giorgio Berta
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Takaharu Kanno
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Eugene Kim
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
| | - Camilla Björkegren
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden.
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5
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Pradhan B, Kanno T, Umeda Igarashi M, Loke MS, Baaske MD, Wong JSK, Jeppsson K, Björkegren C, Kim E. The Smc5/6 complex is a DNA loop-extruding motor. Nature 2023; 616:843-848. [PMID: 37076626 PMCID: PMC10132971 DOI: 10.1038/s41586-023-05963-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 03/16/2023] [Indexed: 04/21/2023]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes1. Whereas cohesin and condensin organize chromosomes by extrusion of DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown2. Using single-molecule imaging, we show that Smc5/6 forms DNA loops by extrusion. Upon ATP hydrolysis, Smc5/6 reels DNA symmetrically into loops at a force-dependent rate of one kilobase pair per second. Smc5/6 extrudes loops in the form of dimers, whereas monomeric Smc5/6 unidirectionally translocates along DNA. We also find that the subunits Nse5 and Nse6 (Nse5/6) act as negative regulators of loop extrusion. Nse5/6 inhibits loop-extrusion initiation by hindering Smc5/6 dimerization but has no influence on ongoing loop extrusion. Our findings reveal functions of Smc5/6 at the molecular level and establish DNA loop extrusion as a conserved mechanism among eukaryotic SMC complexes.
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Affiliation(s)
| | - Takaharu Kanno
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Miki Umeda Igarashi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Mun Siong Loke
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | | | - Kristian Jeppsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Camilla Björkegren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| | - Eugene Kim
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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6
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Xing L, Liu S, Zhang L, Yang H, Sun L. MITF Contributes to the Body Color Differentiation of Sea Cucumbers Apostichopus japonicus through Expression Differences and Regulation of Downstream Genes. BIOLOGY 2022; 12:biology12010001. [PMID: 36671694 PMCID: PMC9854957 DOI: 10.3390/biology12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Melanin, which is a pigment produced in melanocytes, is an important contributor to sea cucumber body color. MITF is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. In this study, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. The mRNA and protein expression levels of MITF were all highest in purple morphs and lowest in white morphs. In situ hybridization indicated that MITF mRNA were mainly expressed in the epidermis. We also identified 984, 732, and 1191 peaks of MITF binding in green, purple, and white sea cucumbers, which were associated with 727, 557, and 887 genes, respectively. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers through expression differences and regulation of downstream genes. These results provided a basis for future studies to determine the mechanisms underlying body color formation and provided insights into gene regulation in sea cucumbers.
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Affiliation(s)
- Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel./Fax: +86-532-8289-8610
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7
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Smc5/6 silences episomal transcription by a three-step function. Nat Struct Mol Biol 2022; 29:922-931. [PMID: 36097294 DOI: 10.1038/s41594-022-00829-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
In addition to its role in chromosome maintenance, the six-membered Smc5/6 complex functions as a restriction factor that binds to and transcriptionally silences viral and other episomal DNA. However, the underlying mechanism is unknown. Here, we show that transcriptional silencing by the human Smc5/6 complex is a three-step process. The first step is entrapment of the episomal DNA by a mechanism dependent on Smc5/6 ATPase activity and a function of its Nse4a subunit for which the Nse4b paralog cannot substitute. The second step results in Smc5/6 recruitment to promyelocytic leukemia nuclear bodies by SLF2 (the human ortholog of Nse6). The third step promotes silencing through a mechanism requiring Nse2 but not its SUMO ligase activity. By contrast, the related cohesin and condensin complexes fail to bind to or silence episomal DNA, indicating a property unique to Smc5/6.
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8
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Condensin-driven loop extrusion on supercoiled DNA. Nat Struct Mol Biol 2022; 29:719-727. [PMID: 35835864 DOI: 10.1038/s41594-022-00802-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping are stimulated by positively supercoiled DNA, and condensin preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.
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9
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Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C. Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks. SCIENCE ADVANCES 2022; 8:eabn7063. [PMID: 35687682 PMCID: PMC9187231 DOI: 10.1126/sciadv.abn7063] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 12/15/2021] [Accepted: 04/27/2022] [Indexed: 05/31/2023]
Abstract
Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes induced by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome-folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin's roles in genome function and stability.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Stefina Milanova
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Katsuhiko Shirahige
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Camilla Björkegren
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
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10
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Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022; 17:1486-1517. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Abstract
Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.
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11
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Breimann L, Morao AK, Kim J, Sebastian Jimenez D, Maryn N, Bikkasani K, Carrozza MJ, Albritton SE, Kramer M, Street LA, Cerimi K, Schumann VF, Bahry E, Preibisch S, Woehler A, Ercan S. The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding. J Cell Sci 2022; 135:jcs258818. [PMID: 34918745 PMCID: PMC8917352 DOI: 10.1242/jcs.258818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Condensin is a multi-subunit structural maintenance of chromosomes (SMC) complex that binds to and compacts chromosomes. Here, we addressed the regulation of condensin binding dynamics using Caenorhabditis elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes DPY-27 binding to X chromosomes. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C sequencing data from the dpy-21 null mutant showed little change compared to wild-type data, uncoupling Hi-C-measured long-range DNA contacts from transcriptional repression of the X chromosomes. Taken together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.
