1
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Yuan X, Yan L, Chen Q, Zhu S, Zhou X, Zeng LH, Liu M, He X, Huang J, Lu W, Zhang L, Yan H, Wang F. Molecular mechanism and functional significance of Wapl interaction with the Cohesin complex. Proc Natl Acad Sci U S A 2024; 121:e2405177121. [PMID: 39110738 PMCID: PMC11331136 DOI: 10.1073/pnas.2405177121] [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: 03/12/2024] [Accepted: 07/01/2024] [Indexed: 08/21/2024] Open
Abstract
The ring-shaped Cohesin complex, consisting of core subunits Smc1, Smc3, Scc1, and SA2 (or its paralog SA1), topologically entraps two duplicated sister DNA molecules to establish sister chromatid cohesion in S-phase. It remains largely elusive how the Cohesin release factor Wapl binds the Cohesin complex, thereby inducing Cohesin disassociation from mitotic chromosomes to allow proper resolution and separation of sister chromatids. Here, we show that Wapl uses two structural modules containing the FGF motif and the YNARHWN motif, respectively, to simultaneously bind distinct pockets in the extensive composite interface between Scc1 and SA2. Strikingly, only when both docking modules are mutated, Wapl completely loses the ability to bind the Scc1-SA2 interface and release Cohesin, leading to erroneous chromosome segregation in mitosis. Surprisingly, Sororin, which contains a conserved FGF motif and functions as a master antagonist of Wapl in S-phase and G2-phase, does not bind the Scc1-SA2 interface. Moreover, Sgo1, the major protector of Cohesin at mitotic centromeres, can only compete with the FGF motif but not the YNARHWN motif of Wapl for binding Scc1-SA2 interface. Our data uncover the molecular mechanism by which Wapl binds Cohesin to ensure precise chromosome segregation.
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Affiliation(s)
- Xueying Yuan
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lu Yan
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qinfu Chen
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shukai Zhu
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xinyu Zhou
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ling-Hui Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Mingjie Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute and MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Weiguo Lu
- Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital of Zhejiang University School of Medicine, and Cancer Center of Zhejiang University, Hangzhou, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute and MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Haiyan Yan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Fangwei Wang
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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2
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Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB. Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. eLife 2024; 13:RP94070. [PMID: 39110499 PMCID: PMC11305675 DOI: 10.7554/elife.94070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Two different models have been proposed to explain how the endpoints of chromatin looped domains ('TADs') in eukaryotic chromosomes are determined. In the first, a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop. In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of MicroC to analyze how TADs are organized, and experimental manipulations of the even skipped TAD boundary, homie, to test the predictions of the 'loop-extrusion' and the 'boundary-pairing' models. Our findings are incompatible with the loop-extrusion model, and instead suggest that the endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their partners, either head-to-head or head-to-tail, with varying degrees of specificity. Although our experiments do not address how partners find each other, the mechanism is unlikely to require loop extrusion.
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Affiliation(s)
- Xinyang Bing
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Amina Kurbidaeva
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Sarah Levitt
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Mike Levine
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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3
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Oldenkamp R, Rowland BD. Cell biology: Converging paths to cohesion. Curr Biol 2024; 34:R680-R682. [PMID: 39043139 DOI: 10.1016/j.cub.2024.05.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Cohesin holds together the sister chromatids from DNA replication onwards. How cohesion is established has long remained a black box. Through recent studies, a model is emerging in which a replisome-cohesin encounter results in the establishment of cohesive linkages at sites of replication termination.
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Affiliation(s)
- Roel Oldenkamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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4
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Prusén Mota I, Galova M, Schleiffer A, Nguyen TT, Kovacikova I, Farias Saad C, Litos G, Nishiyama T, Gregan J, Peters JM, Schlögelhofer P. Sororin is an evolutionary conserved antagonist of WAPL. Nat Commun 2024; 15:4729. [PMID: 38830897 PMCID: PMC11148194 DOI: 10.1038/s41467-024-49178-0] [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: 10/24/2022] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
Cohesin mediates sister chromatid cohesion to enable chromosome segregation and DNA damage repair. To perform these functions, cohesin needs to be protected from WAPL, which otherwise releases cohesin from DNA. It has been proposed that cohesin is protected from WAPL by SORORIN. However, in vivo evidence for this antagonism is missing and SORORIN is only known to exist in vertebrates and insects. It is therefore unknown how important and widespread SORORIN's functions are. Here we report the identification of SORORIN orthologs in Schizosaccharomyces pombe (Sor1) and Arabidopsis thaliana (AtSORORIN). sor1Δ mutants display cohesion defects, which are partially alleviated by wpl1Δ. Atsororin mutant plants display dwarfism, tissue specific cohesion defects and chromosome mis-segregation. Furthermore, Atsororin mutant plants are sterile and separate sister chromatids prematurely at anaphase I. The somatic, but not the meiotic deficiencies can be alleviated by loss of WAPL. These results provide in vivo evidence for SORORIN antagonizing WAPL, reveal that SORORIN is present in organisms beyond the animal kingdom and indicate that it has acquired tissue specific functions in plants.