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Affiliation(s)
- Laura Breimann
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
- Institute for Biology, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - David Sebastian Jimenez
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Nina Maryn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Krishna Bikkasani
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael J. Carrozza
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sarah E. Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Kustrim Cerimi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Vic-Fabienne Schumann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew Woehler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
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12
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Lin Y, Liu Y, Xu D, Guo F, Zhang W, Zhang Y, Bai G. HBxAg promotes HBV replication and EGFR activation in human placental trophoblasts. Exp Ther Med 2021; 22:1211. [PMID: 34584556 PMCID: PMC8422389 DOI: 10.3892/etm.2021.10645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a global epidemic. The main transmission route of chronic HBV infection is from mother to child, yet the mechanisms underlying HBV intrauterine infection remain unclear. In the present study, the effect and the mechanism underlying hepatitis B virus X antigen (HBxAg) on HBV replication and EGFR activation in trophoblasts was investigated. Serum samples from pregnant women with HBV infection were used to infect trophoblasts and HBxAg expression was detected using ELISA. HBV plasmids carrying either full length hepatitis B virus X (HBx) or HBx with a deletion mutation (ΔHBx) were transfected into trophoblasts and expression levels of HBV DNA, hepatitis B e-antigen and pregenomic (pg)RNA, and structural maintenance of chromosomes (Smc) 5/6 were assessed. The association between HBx and EGFR promoters was characterized using a luciferase reporter assay and EGFR/PI3K/phosphorylated (p)-AKT expression and apoptosis rate were also monitored. The results of the present study indicated that HBxAg expression increased with the increasing titre of HBV DNA (P<0.05). Compared with the wild-type group, the amount of HBV DNA in the supernatant and cells was significantly reduced (P<0.05) in the ΔHBx group and the intracellular HBeAg and pgRNA levels were also significantly decreased (P<0.05). In addition, Smc5/6 expression was also significantly decreased (P<0.05) when the intracellular HBx protein was expressed compared with mock-transfected cells. Co-transfection of HBx and EGFR promoter plasmids in JEG-3 and HTR-8 cells significantly elevated EGFR promoter driven luciferase expression relative to the control group (P<0.01). In EGFR overexpressing cells, the expression of PI3K/p-AKT was significantly increased, whereas the apoptosis rate was significantly decreased (P<0.05). These results were reversed in the EGFR-knockdown group. In conclusion, the present study demonstrated that HBx promotes HBV replication in trophoblasts via downregulation of Smc5/6, activates the EGFR promoter and inhibits trophoblast apoptosis via the PI3K/p-AKT downstream signalling pathway, thereby increasing the risk of HBV intrauterine infection.
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Affiliation(s)
- Yayun Lin
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yan Liu
- Institute of Infectious Diseases, 5th Medical Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Dongping Xu
- Institute of Infectious Diseases, 5th Medical Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Fanfan Guo
- College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Wentao Zhang
- College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yidan Zhang
- College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Guiqin Bai
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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13
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Parts L, Batté A, Lopes M, Yuen MW, Laver M, San Luis B, Yue J, Pons C, Eray E, Aloy P, Liti G, van Leeuwen J. Natural variants suppress mutations in hundreds of essential genes. Mol Syst Biol 2021; 17:e10138. [PMID: 34042294 PMCID: PMC8156963 DOI: 10.15252/msb.202010138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
The consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, and lethal in another. The extent to which mutant phenotypes are malleable, the architecture of modifiers and the identities of causal genes remain largely unknown. Here, we measure the fitness effects of ~ 1,100 temperature-sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds and map the modifiers for 19 combinations. Altogether, fitness defects for 149 of the 580 tested genes (26%) could be suppressed by genetic variation in at least one yeast strain. Suppression was generally driven by gain-of-function of a single, strong modifier gene, and involved both genes encoding complex or pathway partners suppressing specific temperature-sensitive alleles, as well as general modifiers altering the effect of many alleles. The emerging frequency of suppression and range of possible mechanisms suggest that a substantial fraction of monogenic diseases could be managed by modulating other gene products.
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Affiliation(s)
- Leopold Parts
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- Wellcome Sanger InstituteWellcome Genome CampusHinxtonUK
- Department of Computer ScienceUniversity of TartuTartuEstonia
| | - Amandine Batté
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Maykel Lopes
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Michael W Yuen
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Meredith Laver
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Bryan‐Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Jia‐Xing Yue
- University of Côte d’AzurCNRSINSERMIRCANNiceFrance
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute for Science and TechnologyBarcelonaSpain
| | - Elise Eray
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute for Science and TechnologyBarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Gianni Liti
- University of Côte d’AzurCNRSINSERMIRCANNiceFrance
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14
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Etheridge TJ, Villahermosa D, Campillo-Funollet E, Herbert AD, Irmisch A, Watson AT, Dang HQ, Osborne MA, Oliver AW, Carr AM, Murray JM. Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo. eLife 2021; 10:e68579. [PMID: 33860765 PMCID: PMC8075580 DOI: 10.7554/elife.68579] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.
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Affiliation(s)
- Thomas J Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Desiree Villahermosa
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Eduard Campillo-Funollet
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Alex David Herbert
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Anja Irmisch
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Adam T Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Hung Q Dang
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Mark A Osborne
- Chemistry Department, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
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15
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Bradley AI, Marsh NM, Borror HR, Mostoller KE, Gama AI, Gardner RG. Acute ethanol stress induces sumoylation of conserved chromatin structural proteins in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:1121-1133. [PMID: 33788582 PMCID: PMC8351541 DOI: 10.1091/mbc.e20-11-0715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Stress is ubiquitous to life and can irreparably damage essential biomolecules and organelles in cells. To survive, organisms must sense and adapt to stressful conditions. One highly conserved adaptive stress response is through the posttranslational modification of proteins by the small ubiquitin-like modifier (SUMO). Here, we examine the effects of acute ethanol stress on protein sumoylation in the budding yeast Saccharomyces cerevisiae. We found that cells exhibit a transient sumoylation response after acute exposure to ≤7.5% vol/vol ethanol. By contrast, the sumoylation response becomes chronic at 10% ethanol exposure. Mass spectrometry analyses identified 18 proteins that are sumoylated after acute ethanol exposure, with 15 known to associate with chromatin. Upon further analysis, we found that the chromatin structural proteins Smc5 and Smc6 undergo ethanol-induced sumoylation that depends on the activity of the E3 SUMO ligase Mms21. Using cell-cycle arrest assays, we observed that Smc5 and Smc6 ethanol-induced sumoylation occurs during G1 and G2/M phases but not S phase. Acute ethanol exposure also resulted in the formation of Rad52 foci at levels comparable to Rad52 foci formation after exposure to the DNA alkylating agent methyl methanesulfonate (MMS). MMS exposure is known to induce the intra-S-phase DNA damage checkpoint via Rad53 phosphorylation, but ethanol exposure did not induce Rad53 phosphorylation. Ethanol abrogated the effect of MMS on Rad53 phosphorylation when added simultaneously. From these studies, we propose that acute ethanol exposure induces a change in chromatin leading to sumoylation of specific chromatin structural proteins.