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Affiliation(s)
- Ignacio Prusén Mota
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Marta Galova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tan-Trung Nguyen
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
| | - Ines Kovacikova
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
| | - Carolina Farias Saad
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tomoko Nishiyama
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Juraj Gregan
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria.
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Tulln an der Donau, Austria.
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
| | - Peter Schlögelhofer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria.
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5
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Xu JJ, Viny AD. Chromatin organization in myelodysplastic syndrome. Exp Hematol 2024; 134:104216. [PMID: 38582293 DOI: 10.1016/j.exphem.2024.104216] [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: 01/10/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Disordered chromatin organization has emerged as a new aspect of the pathogenesis of myelodysplastic syndrome (MDS). Characterized by lineage dysplasia and a high transformation rate to acute myeloid leukemia (AML), the genetic determinant of MDS is thought to be the main driver of the disease's progression. Among the recurrently mutated pathways, alterations in chromatin organization, such as the cohesin complex, have a profound impact on hematopoietic stem cell (HSC) function and lineage commitment. The cohesin complex is a ring-like structure comprised of structural maintenance of chromosomes (SMC), RAD21, and STAG proteins that involve three-dimensional (3D) genome organization via loop extrusion in mammalian cells. The partial loss of the functional cohesin ring leads to altered chromatin accessibility specific to key hematopoietic transcription factors, which is thought to be the molecular mechanism of cohesin dysfunction. Currently, there are no specific targeting agents for cohesin mutant MDS/AML. Potential therapeutic strategies have been proposed based on the current understanding of cohesin mutant leukemogenesis. Here, we will review the recent advances in investigation and targeting approaches against cohesin mutant MDS/AML.
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Affiliation(s)
- Jane Jialu Xu
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York.
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6
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McDonald A, Murre C, Sedat J. Helical Coiled Nucleosome Chromosome Architectures during Cell Cycle Progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595892. [PMID: 38826250 PMCID: PMC11142257 DOI: 10.1101/2024.05.25.595892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Recent studies showed an interphase chromosome architecture, --- a specific coiled nucleosome structure, --- derived from cryo-preserved EM tomograms, and dispersed throughout the nucleus. The images were computationally processed to fill in the missing wedges of data caused by incomplete tomographic tilts. The resulting structures increased z-resolution enabling an extension of the proposed architecture to that of mitotic chromosomes. Here we provide additional insights and details into the coiled nucleosome chromosome architectures. We build on the defined chromosomes time-dependent structures in an effort to probe their dynamics. Variants of the coiled chromosome structures, possibly further defining specific regions, are discussed. We propose, based on generalized specific uncoiling of mitotic chromosomes in telophase, large-scale re-organization of interphase chromosomes. Chromosome territories, organized as micron-sized small patches, are constructed, satisfying complex volume considerations. Finally, we unveiled the structures of replicated coiled chromosomes, still attached to centromeres, as part of chromosome architecture. Significance Statement This study places all 46 sequenced human chromosomes, --- correctly filled with nucleosomes and in micron sized chromosome territories - into 10micron (average sized) nuclei. The chromosome architecture used a helical nucleosome coiled structure discerned from cryo-EM tomography, as was recently published ( https://doi.org/10.1073/pnas.2119101119 ). This chromosome architecture was further modeled to dynamic structures, structure variations and chromosome replication centromere complications. Finally, this chromosome architecture was modified to allow seamless transition through the cell cycle.
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7
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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8
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Golov AK, Gavrilov AA. Cohesin Complex: Structure and Principles of Interaction with DNA. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:585-600. [PMID: 38831498 DOI: 10.1134/s0006297924040011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 06/05/2024]
Abstract
Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of cohesin-DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in the not-so-distant future.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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9
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Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R. Sister chromatid cohesion halts DNA loop expansion. Mol Cell 2024; 84:1139-1148.e5. [PMID: 38452765 DOI: 10.1016/j.molcel.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are folded into DNA loops mediated by structural maintenance of chromosomes (SMC) complexes such as cohesin, condensin, and Smc5/6. This organization regulates different DNA-related processes along the cell cycle, such as transcription, recombination, segregation, and DNA repair. During the G2 stage, SMC-mediated DNA loops coexist with cohesin complexes involved in sister chromatid cohesion (SCC). However, the articulation between the establishment of SCC and the formation of SMC-mediated DNA loops along the chromatin remains unknown. Here, we show that SCC is indeed a barrier to cohesin-mediated DNA loop expansion along G2/M Saccharomyces cerevisiae chromosomes.
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Affiliation(s)
- Nathalie Bastié
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Christophe Chapard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Axel Cournac
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Sanae Nejmi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
| | - Henri Mboumba
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Gadal
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Frederic Beckouët
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France.
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10
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Fisher AG. Cell and developmental biology: grand challenges. Front Cell Dev Biol 2024; 12:1377073. [PMID: 38559812 PMCID: PMC10978741 DOI: 10.3389/fcell.2024.1377073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Amanda G. Fisher
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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11
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Ochs F, Green C, Szczurek AT, Pytowski L, Kolesnikova S, Brown J, Gerlich DW, Buckle V, Schermelleh L, Nasmyth KA. Sister chromatid cohesion is mediated by individual cohesin complexes. Science 2024; 383:1122-1130. [PMID: 38452070 DOI: 10.1126/science.adl4606] [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: 10/20/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are organized by loop extrusion and sister chromatid cohesion, both mediated by the multimeric cohesin protein complex. Understanding how cohesin holds sister DNAs together, and how loss of cohesion causes age-related infertility in females, requires knowledge as to cohesin's stoichiometry in vivo. Using quantitative super-resolution imaging, we identified two discrete populations of chromatin-bound cohesin in postreplicative human cells. Whereas most complexes appear dimeric, cohesin that localized to sites of sister chromatid cohesion and associated with sororin was exclusively monomeric. The monomeric stoichiometry of sororin:cohesin complexes demonstrates that sister chromatid cohesion is conferred by individual cohesin rings, a key prediction of the proposal that cohesion arises from the co-entrapment of sister DNAs.
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Affiliation(s)
- Fena Ochs
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Charlotte Green
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sofia Kolesnikova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna Austria
| | - Jill Brown
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daniel Wolfram Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna Austria
| | - Veronica Buckle
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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12
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Pati D. Role of chromosomal cohesion and separation in aneuploidy and tumorigenesis. Cell Mol Life Sci 2024; 81:100. [PMID: 38388697 PMCID: PMC10884101 DOI: 10.1007/s00018-024-05122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Cell division is a crucial process, and one of its essential steps involves copying the genetic material, which is organized into structures called chromosomes. Before a cell can divide into two, it needs to ensure that each newly copied chromosome is paired tightly with its identical twin. This pairing is maintained by a protein complex known as cohesin, which is conserved in various organisms, from single-celled ones to humans. Cohesin essentially encircles the DNA, creating a ring-like structure to handcuff, to keep the newly synthesized sister chromosomes together in pairs. Therefore, chromosomal cohesion and separation are fundamental processes governing the attachment and segregation of sister chromatids during cell division. Metaphase-to-anaphase transition requires dissolution of cohesins by the enzyme Separase. The tight regulation of these processes is vital for safeguarding genomic stability. Dysregulation in chromosomal cohesion and separation resulting in aneuploidy, a condition characterized by an abnormal chromosome count in a cell, is strongly associated with cancer. Aneuploidy is a recurring hallmark in many cancer types, and abnormalities in chromosomal cohesion and separation have been identified as significant contributors to various cancers, such as acute myeloid leukemia, myelodysplastic syndrome, colorectal, bladder, and other solid cancers. Mutations within the cohesin complex have been associated with these cancers, as they interfere with chromosomal segregation, genome organization, and gene expression, promoting aneuploidy and contributing to the initiation of malignancy. In summary, chromosomal cohesion and separation processes play a pivotal role in preserving genomic stability, and aberrations in these mechanisms can lead to aneuploidy and cancer. Gaining a deeper understanding of the molecular intricacies of chromosomal cohesion and separation offers promising prospects for the development of innovative therapeutic approaches in the battle against cancer.
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Affiliation(s)
- Debananda Pati
- Texas Children's Cancer Center, Department of Pediatrics Hematology/Oncology, Molecular and Cellular Biology, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA.
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13
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Richeldi M, Pobegalov G, Higashi TL, Gmurczyk K, Uhlmann F, Molodtsov MI. Mechanical disengagement of the cohesin ring. Nat Struct Mol Biol 2024; 31:23-31. [PMID: 37872232 DOI: 10.1038/s41594-023-01122-4] [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: 11/11/2022] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Cohesin forms a proteinaceous ring that is thought to link sister chromatids by entrapping DNA and counteracting the forces generated by the mitotic spindle. Whether individual cohesins encircle both sister DNAs and how cohesin opposes spindle-generated forces remains unknown. Here we perform force measurements on individual yeast cohesin complexes either bound to DNA or holding together two DNAs. By covalently closing the hinge and Smc3Psm3-kleisin interfaces we find that the mechanical stability of the cohesin ring entrapping DNA is determined by the hinge domain. Forces of ~20 pN disengage cohesin at the hinge and release DNA, indicating that ~40 cohesin molecules are sufficient to counteract known spindle forces. Our findings provide a mechanical framework for understanding how cohesin interacts with sister chromatids and opposes the spindle-generated tension during mitosis, with implications for other force-generating chromosomal processes including transcription and DNA replication.
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Affiliation(s)
- Martina Richeldi
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Georgii Pobegalov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Kamakura Research Laboratories, Chugai Pharmaceutical Co., Kamakura City, Japan
| | - Karolina Gmurczyk
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | - Maxim I Molodtsov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics and Astronomy, University College London, London, UK.
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14
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Nasmyth KA, Lee BG, Roig MB, Löwe J. What AlphaFold tells us about cohesin's retention on and release from chromosomes. eLife 2023; 12:RP88656. [PMID: 37975572 PMCID: PMC10656103 DOI: 10.7554/elife.88656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1's association with two large hook-shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latter's replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1's N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the 20 years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1's NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapl's C-terminal domain. AF also reveals how Scc1's dissociation from Smc3 arises from a distortion of Smc3's CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.