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Affiliation(s)
- Amanda I Bradley
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
| | - Nicole M Marsh
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Heather R Borror
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | | | - Amber I Gama
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
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16
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Nakato R, Sakata T. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods 2021; 187:44-53. [PMID: 32240773 DOI: 10.1016/j.ymeth.2020.03.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/13/2022] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in epigenomic research. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, enables systematic analysis of how the epigenomic landscape contributes to cell identity, development, lineage specification, and disease. In this review, we first present a typical ChIP-seq analysis workflow, from quality assessment to chromatin-state annotation. We focus on practical, rather than theoretical, approaches for biological studies. Next, we outline various advanced ChIP-seq applications and introduce several state-of-the-art methods, including prediction of gene expression level and chromatin loops from epigenome data and data imputation. Finally, we discuss recently developed single-cell ChIP-seq analysis methodologies that elucidate the cellular diversity within complex tissues and cancers.
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Affiliation(s)
- Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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17
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Gutierrez-Escribano P, Hormeño S, Madariaga-Marcos J, Solé-Soler R, O'Reilly FJ, Morris K, Aicart-Ramos C, Aramayo R, Montoya A, Kramer H, Rappsilber J, Torres-Rosell J, Moreno-Herrero F, Aragon L. Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction. Mol Cell 2020; 80:1039-1054.e6. [PMID: 33301732 PMCID: PMC7758880 DOI: 10.1016/j.molcel.2020.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
Eukaryotic SMC complexes, cohesin, condensin, and Smc5/6, use ATP hydrolysis to power a plethora of functions requiring organization and restructuring of eukaryotic chromosomes in interphase and during mitosis. The Smc5/6 mechanism of action and its activity on DNA are largely unknown. Here we purified the budding yeast Smc5/6 holocomplex and characterized its core biochemical and biophysical activities. Purified Smc5/6 exhibits DNA-dependent ATP hydrolysis and SUMO E3 ligase activity. We show that Smc5/6 binds DNA topologically with affinity for supercoiled and catenated DNA templates. Employing single-molecule assays to analyze the functional and dynamic characteristics of Smc5/6 bound to DNA, we show that Smc5/6 locks DNA plectonemes and can compact DNA in an ATP-dependent manner. These results demonstrate that the Smc5/6 complex recognizes DNA tertiary structures involving juxtaposed helices and might modulate DNA topology by plectoneme stabilization and local compaction.
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Affiliation(s)
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roger Solé-Soler
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kyle Morris
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ricardo Aramayo
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jordi Torres-Rosell
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Luis Aragon
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK.
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18
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The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Mol Cell 2020; 80:1025-1038.e5. [PMID: 33301731 DOI: 10.1016/j.molcel.2020.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
The structural organization of chromosomes is a crucial feature that defines the functional state of genes and genomes. The extent of structural changes experienced by genomes of eukaryotic cells can be dramatic and spans several orders of magnitude. At the core of these changes lies a unique group of ATPases-the SMC proteins-that act as major effectors of chromosome behavior in cells. The Smc5/6 proteins play essential roles in the maintenance of genome stability, yet their mode of action is not fully understood. Here we show that the human Smc5/6 complex recognizes unusual DNA configurations and uses the energy of ATP hydrolysis to promote their compaction. Structural analyses reveal subunit interfaces responsible for the functionality of the Smc5/6 complex and how mutations in these regions may lead to chromosome breakage syndromes in humans. Collectively, our results suggest that the Smc5/6 complex promotes genome stability as a DNA micro-compaction machine.
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19
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Minchell NE, Keszthelyi A, Baxter J. Cohesin Causes Replicative DNA Damage by Trapping DNA Topological Stress. Mol Cell 2020; 78:739-751.e8. [PMID: 32259483 PMCID: PMC7242899 DOI: 10.1016/j.molcel.2020.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/12/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
Abstract
DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae, we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological-stress-linked damage in these regions. At cohesin-enriched centromeres, cohesin activity causes the accumulation of DNA damage, RF rotation, and pre-catenation, confirming that cohesin-dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA, cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that, as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.
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Affiliation(s)
- Nicola Elizabeth Minchell
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK.
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20
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Zapatka M, Pociño-Merino I, Heluani-Gahete H, Bermúdez-López M, Tarrés M, Ibars E, Solé-Soler R, Gutiérrez-Escribano P, Apostolova S, Casas C, Aragon L, Wellinger R, Colomina N, Torres-Rosell J. Sumoylation of Smc5 Promotes Error-free Bypass at Damaged Replication Forks. Cell Rep 2019; 29:3160-3172.e4. [DOI: 10.1016/j.celrep.2019.10.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
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21
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Winczura A, Appanah R, Tatham MH, Hay RT, De Piccoli G. The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε. PLoS Genet 2019; 15:e1008427. [PMID: 31765407 PMCID: PMC6876773 DOI: 10.1371/journal.pgen.1008427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Replication fork stalling and accumulation of single-stranded DNA trigger the S phase checkpoint, a signalling cascade that, in budding yeast, leads to the activation of the Rad53 kinase. Rad53 is essential in maintaining cell viability, but its targets of regulation are still partially unknown. Here we show that Rad53 drives the hyper-SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε, principally following replication forks stalling induced by nucleotide depletion. Pol2 is the main target of SUMOylation within the replisome and its modification requires the SUMO-ligase Mms21, a subunit of the Smc5/6 complex. Moreover, the Smc5/6 complex co-purifies with Pol ε, independently of other replisome components. Finally, we map Pol2 SUMOylation to a single site within the N-terminal catalytic domain and identify a SUMO-interacting motif at the C-terminus of Pol2. These data suggest that the S phase checkpoint regulate Pol ε during replication stress through Pol2 SUMOylation and SUMO-binding ability.
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Affiliation(s)
- Alicja Winczura
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Rowin Appanah
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Michael H. Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
| | - Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, United Kingdom
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22
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Abstract
Smc5 and Smc6, together with the kleisin Nse4, form the heart of the enigmatic and poorly understood Smc5/6 complex, which is frequently viewed as a cousin of cohesin and condensin with functions in DNA repair. As novel functions for cohesin and condensin complexes in the organization of long-range chromatin architecture have recently emerged, new unsuspected roles for Smc5/6 have also surfaced. Here, I aim to provide a comprehensive overview of our current knowledge of the Smc5/6 complex, including its long-established function in genome stability, its multiple roles in DNA repair, and its recently discovered connection to the transcription inhibition of hepatitis B virus genomes. In addition, I summarize new research that is beginning to tease out the molecular details of Smc5/6 structure and function, knowledge that will illuminate the nuclear activities of Smc5/6 in the stability and dynamics of eukaryotic genomes.
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Affiliation(s)
- Luis Aragón
- Cell Cycle Group, MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, United Kingdom;
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23
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Díaz M, Pečinková P, Nowicka A, Baroux C, Sakamoto T, Gandha PY, Jeřábková H, Matsunaga S, Grossniklaus U, Pecinka A. The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. THE PLANT CELL 2019; 31:1579-1597. [PMID: 31036599 PMCID: PMC6635853 DOI: 10.1105/tpc.18.00043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2019] [Accepted: 04/26/2019] [Indexed: 05/04/2023]
Abstract
The maintenance of genome integrity over cell divisions is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is the STRUCTURAL MAINTENANCE OF CHROMOSOME5 (SMC5) and SMC6 (SMC5/6) complex, related to the cohesin and condensin complexes that control sister chromatid alignment and chromosome condensation, respectively. Here, we characterize NON-SMC ELEMENT4 (NSE4) paralogs of the SMC5/6 complex in Arabidopsis (Arabidopsis thaliana). NSE4A is expressed in meristems and accumulates during DNA damage repair. Partial loss-of-function nse4a mutants are viable but hypersensitive to DNA damage induced by zebularine. In addition, nse4a mutants produce abnormal seeds, with noncellularized endosperm and embryos that maximally develop to the heart or torpedo stage. This phenotype resembles the defects in cohesin and condensin mutants and suggests a role for all three SMC complexes in differentiation during seed development. By contrast, NSE4B is expressed in only a few cell types, and loss-of-function mutants do not have any obvious abnormal phenotype. In summary, our study shows that the NSE4A subunit of the SMC5-SMC6 complex is essential for DNA damage repair in somatic tissues and plays a role in plant reproduction.
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Affiliation(s)
- Mariana Díaz
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Petra Pečinková
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Anna Nowicka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Polish Academy of Sciences, Franciszek Gorski Institute of Plant Physiology, 30-239 Krakow, Poland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Priscilla Yuliani Gandha
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
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24
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Zelkowski M, Zelkowska K, Conrad U, Hesse S, Lermontova I, Marzec M, Meister A, Houben A, Schubert V. Arabidopsis NSE4 Proteins Act in Somatic Nuclei and Meiosis to Ensure Plant Viability and Fertility. FRONTIERS IN PLANT SCIENCE 2019; 10:774. [PMID: 31281325 PMCID: PMC6596448 DOI: 10.3389/fpls.2019.00774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/28/2019] [Indexed: 05/02/2023]
Abstract
The SMC 5/6 complex together with cohesin and condensin is a member of the structural maintenance of chromosome (SMC) protein family. In non-plant organisms SMC5/6 is engaged in DNA repair, meiotic synapsis, genome organization and stability. In plants, the function of SMC5/6 is still enigmatic. Therefore, we analyzed the crucial δ-kleisin component NSE4 of the SMC5/6 complex in the model plant Arabidopsis thaliana. Two functional conserved Nse4 paralogs (Nse4A and Nse4B) are present in A. thaliana, which may have evolved via gene subfunctionalization. Due to its high expression level, Nse4A seems to be the more essential gene, whereas Nse4B appears to be involved mainly in seed development. The morphological characterization of A. thaliana T-DNA mutants suggests that the NSE4 proteins are essential for plant growth and fertility. Detailed investigations in wild-type and the mutants based on live cell imaging of transgenic GFP lines, fluorescence in situ hybridization (FISH), immunolabeling and super-resolution microscopy suggest that NSE4A acts in several processes during plant development, such as mitosis, meiosis and chromatin organization of differentiated nuclei, and that NSE4A operates in a cell cycle-dependent manner. Differential response of NSE4A and NSE4B mutants after induced DNA double strand breaks (DSBs) suggests their involvement in DNA repair processes.
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Affiliation(s)
- Mateusz Zelkowski
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Susann Hesse
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Marzec
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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25
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Deiss K, Lockwood N, Howell M, Segeren HA, Saunders RE, Chakravarty P, Soliman TN, Martini S, Rocha N, Semple R, Zalmas LP, Parker PJ. A genome-wide RNAi screen identifies the SMC5/6 complex as a non-redundant regulator of a Topo2a-dependent G2 arrest. Nucleic Acids Res 2019; 47:2906-2921. [PMID: 30590722 PMCID: PMC6451093 DOI: 10.1093/nar/gky1295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
The Topo2a-dependent arrest is associated with faithful segregation of sister chromatids and has been identified as dysfunctional in numerous tumour cell lines. This genome-protecting pathway is poorly understood and its characterization is of significant interest, potentially offering interventional opportunities in relation to synthetic lethal behaviours in arrest-defective tumours. Using the catalytic Topo2a inhibitor ICRF193, we have performed a genome-wide siRNA screen in arrest-competent, non-transformed cells, to identify genes essential for this arrest mechanism. In addition, we have counter-screened several DNA-damaging agents and demonstrate that the Topo2a-dependent arrest is genetically distinct from DNA damage checkpoints. We identify the components of the SMC5/6 complex, including the activity of the E3 SUMO ligase NSE2, as non-redundant players that control the timing of the Topo2a-dependent arrest in G2. We have independently verified the NSE2 requirement in fibroblasts from patients with germline mutations that cause severely reduced levels of NSE2. Through imaging Topo2a-dependent G2 arrested cells, an increased interaction between Topo2a and NSE2 is observed at PML bodies, which are known SUMOylation hotspots. We demonstrate that Topo2a is SUMOylated in an ICRF193-dependent manner by NSE2 at a novel non-canonical site (K1520) and that K1520 sumoylation is required for chromosome segregation but not the G2 arrest.
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Affiliation(s)
- Katharina Deiss
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicola Lockwood
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hendrika Alida Segeren
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rebecca E Saunders
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Probir Chakravarty
- Bioinformatics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tanya N Soliman
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Silvia Martini
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nuno Rocha
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Robert Semple
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | | | - Peter J Parker
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
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26
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Chowdhury SR, Majumder HK. DNA Topoisomerases in Unicellular Pathogens: Structure, Function, and Druggability. Trends Biochem Sci 2019; 44:415-432. [PMID: 30609953 DOI: 10.1016/j.tibs.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
All organisms, including unicellular pathogens, compulsorily possess DNA topoisomerases for successful nucleic acid metabolism. But particular subtypes of topoisomerases exist, in all prokaryotes and in some unicellular eukaryotes, that are absent in higher eukaryotes. Moreover, topoisomerases from pathogenic members of a niche possess some unique molecular architecture and functionalities completely distinct from their nonpathogenic colleagues. This review will highlight the unique attributes associated with the structures and functions of topoisomerases from the unicellular pathogens, with special reference to bacteria and protozoan parasites. It will also summarise the progress made in the domain pertaining to the druggability of these topoisomerases, upon which a future platform for therapeutic development can be successfully constructed.