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Affiliation(s)
- Kim A Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Byung-Gil Lee
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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15
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Bhattacharya SA, Dias E, Nieto-Aliseda A, Buschbeck M. The consequences of cohesin mutations in myeloid malignancies. Front Mol Biosci 2023; 10:1319804. [PMID: 38033389 PMCID: PMC10684907 DOI: 10.3389/fmolb.2023.1319804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Recurrent somatic mutations in the genes encoding the chromatin-regulatory cohesin complex and its modulators occur in a wide range of human malignancies including a high frequency in myeloid neoplasms. The cohesin complex has a ring-like structure which can enclose two strands of DNA. A first function for the complex was described in sister chromatid cohesion during metaphase avoiding defects in chromosome segregation. Later studies identified additional functions of the cohesin complex functions in DNA replication, DNA damage response, 3D genome organisation, and transcriptional regulation through chromatin looping. In this review, we will focus on STAG2 which is the most frequently mutated cohesin subunit in myeloid malignancies. STAG2 loss of function mutations are not associated with chromosomal aneuploidies or genomic instability. We hypothesize that this points to changes in gene expression as disease-promoting mechanism and summarize the current state of knowledge on affected genes and pathways. Finally, we discuss potential strategies for targeting cohesion-deficient disease cells.
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Affiliation(s)
- Shubhra Ashish Bhattacharya
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Eve Dias
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Andrea Nieto-Aliseda
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Marcus Buschbeck
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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16
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Rosa C, Singh P, Chen P, Sinha A, Claës A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM. Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite. EMBO Rep 2023; 24:e57090. [PMID: 37592911 PMCID: PMC10561359 DOI: 10.15252/embr.202357090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
The complex life cycle of the human malaria parasite, Plasmodium falciparum, is driven by specific transcriptional programs, but it is unclear how most genes are activated or silenced at specific times. There is an association between transcription and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome-organizing proteins found in metazoans, it has all core components of the cohesin complex. To investigate the role of cohesin in P. falciparum, we functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown during early stages of the intraerythrocytic developmental cycle (IDC) upregulates a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq analyses reveal that during the IDC, SMC3 enrichment at the promoter regions of these genes inversely correlates with gene expression and chromatin accessibility. These data suggest that SMC3 binding contributes to the repression of specific genes until their appropriate time of expression, revealing a new mode of stage-specific gene repression in P. falciparum.
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Affiliation(s)
- Catarina Rosa
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
- Sorbonne Université, Collège Doctoral Complexité du Vivant ED515ParisFrance
| | - Parul Singh
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Patty Chen
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | | | - Artur Scherf
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Jessica M Bryant
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
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17
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Agarwal A, Korsak S, Choudhury A, Plewczynski D. The dynamic role of cohesin in maintaining human genome architecture. Bioessays 2023; 45:e2200240. [PMID: 37603403 DOI: 10.1002/bies.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.
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Affiliation(s)
- Abhishek Agarwal
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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18
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Kaushik A, Than T, Petela NJ, Voulgaris M, Percival C, Daniels P, Rafferty JB, Nasmyth KA, Hu B. Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding. Nat Commun 2023; 14:5929. [PMID: 37739959 PMCID: PMC10516938 DOI: 10.1038/s41467-023-41596-w] [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: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
The ring-shaped cohesin complex is a key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is hindered by Smc3 acetylation. However, the molecular mechanism underlying this inhibition remains mysterious. Here, using Saccharomyces cerevisiae as a model system, we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3's head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.
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Affiliation(s)
- Aditi Kaushik
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Thane Than
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Naomi J Petela
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Charlotte Percival
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter Daniels
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bin Hu
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
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19
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Litwin I, Nowicka M, Markowska K, Maciaszczyk-Dziubińska E, Tomaszewska P, Wysocki R, Kramarz K. ISW1a modulates cohesin distribution in centromeric and pericentromeric regions. Nucleic Acids Res 2023; 51:9101-9121. [PMID: 37486771 PMCID: PMC10516642 DOI: 10.1093/nar/gkad612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Cohesin is a highly conserved, multiprotein complex whose canonical function is to hold sister chromatids together to ensure accurate chromosome segregation. Cohesin association with chromatin relies on the Scc2-Scc4 cohesin loading complex that enables cohesin ring opening and topological entrapment of sister DNAs. To better understand how sister chromatid cohesion is regulated, we performed a proteomic screen in budding yeast that identified the Isw1 chromatin remodeler as a cohesin binding partner. In addition, we found that Isw1 also interacts with Scc2-Scc4. Lack of Isw1 protein, the Ioc3 subunit of ISW1a or Isw1 chromatin remodeling activity resulted in increased accumulation of cohesin at centromeres and pericentromeres, suggesting that ISW1a may promote efficient translocation of cohesin from the centromeric site of loading to neighboring regions. Consistent with the role of ISW1a in the chromatin organization of centromeric regions, Isw1 was found to be recruited to centromeres. In its absence we observed changes in the nucleosomal landscape at centromeres and pericentromeres. Finally, we discovered that upon loss of RSC functionality, ISW1a activity leads to reduced cohesin binding and cohesion defect. Taken together, our results support the notion of a key role of chromatin remodelers in the regulation of cohesin distribution on chromosomes.