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Affiliation(s)
- Somenath Roy Chowdhury
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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27
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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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28
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Diaz M, Pecinka A. Scaffolding for Repair: Understanding Molecular Functions of the SMC5/6 Complex. Genes (Basel) 2018; 9:genes9010036. [PMID: 29329249 PMCID: PMC5793187 DOI: 10.3390/genes9010036] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 12/17/2022] Open
Abstract
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex. SMC5/6 complex was originally identified based on the sensitivity of its mutants to genotoxic stress but there is increasing number of studies demonstrating its roles in the control of DNA replication, sister chromatid resolution and genomic location-dependent promotion or suppression of homologous recombination. Some of these functions appear to be due to a very dynamic interaction with cohesin or other repair complexes. Studies in Arabidopsis indicate that, besides its canonical function in repair of damaged DNA, the SMC5/6 complex plays important roles in regulating plant development, abiotic stress responses, suppression of autoimmune responses and sexual reproduction.
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Affiliation(s)
- Mariana Diaz
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
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29
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Piskadlo E, Oliveira RA. A Topology-Centric View on Mitotic Chromosome Architecture. Int J Mol Sci 2017; 18:E2751. [PMID: 29258269 PMCID: PMC5751350 DOI: 10.3390/ijms18122751] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 02/04/2023] Open
Abstract
Mitotic chromosomes are long-known structures, but their internal organization and the exact process by which they are assembled are still a great mystery in biology. Topoisomerase II is crucial for various aspects of mitotic chromosome organization. The unique ability of this enzyme to untangle topologically intertwined DNA molecules (catenations) is of utmost importance for the resolution of sister chromatid intertwines. Although still controversial, topoisomerase II has also been proposed to directly contribute to chromosome compaction, possibly by promoting chromosome self-entanglements. These two functions raise a strong directionality issue towards topoisomerase II reactions that are able to disentangle sister DNA molecules (in trans) while compacting the same DNA molecule (in cis). Here, we review the current knowledge on topoisomerase II role specifically during mitosis, and the mechanisms that directly or indirectly regulate its activity to ensure faithful chromosome segregation. In particular, we discuss how the activity or directionality of this enzyme could be regulated by the SMC (structural maintenance of chromosomes) complexes, predominantly cohesin and condensin, throughout mitosis.
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Affiliation(s)
- Ewa Piskadlo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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30
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Eeftens J, Dekker C. Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins. Nat Struct Mol Biol 2017; 24:1012-1020. [DOI: 10.1038/nsmb.3507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
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31
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Kuzminov A. When DNA Topology Turns Deadly - RNA Polymerases Dig in Their R-Loops to Stand Their Ground: New Positive and Negative (Super)Twists in the Replication-Transcription Conflict. Trends Genet 2017; 34:111-120. [PMID: 29179918 DOI: 10.1016/j.tig.2017.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022]
Abstract
Head-on replication-transcription conflict is especially bitter in bacterial chromosomes, explaining why actively transcribed genes are always co-oriented with replication. The mechanism of this conflict remains unclear, besides the anticipated accumulation of positive supercoils between head-on-conflicting polymerases. Unexpectedly, experiments in bacterial and human cells reveal that head-on replication-transcription conflict induces R-loops, indicating hypernegative supercoiling [(-)sc] in the region - precisely the opposite of that assumed. Further, as a result of these R-loops, both replication and transcription in the affected region permanently stall, so the failure of R-loop removal in RNase H-deficient bacteria becomes lethal. How hyper(-)sc emerges in the middle of a positively supercoiled chromosomal domain is a mystery that requires rethinking of topoisomerase action around polymerases.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 South Goodwin Avenue, Urbana, IL 61801-3709, USA.
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32
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Nakato R, Shirahige K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Brief Bioinform 2017; 18:279-290. [PMID: 26979602 PMCID: PMC5444249 DOI: 10.1093/bib/bbw023] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 02/06/2023] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.
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Affiliation(s)
- Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Japan
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33
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Mariezcurrena A, Uhlmann F. Observation of DNA intertwining along authentic budding yeast chromosomes. Genes Dev 2017; 31:2151-2161. [PMID: 29208645 PMCID: PMC5749163 DOI: 10.1101/gad.305557.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
DNA replication of circular genomes generates physically interlinked or catenated sister DNAs. These are resolved through transient DNA fracture by type II topoisomerases to permit chromosome segregation during cell division. Topoisomerase II is similarly required for linear chromosome segregation, suggesting that linear chromosomes also remain intertwined following DNA replication. Indeed, chromosome resolution defects are a frequent cause of chromosome segregation failure and consequent aneuploidies. When and where intertwines arise and persist along linear chromosomes are not known, owing to the difficulty of demonstrating intertwining of linear DNAs. Here, we used excision of chromosomal regions as circular "loop outs" to convert sister chromatid intertwines into catenated circles. This revealed intertwining at replication termination and cohesin-binding sites, where intertwines are thought to arise and persist but not to a greater extent than elsewhere in the genome. Intertwining appears to spread evenly along chromosomes but is excluded from heterochromatin. We found that intertwines arise before replication termination, suggesting that replication forks rotate during replication elongation to dissipate torsion ahead of the forks. Our approach provides previously inaccessible insight into the topology of eukaryotic chromosomes and illuminates a process critical for successful chromosome segregation.