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Affiliation(s)
- Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Małgorzata Nowicka
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Katarzyna Markowska
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubińska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Paulina Tomaszewska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Karol Kramarz
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
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20
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Elias M, Gani S, Lerner Y, Yamin K, Tor C, Patel A, Matityahu A, Dessau M, Qvit N, Onn I. Developing a peptide to disrupt cohesin head domain interactions. iScience 2023; 26:107498. [PMID: 37664609 PMCID: PMC10470313 DOI: 10.1016/j.isci.2023.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Cohesin mediates the 3-D structure of chromatin and is involved in maintaining genome stability and function. The cohesin core comprises Smc1 and Smc3, elongated-shaped proteins that dimerize through globular domains at their edges, called head and hinge. ATP binding to the Smc heads induces their dimerization and the formation of two active sites, while ATP hydrolysis results in head disengagement. This ATPase cycle is essential for driving cohesin activity. We report on the development of the first cohesin-inhibiting peptide (CIP). The CIP binds Smc3 in vitro and inhibits the ATPase activity of the holocomplex. Treating yeast cells with the CIP prevents cohesin's tethering activity and, interestingly, leads to the accumulation of cohesin on chromatin. CIP3 also affects cohesin activity in human cells. Altogether, we demonstrate the power of peptides to inhibit cohesin in cells and discuss the potential application of CIPs as a therapeutic approach.
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Affiliation(s)
- Maria Elias
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Samar Gani
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yana Lerner
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Katreen Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Chen Tor
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Adarsh Patel
- The Lab for Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Moshe Dessau
- The Lab for Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Nir Qvit
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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21
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Pobegalov G, Chu LY, Peters JM, Molodtsov MI. Single cohesin molecules generate force by two distinct mechanisms. Nat Commun 2023; 14:3946. [PMID: 37402740 DOI: 10.1038/s41467-023-39696-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Spatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
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Affiliation(s)
- Georgii Pobegalov
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Lee-Ya Chu
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria
| | - Maxim I Molodtsov
- The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria.
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22
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Borrie MS, Kraycer PM, Gartenberg MR. Transcription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo. Mol Cell Biol 2023; 43:254-268. [PMID: 37178128 PMCID: PMC10251789 DOI: 10.1080/10985549.2023.2199660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cohesin is a central architectural element of chromosomes that regulates numerous DNA-based events. The complex holds sister chromatids together until anaphase onset and organizes individual chromosomal DNAs into loops and self-associating domains. Purified cohesin diffuses along DNA in an ATP-independent manner but can be propelled by transcribing RNA polymerase. In conjunction with a cofactor, the complex also extrudes DNA loops in an ATP-dependent manner. In this study we examine transcription-driven translocation of cohesin under various conditions in yeast. To this end, obstacles of increasing size were tethered to DNA to act as roadblocks to complexes mobilized by an inducible gene. The obstacles were built from a GFP-lacI core fused to one or more mCherries. A chimera with four mCherries blocked cohesin passage in late G1. During M phase, the threshold barrier depended on the state of cohesion: non-cohesive complexes were also blocked by four mCherries whereas cohesive complexes were blocked by as few as three mCherries. Furthermore cohesive complexes that were stalled at obstacles, in turn, blocked the passage of non-cohesive complexes. That synthetic barriers capture mobilized cohesin demonstrates that transcription-driven complexes translocate processively in vivo. Together, this study reveals unexplored limitations to cohesin movement on chromosomes.
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Affiliation(s)
- Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Paul M. Kraycer
- Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Member of The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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23
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Taschner M, Gruber S. DNA segment capture by Smc5/6 holocomplexes. Nat Struct Mol Biol 2023; 30:619-628. [PMID: 37012407 DOI: 10.1038/s41594-023-00956-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Three distinct structural maintenance of chromosomes (SMC) complexes facilitate chromosome folding and segregation in eukaryotes, presumably by DNA loop extrusion. How SMCs interact with DNA to extrude loops is not well understood. Among the SMC complexes, Smc5/6 has dedicated roles in DNA repair and preventing a buildup of aberrant DNA junctions. In the present study, we describe the reconstitution of ATP-dependent DNA loading by yeast Smc5/6 rings. Loading strictly requires the Nse5/6 subcomplex which opens the kleisin neck gate. We show that plasmid molecules are topologically entrapped in the kleisin and two SMC subcompartments, but not in the full SMC compartment. This is explained by the SMC compartment holding a looped DNA segment and by kleisin locking it in place when passing between the two flanks of the loop for neck-gate closure. Related segment capture events may provide the power stroke in subsequent DNA extrusion steps, possibly also in other SMC complexes, thus providing a unifying principle for DNA loading and extrusion.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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24
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Choudhary K, Kupiec M. The cohesin complex of yeasts: sister chromatid cohesion and beyond. FEMS Microbiol Rev 2023; 47:6825453. [PMID: 36370456 DOI: 10.1093/femsre/fuac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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25