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Affiliation(s)
- Ainhoa Mariezcurrena
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
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34
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Identifying and Characterizing Interplay between Hepatitis B Virus X Protein and Smc5/6. Viruses 2017; 9:v9040069. [PMID: 28368357 PMCID: PMC5408675 DOI: 10.3390/v9040069] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B X protein (HBx) plays an essential role in the hepatitis B virus (HBV) replication cycle, but the function of HBx has been elusive until recently. It was recently shown that transcription from the HBV genome (covalently-closed circular DNA, cccDNA) is inhibited by the structural maintenance of chromosome 5/6 complex (Smc5/6), and that a key function of HBx is to redirect the DNA-damage binding protein 1 (DDB1) E3 ubiquitin ligase to target this complex for degradation. By doing so, HBx alleviates transcriptional repression by Smc5/6 and stimulates HBV gene expression. In this review, we discuss in detail how the interplay between HBx and Smc5/6 was identified and characterized. We also discuss what is known regarding the repression of cccDNA transcription by Smc5/6, the timing of HBx expression, and the potential role of HBx in promoting hepatocellular carcinoma (HCC).
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35
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Li G, Zou W, Jian L, Qian J, Deng Y, Zhao J. Non-SMC elements 1 and 3 are required for early embryo and seedling development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1039-1054. [PMID: 28207059 PMCID: PMC5441860 DOI: 10.1093/jxb/erx016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Early embryo development from the zygote is an essential stage in the formation of the seed, while seedling development is the beginning of the formation of an individual plant. AtNSE1 and AtNSE3 are subunits of the structural maintenance of chromosomes (SMC) 5/6 complex and have been identified as non-SMC elements, but their functions in Arabidopsis growth and development remain as yet unknown. In this study, we found that loss of function of AtNSE1 and AtNSE3 led to severe defects in early embryo development. Partially complemented mutants showed that the development of mutant seedlings was inhibited, that chromosome fragments occurred during anaphase, and that the cell cycle was delayed at G2/M, which led to the occurrence of endoreduplication. Further, a large number of DNA double-strand breaks (DSBs) occurred in the nse1 and nse3 mutants, and the expression of AtNSE1 and AtNSE3 was up-regulated following treatment of the plants with DSB inducer compounds, suggesting that AtNSE1 and AtNSE3 have a role in DNA damage repair. Therefore, we conclude that AtNSE1 and AtNSE3 facilitate DSB repair and contribute to maintaining genome stability and cell division in mitotic cells. Thus, we think that AtNSE1 and AtNSE3 may be crucial factors for maintaining proper early embryonic and post-embryonic development.
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Affiliation(s)
- Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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36
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Abstract
DNA topological transitions occur when replication forks encounter other DNA transactions such as transcription. Failure in resolving such conflicts leads to generation of aberrant replication and transcription intermediates that might have adverse effects on genome stability. Cells have evolved numerous surveillance mechanisms to avoid, tolerate, and resolve such replication-transcription conflicts. Defects or non-coordination in such cellular mechanisms might have catastrophic effect on cell viability. In this chapter, we review consequences of replication encounters with transcription and its associated events, topological challenges, and how these inevitable conflicts alter the genome structure and functions.
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37
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The Causes and Consequences of Topological Stress during DNA Replication. Genes (Basel) 2016; 7:genes7120134. [PMID: 28009828 PMCID: PMC5192510 DOI: 10.3390/genes7120134] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/11/2016] [Accepted: 12/14/2016] [Indexed: 01/08/2023] Open
Abstract
The faithful replication of sister chromatids is essential for genomic integrity in every cell division. The replication machinery must overcome numerous difficulties in every round of replication, including DNA topological stress. Topological stress arises due to the double-stranded helical nature of DNA. When the strands are pulled apart for replication to occur, the intertwining of the double helix must also be resolved or topological stress will arise. This intrinsic problem is exacerbated by specific chromosomal contexts encountered during DNA replication. The convergence of two replicons during termination, the presence of stable protein-DNA complexes and active transcription can all lead to topological stresses being imposed upon DNA replication. Here we describe how replication forks respond to topological stress by replication fork rotation and fork reversal. We also discuss the genomic contexts where topological stress is likely to occur in eukaryotes, focusing on the contribution of transcription. Finally, we describe how topological stress, and the ways forks respond to it, may contribute to genomic instability in cells.
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38
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Lin SJ, Tapia-Alveal C, Jabado OJ, Germain D, O'Connell MJ. An acetyltransferase-independent function of Eso1 regulates centromere cohesion. Mol Biol Cell 2016; 27:4002-4010. [PMID: 27798241 PMCID: PMC5156541 DOI: 10.1091/mbc.e16-08-0596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Eukaryotes contain three essential Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin, and Smc5/6. Cohesin forms a ring-shaped structure that embraces sister chromatids to promote their cohesion. The cohesiveness of cohesin is promoted by acetylation of N-terminal lysines of the Smc3 subunit by the acetyltransferases Eco1 in Saccharomyces cerevisiae and the homologue, Eso1, in Schizosaccharomyces pombe. In both yeasts, these acetyltransferases are essential for cell viability. However, whereas nonacetylatable Smc3 mutants are lethal in S. cerevisiae, they are not in S. pombe We show that the lethality of a temperature-sensitive allele of eso1 (eso1-H17) is due to activation of the spindle assembly checkpoint (SAC) and is associated with premature centromere separation. The lack of cohesion at the centromeres does not correlate with Psm3 acetylation or cohesin levels at the centromeres, but is associated ith significantly reduced recruitment of the cohesin regulator Pds5. The SAC activation in this context is dependent on Smc5/6 function, which is required to remove cohesin from chromosome arms but not centromeres. The mitotic defects caused by Smc5/6 and Eso1 dysfunction are cosuppressed in double mutants. This identifies a novel function (or functions) for Eso1 and Smc5/6 at centromeres and extends the functional relationships between these SMC complexes.
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Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Omar J Jabado
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Doris Germain
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei. PLoS Genet 2016; 12:e1006169. [PMID: 27541002 PMCID: PMC4991795 DOI: 10.1371/journal.pgen.1006169] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Following DNA replication, sister chromatids must stay connected for the remainder of the cell cycle in order to ensure accurate segregation in the subsequent cell division. This important function involves an evolutionarily conserved protein complex known as cohesin; any loss of cohesin causes premature sister chromatid separation in mitosis. Here, we examined the role of cohesin in sister chromatid cohesion prior to mitosis, using fluorescence in situ hybridization (FISH) to assay the alignment of sister chromatids in interphase Drosophila cells. Surprisingly, we found that sister chromatid cohesion can be maintained in G2 with little to no cohesin. This capacity to maintain cohesion is widespread in Drosophila, unlike in other systems where a reduced dependence on cohesin for sister chromatid segregation has been observed only at specific chromosomal regions, such as the rDNA locus in budding yeast. Additionally, we show that condensin II antagonizes the alignment of sister chromatids in interphase, supporting a model wherein cohesin and condensin II oppose each other’s functions in the alignment of sister chromatids. Finally, because the maternal and paternal homologs are paired in the somatic cells of Drosophila, and because condensin II has been shown to antagonize this pairing, we consider the possibility that condensin II-regulated mechanisms for aligning homologous chromosomes may also contribute to sister chromatid cohesion. As cells grow, they replicate their DNA to give rise to two copies of each chromosome, known as sister chromatids, which separate from each other once the cell divides. To ensure that sister chromatids end up in different daughter cells, they are kept together from DNA replication until mitosis via a connection known as cohesion. A protein complex known as cohesin is essential for this process. Our work in Drosophila cells suggests that factors other than cohesin also contribute to sister chromatid cohesion in interphase. Additionally, we observed that the alignment of sister chromatids is regulated by condensin II, a protein complex involved in the compaction of chromosomes prior to division as well as the regulation of inter-chromosomal associations. These findings highlight that, in addition to their important individual functions, cohesin and condensin II proteins may interact to organize chromosomes over the course of the cell cycle. Finally, building on prior observations that condensin II is involved in the regulation of somatic homolog pairing in Drosophila, our work suggests that the mechanisms underlying homolog pairing may also contribute to sister chromatid cohesion.
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40
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Pakchuen S, Ishibashi M, Takakusagi E, Shirahige K, Sutani T. Physical Association of Saccharomyces cerevisiae Polo-like Kinase Cdc5 with Chromosomal Cohesin Facilitates DNA Damage Response. J Biol Chem 2016; 291:17228-46. [PMID: 27325700 PMCID: PMC5016123 DOI: 10.1074/jbc.m116.727438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/13/2016] [Indexed: 12/03/2022] Open
Abstract
At the onset of anaphase, a protease called separase breaks the link between sister chromatids by cleaving the cohesin subunit Scc1. This irreversible step in the cell cycle is promoted by degradation of the separase inhibitor, securin, and polo-like kinase (Plk) 1-dependent phosphorylation of the Scc1 subunit. Plk could recognize substrates through interaction between its phosphopeptide interaction domain, the polo-box domain, and a phosphorylated priming site in the substrate, which has been generated by a priming kinase beforehand. However, the physiological relevance of this targeting mechanism remains to be addressed for many of the Plk1 substrates. Here, we show that budding yeast Plk1, Cdc5, is pre-deposited onto cohesin engaged in cohesion on chromosome arms in G2/M phase cells. The Cdc5-cohesin association is mediated by direct interaction between the polo-box domain of Cdc5 and Scc1 phosphorylated at multiple sites in its middle region. Alanine substitutions of the possible priming phosphorylation sites (scc1-15A) impair Cdc5 association with chromosomal cohesin, but they make only a moderate impact on mitotic cell growth even in securin-deleted cells (pds1Δ), where Scc1 phosphorylation by Cdc5 is indispensable. The same scc1-15A pds1Δ double mutant, however, exhibits marked sensitivity to the DNA-damaging agent phleomycin, suggesting that the priming phosphorylation of Scc1 poses an additional layer of regulation that enables yeast cells to adapt to genotoxic environments.
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Affiliation(s)
- Sujiraporn Pakchuen
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and the Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Mai Ishibashi
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Emi Takakusagi
- the Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Katsuhiko Shirahige
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Takashi Sutani
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
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41
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Tran M, Tsarouhas V, Kegel A. Early development of Drosophila embryos requires Smc5/6 function during oogenesis. Biol Open 2016; 5:928-41. [PMID: 27288507 PMCID: PMC4958276 DOI: 10.1242/bio.019000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mutations in structural maintenance of chromosomes (Smc) proteins are frequently associated with chromosomal abnormalities commonly observed in developmental disorders. However, the role of Smc proteins in development still remains elusive. To investigate Smc5/6 function during early embryogenesis we examined smc5 and smc6 mutants of the fruit fly Drosophila melanogaster using a combination of reverse genetics and microscopy approaches. Smc5/6 exhibited a maternally contributed function in maintaining chromosome stability during early embryo development, which manifested as female subfertility in its absence. Loss of Smc5/6 caused an arrest and a considerable delay in embryo development accompanied by fragmented nuclei and increased anaphase-bridge formation, respectively. Surprisingly, early embryonic arrest was attributable to the absence of Smc5/6 during oogenesis, which resulted in insufficient repair of pre-meiotic and meiotic DNA double-strand breaks. Thus, our findings contribute to the understanding of Smc proteins in higher eukaryotic development by highlighting a maternal function in chromosome maintenance and a link between oogenesis and early embryogenesis. Summary: Early emerging problems during oogenesis, such as DNA double-strand breaks, can affect chromosome duplication and segregation in embryogenesis in Drosophila. Moreover, environmental cues including temperature are important for proper oogenesis.
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Affiliation(s)
- Martin Tran
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
| | - Vasilios Tsarouhas
- Department of Molecular Bioscience, The Wenner-Gren Institute, Stockholm University, Stockholm S-10691, Sweden
| | - Andreas Kegel
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
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42
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Ocampo-Hafalla M, Muñoz S, Samora CP, Uhlmann F. Evidence for cohesin sliding along budding yeast chromosomes. Open Biol 2016; 6:150178. [PMID: 27278645 PMCID: PMC4929932 DOI: 10.1098/rsob.150178] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 05/13/2016] [Indexed: 11/12/2022] Open
Abstract
The ring-shaped cohesin complex is thought to topologically hold sister chromatids together from their synthesis in S phase until chromosome segregation in mitosis. How cohesin stably binds to chromosomes for extended periods, without impeding other chromosomal processes that also require access to the DNA, is poorly understood. Budding yeast cohesin is loaded onto DNA by the Scc2-Scc4 cohesin loader at centromeres and promoters of active genes, from where cohesin translocates to more permanent places of residence at transcription termination sites. Here we show that, at the GAL2 and MET17 loci, pre-existing cohesin is pushed downstream along the DNA in response to transcriptional gene activation, apparently without need for intermittent dissociation or reloading. We observe translocation intermediates and find that the distribution of most chromosomal cohesin is shaped by transcription. Our observations support a model in which cohesin is able to slide laterally along chromosomes while maintaining topological contact with DNA. In this way, stable cohesin binding to DNA and enduring sister chromatid cohesion become compatible with simultaneous underlying chromosomal activities, including but maybe not limited to transcription.