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Xu X, Yanagida M. Cohesin organization, dynamics, and subdomain functions revealed by genetic suppressor screening. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:61-74. [PMID: 36908173 PMCID: PMC10170060 DOI: 10.2183/pjab.99.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cohesin is a heteropentameric protein complex that contributes to various aspects of chromosome structure and function, such as sister chromatid cohesion, genome compaction, and DNA damage response. Previous studies have provided abundant information on architecture and regional structures of the cohesin complex, but the configuration and structural dynamics of the whole cohesin complex are still largely unknown, partly due to flexibility of its coiled coils. We studied cohesin organization and dynamics using in vivo functional mutation compensation. Specifically, we developed and applied genetic suppressor screening methods to identify second mutations in cohesin complex genes that rescue lethality caused by various site-specific abnormalities in the cohesin complex. Functional analysis of these missense suppressor mutations revealed novel features of cohesin. Here, we summarize recent genetic suppressor screening results and insights into: 1) cohesin's structural organization when holding chromosomal DNAs; 2) interaction between cohesin head-kleisin and hinge; 3) ATP-driven cohesin conformational changes for genome packaging.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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26
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Collier JE, Nasmyth KA. DNA passes through cohesin's hinge as well as its Smc3-kleisin interface. eLife 2022; 11:80310. [PMID: 36094369 PMCID: PMC9467508 DOI: 10.7554/elife.80310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/29/2022] [Indexed: 12/17/2022] Open
Abstract
The ring model proposes that sister chromatid cohesion is mediated by co-entrapment of sister DNAs inside a single tripartite cohesin ring. The model explains how Scc1 cleavage triggers anaphase but has hitherto only been rigorously tested using small circular mini-chromosomes in yeast, where covalently circularizing the ring by crosslinking its three interfaces induces catenation of individual and sister DNAs. If the model applies to real chromatids, then the ring must have a DNA entry gate essential for mitosis. Whether this is situated at the Smc3/Scc1 or Smc1/Smc3 hinge interface is an open question. We have previously demonstrated DNA entrapment by cohesin in vitro (Collier et al., 2020). Here we show that cohesin in fact possesses two DNA gates, one at the Smc3/Scc1 interface and a second at the Smc1/3 hinge. Unlike the Smc3/Scc1 interface, passage of DNAs through SMC hinges depends on both Scc2 and Scc3, a pair of regulatory subunits necessary for entrapment in vivo. This property together with the lethality caused by locking this interface but not that between Smc3 and Scc1 in vivo suggests that passage of DNAs through the hinge is essential for building sister chromatid cohesion. Passage of DNAs through the Smc3/Scc1 interface is necessary for cohesin’s separase-independent release from chromosomes and may therefore largely serve as an exit gate.
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Affiliation(s)
- James E Collier
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Bock FP, Liu HW, Anchimiuk A, Diebold-Durand ML, Gruber S. A joint-ParB interface promotes Smc DNA recruitment. Cell Rep 2022; 40:111273. [PMID: 36044845 PMCID: PMC9449133 DOI: 10.1016/j.celrep.2022.111273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomes readily unlink and segregate to daughter cells during cell division, highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes promote DNA organization by loop extrusion. In most bacteria, chromosome folding initiates at dedicated start sites marked by the ParB/parS partition complexes. Whether SMC complexes recognize a specific DNA structure in the partition complex or a protein component is unclear. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate foreign chromosomes. Using chimeric proteins and chemical cross-linking, we find that ParB directly binds the Smc subunit. We map an interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex, presumably to initiate DNA loop extrusion. The bacterial DNA-binding protein ParB interacts with the condensin-like Smc-ScpAB Genetic mapping and structure predictions reveal an Smc joint-ParB binding interface Mutating the binding interface hampers Smc recruitment but not other ParB functions ParB and Smc-ScpAB form a transplantable unit for chromosome segregation in bacteria
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Affiliation(s)
- Florian P Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Anchimiuk
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Marie-Laure Diebold-Durand
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland.
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28
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Hallett ST, Campbell Harry I, Schellenberger P, Zhou L, Cronin N, Baxter J, Etheridge T, Murray J, Oliver A. Cryo-EM structure of the Smc5/6 holo-complex. Nucleic Acids Res 2022; 50:9505-9520. [PMID: 35993814 PMCID: PMC9458440 DOI: 10.1093/nar/gkac692] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023] Open
Abstract
The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells - providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the 'W-loop' of Smc4 or 'F-loop' of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes.
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Affiliation(s)
- Stephen T Hallett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Isabella Campbell Harry
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Pascale Schellenberger
- Electron Microscopy Imaging Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Nora B Cronin
- London Consortium for CryoEM (LonCEM) Facility, The Francis Crick Institute, London, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Thomas J Etheridge
- Correspondence may also be addressed to Thomas J. Etheridge. Tel: +44 1273 678123;
| | - Johanne M Murray
- Correspondence may also be addressed to Johanne M. Murray. Tel: +44 1273 877191;
| | - Antony W Oliver
- To whom correspondence should be addressed. Tel: +44 1273 678349;
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29
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Cohesin ATPase activities regulate DNA binding and coiled-coil configuration. Proc Natl Acad Sci U S A 2022; 119:e2208004119. [PMID: 35939705 PMCID: PMC9388089 DOI: 10.1073/pnas.2208004119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cohesin is a heteropentameric protein complex consisting of two structural maintenance of chromosomes (SMC) subunits and three non-SMC subunits. The two SMC subunits form a heterodimer with an ATPase head and hinge that are connected by long coiled coils. Isolation of ATPase mutants followed by comprehensive identification of suppressor mutations in SMC subunits that can bypass ATPase defects was performed. Locations and properties of mutant alleles reflect how ATPase activities could be compromised by structural adaptation. ATP-driven conformational changes may enhance DNA anchoring by the head, alter interactions of coiled coils at the head with other subunits for DNA to go through, and fold/extend coiled coils near break sites around midpoint to bring together DNA elements far from each other. The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs.
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30
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Mattingly M, Seidel C, Muñoz S, Hao Y, Zhang Y, Wen Z, Florens L, Uhlmann F, Gerton JL. Mediator recruits the cohesin loader Scc2 to RNA Pol II-transcribed genes and promotes sister chromatid cohesion. Curr Biol 2022; 32:2884-2896.e6. [PMID: 35654035 PMCID: PMC9286023 DOI: 10.1016/j.cub.2022.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/07/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022]
Abstract
The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 functions as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate the localization of the Scc2-Scc4 cohesin loader. Here, we identify a broad range of Scc2-chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in the recruitment of the cohesin loader. We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and the decreased binding of Scc2 at RNA Pol II-transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in the direct recruitment of Scc2 to RNA Pol II-transcribed genes.
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Affiliation(s)
- Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chris Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zhihui Wen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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31
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A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence. Proc Natl Acad Sci U S A 2022; 119:e2119101119. [PMID: 35749363 PMCID: PMC9245672 DOI: 10.1073/pnas.2119101119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cryopreservation of the nuclear interior allows a large-scale interphase chromosome structure—present throughout the nucleus—to be seen in its native state by electron tomography. This structure appears as a coiled chain of nucleosomes, wrapped like a Slinky toy. This coiled structure can be further used to explain the enigmatic architectures of polytene and lampbrush chromosomes. In addition, this new structure can further be organized as chromosome territories: for example, all 46 human interphase chromosomes easily fit into a 10-μm-diameter nucleus. Thus, interphase chromosomes can be unified into a flexibly defined structure. Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman et al., eLife 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.
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32
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Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem 2022; 298:102117. [PMID: 35691341 PMCID: PMC9283939 DOI: 10.1016/j.jbc.2022.102117] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022] Open
Abstract
In mammalian organisms, enhancers can regulate transcription from great genomic distances. How enhancers affect distal gene expression has been a major question in the field of gene regulation. One model to explain how enhancers communicate with their target promoters, the chromatin looping model, posits that enhancers and promoters come in close spatial proximity to mediate communication. Chromatin looping has been broadly accepted as a means for enhancer–promoter communication, driven by accumulating in vitro and in vivo evidence. The genome is now known to be folded into a complex 3D arrangement, created and maintained in part by the interplay of the Cohesin complex and the DNA-binding protein CTCF. In the last few years, however, doubt over the relationship between looping and transcriptional activation has emerged, driven by studies finding that only a modest number of genes are perturbed with acute degradation of looping machinery components. In parallel, newer models describing distal enhancer action have also come to prominence. In this article, we explore the emergence and development of the looping model as a means for enhancer–promoter communication and review the contrasting evidence between historical gene-specific and current global data for the role of chromatin looping in transcriptional regulation. We also discuss evidence for alternative models to chromatin looping and their support in the literature. We suggest that, while there is abundant evidence for chromatin looping as a major mechanism for enhancer function, enhancer–promoter communication is likely mediated by more than one mechanism in an enhancer- and context-dependent manner.
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Affiliation(s)
- Tessa M Popay
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R Dixon
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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33
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Shaltiel IA, Datta S, Lecomte L, Hassler M, Kschonsak M, Bravo S, Stober C, Ormanns J, Eustermann S, Haering CH. A hold-and-feed mechanism drives directional DNA loop extrusion by condensin. Science 2022; 376:1087-1094. [PMID: 35653469 DOI: 10.1126/science.abm4012] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop transiently in two separate chambers. Single-molecule imaging and cryo-electron microscopy suggest a putative power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon adenosine triphosphate binding, whereas the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of "motor" and "anchor" chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the SMC reaction cycle determines the directionality of DNA loop extrusion.