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Affiliation(s)
- Maria Ocampo-Hafalla
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Sofía Muñoz
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Catarina P Samora
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Frank Uhlmann
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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43
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Abstract
SMC (structural maintenance of chromosomes) complexes - which include condensin, cohesin and the SMC5-SMC6 complex - are major components of chromosomes in all living organisms, from bacteria to humans. These ring-shaped protein machines, which are powered by ATP hydrolysis, topologically encircle DNA. With their ability to hold more than one strand of DNA together, SMC complexes control a plethora of chromosomal activities. Notable among these are chromosome condensation and sister chromatid cohesion. Moreover, SMC complexes have an important role in DNA repair. Recent mechanistic insight into the function and regulation of these universal chromosomal machines enables us to propose molecular models of chromosome structure, dynamics and function, illuminating one of the fundamental entities in biology.
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44
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Menolfi D, Delamarre A, Lengronne A, Pasero P, Branzei D. Essential Roles of the Smc5/6 Complex in Replication through Natural Pausing Sites and Endogenous DNA Damage Tolerance. Mol Cell 2015; 60:835-46. [PMID: 26698660 PMCID: PMC4691243 DOI: 10.1016/j.molcel.2015.10.023] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/02/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023]
Abstract
The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell-cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders. Cell-cycle-regulated alleles reveal Smc5/6-essential functions to segregate in G2/M Genetic screen with new hypomorphic allele identifies processes relying on Smc5/6 Smc5/6 acts on recombination structures triggered by endogenous replication stress Smc5/6 prevents fragility and mediates replication through natural pausing sites
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Affiliation(s)
- Demis Menolfi
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Axel Delamarre
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Armelle Lengronne
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Philippe Pasero
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
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45
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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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46
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Schalbetter SA, Mansoubi S, Chambers AL, Downs JA, Baxter J. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proc Natl Acad Sci U S A 2015; 112:E4565-70. [PMID: 26240319 PMCID: PMC4547287 DOI: 10.1073/pnas.1505356112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.
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Affiliation(s)
- Stephanie A Schalbetter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Sahar Mansoubi
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Anna L Chambers
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom; School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Jonathan Baxter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom;
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47
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Tong K, Skibbens RV. Pds5 regulators segregate cohesion and condensation pathways in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2015; 112:7021-6. [PMID: 25986377 PMCID: PMC4460518 DOI: 10.1073/pnas.1501369112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cohesins are required both for the tethering together of sister chromatids (termed cohesion) and subsequent condensation into discrete structures-processes fundamental for faithful chromosome segregation into daughter cells. Differentiating between cohesin roles in cohesion and condensation would provide an important advance in studying chromatin metabolism. Pds5 is a cohesin-associated factor that is essential for both cohesion maintenance and condensation. Recent studies revealed that ELG1 deletion suppresses the temperature sensitivity of pds5 mutant cells. However, the mechanisms through which Elg1 may regulate cohesion and condensation remain unknown. Here, we report that ELG1 deletion from pds5-1 mutant cells results in a significant rescue of cohesion, but not condensation, defects. Based on evidence that Elg1 unloads the DNA replication clamp PCNA from DNA, we tested whether PCNA overexpression would similarly rescue pds5-1 mutant cell cohesion defects. The results indeed reveal that elevated levels of PCNA rescue pds5-1 temperature sensitivity and cohesion defects, but do not rescue pds5-1 mutant cell condensation defects. In contrast, RAD61 deletion rescues the condensation defect, but importantly, neither the temperature sensitivity nor cohesion defects exhibited by pds5-1 mutant cells. In combination, these findings reveal that cohesion and condensation are separable pathways and regulated in nonredundant mechanisms. These results are discussed in terms of a new model through which cohesion and condensation are spatially regulated.
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Affiliation(s)
- Kevin Tong
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
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48
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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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49
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Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6. Chromosoma 2015; 125:15-27. [PMID: 25947290 PMCID: PMC4761004 DOI: 10.1007/s00412-015-0518-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/02/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
Abstract
The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homologous recombination, restart of stalled replication forks, maintenance of ribosomal DNA (rDNA) and heterochromatin, telomerase-independent telomere elongation, and regulation of chromosome topology. The nature of these functions implies that the Smc5/6 complex also contributes to the profound chromatin changes, including meiotic recombination, that characterize meiosis. Only recently, studies in diverse model organisms have focused on the potential meiotic roles of the Smc5/6 complex. Indeed, Smc5/6 appears to be essential for meiotic recombination. However, due to both the complexity of the process of meiosis and the versatility of the Smc5/6 complex, many additional meiotic functions have been described. In this review, we provide a clear overview of the multiple functions found so far for the Smc5/6 complex in meiosis. Additionally, we compare these meiotic functions with the known mitotic functions in an attempt to find a common denominator and thereby create clarity in the field of Smc5/6 research.
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50
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Shav-Tal Y, Lammerding J. Design (and) principles of nuclear dynamics in Stockholm. Nucleus 2015; 6:425-9. [PMID: 26730816 PMCID: PMC4915483 DOI: 10.1080/19491034.2015.1128609] [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: 11/04/2015] [Revised: 11/26/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022] Open
Abstract
The structural organization of the nucleus and its content has drawn increasing interest in recent years, as it is has become evident that the spatial and temporal arrangement of the genome and associated structures plays a crucial role in transcriptional regulation and numerous other functions. Shining light on the dynamic nature of this organization, along with the processes controlling it, were the topics of the Wenner-Gren Foundations international symposium "Nuclear Dynamics: Design (and) Principles." The meeting, organized by Piorgiogio Percipalle, Maria Vartiainen, Neus Visa, and Ann-Kristin Östlund-Farrants, brought over 60 participants, including 20 international speakers, to Stockholm, Sweden from August 19-22, 2015 to share the latest developments in the field. Given the unpublished nature of many of the talks, we have focused on covering the discussed topics and highlighting the latest trends in this exciting and rapidly evolving field.
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Affiliation(s)
- Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology; Bar-Ilan University; Ramat Gan, Israel
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology; Meinig School of Biomedical Engineering; Cornell University; Ithaca, NY USA
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