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Affiliation(s)
- Indra A Shaltiel
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sumanjit Datta
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Léa Lecomte
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Markus Hassler
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Catherine Stober
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jenny Ormanns
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany
| | | | - Christian H Haering
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, EMBL, 69117 Heidelberg, Germany
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34
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Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
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Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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35
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Abstract
The significance of this proposed mitotic chromosome architecture is that a specific, sequenced chromosome, human chromosome 10, can be built into a specific architecture that accounts for the dimensional values and cytological descriptions. Since this molecular architecture is an extension of the interphase chromosome structure, a coiling of the 11-nm nucleosome fiber with further coiling, a unifying molecular structure motif is present throughout the entire mitotic cycle, interphase through mitosis. A molecular architecture is proposed for a representative mitotic chromosome, human chromosome 10. This architecture is built on an interphase chromosome structure based on cryo-electron microscopy (cryo-EM) cellular tomography [J. Sedat et al., Proc. Natl. Acad. Sci. U.S.A., in press], thus unifying chromosome structure throughout the complete mitotic cycle. The basic organizational principle for mitotic chromosomes is specific coiling of the 11-nm nucleosome fiber into large scale, ∼200-nm interphase structures, a Slinky [https://en.wikipedia.org/wiki/Slinky; motif cited in S. Bowerman et al., eLife 10, e65587 (2021)], then further modified with subsequent additional coiling for the final mitotic chromosome structure. The final mitotic chromosome architecture accounts for the dimensional values as well as the well-known cytological configurations. In addition, proof is experimentally provided by digital PCR technology that G1 T cell nuclei are diploid with one DNA molecule per chromosome. Many nucleosome linker DNA sequences, the promotors and enhancers, are suggestive of optimal exposure on the surfaces of the large-scale coils.
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36
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Nomidis SK, Carlon E, Gruber S, Marko JF. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nucleic Acids Res 2022; 50:4974-4987. [PMID: 35474142 PMCID: PMC9122525 DOI: 10.1093/nar/gkac268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 12/19/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced ‘power stroke’ to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site (‘safety belt’), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.
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Affiliation(s)
- Stefanos K Nomidis
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
| | - John F Marko
- To whom correspondence should be addressed. Tel: +1 847 467 1276; Fax: +1 847 467 1380;
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37
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A walk through the SMC cycle: From catching DNAs to shaping the genome. Mol Cell 2022; 82:1616-1630. [PMID: 35477004 DOI: 10.1016/j.molcel.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes such as transcription, recombination, repair, and mitosis.
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38
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Intersubunit and intrasubunit interactions driving the MukBEF ATPase. J Biol Chem 2022; 298:101964. [PMID: 35452680 PMCID: PMC9127220 DOI: 10.1016/j.jbc.2022.101964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/23/2022] Open
Abstract
MukBEF, a structural maintenance of chromosome-like protein complex consisting of an ATPase, MukB, and two interacting subunits, MukE and MukF, functions as the bacterial condensin. It is likely that MukBEF compacts DNA via an ATP hydrolysis-dependent DNA loop-extrusion reaction similar to that demonstrated for the yeast structural maintenance of chromosome proteins condensin and cohesin. MukB also interacts with the ParC subunit of the cellular chromosomal decatenase topoisomerase IV, an interaction that is required for proper chromosome condensation and segregation in Escherichia coli, although it suppresses the MukB ATPase activity. Other structural determinants and interactions that regulate the ATPase activity of MukBEF are not clear. Here, we have investigated the MukBEF ATPase activity, identifying intersubunit and intrasubunit interactions by protein-protein crosslinking and site-specific mutagenesis. We show that interactions between the hinge of MukB and its neck region are essential for the ATPase activity, that the ParC subunit of topoisomerase IV inhibits the MukB ATPase by preventing this interaction, that MukE interaction with DNA is likely essential for viability, and that interactions between MukF and the MukB neck region are necessary for ATPase activity and viability.
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39
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Lee BG, Rhodes J, Löwe J. Clamping of DNA shuts the condensin neck gate. Proc Natl Acad Sci U S A 2022; 119:e2120006119. [PMID: 35349345 PMCID: PMC9168836 DOI: 10.1073/pnas.2120006119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/24/2022] [Indexed: 01/05/2023] Open
Abstract
SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolyzed. The DNA is clamped within a compartment that has been reported previously in other structural maintenance of chromosomes (SMC) complexes, including Rad50, cohesin, and MukBEF. With the caveat of important differences, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolyzing ATP and translocating DNA.
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Affiliation(s)
- Byung-Gil Lee
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - James Rhodes
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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40
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Xu X, Kanai R, Wang L, Yanagida M. Single amino acid substitutions in hydrophobic cores at a head-coiled coil junction region of cohesin facilitate its release of DNA during anaphase. Open Biol 2022; 12:210275. [PMID: 35472286 PMCID: PMC9042573 DOI: 10.1098/rsob.210275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
Cohesin holds sister chromatids together and is cleaved by separase/Cut1 to release DNA during the transition from mitotic metaphase to anaphase. The cohesin complex consists of heterodimeric structural maintenance of chromosomes (SMC) subunits (Psm1 and Psm3), which possess a head and a hinge, separated by long coiled coils. Non-SMC subunits (Rad21, Psc3 and Mis4) bind to the SMC heads. Kleisin/Rad21's N-terminal domain (Rad21-NTD) interacts with Psm3's head-coiled coil junction (Psm3-HCJ). Spontaneous mutations that rescued the cleavage defects in temperature-sensitive (ts) separase mutants were identified in the interaction interface, but the underlying mechanism is yet to be understood. Here, we performed site-directed random mutagenesis to introduce single amino acid substitutions in Psm3-HCJ and Rad21-NTD, and then identified 300 mutations that rescued the cohesin-releasing defects in a separase ts mutant. Mutational analysis indicated that the amino acids involved in hydrophobic cores (which may be in close contact) in Psm3-HCJ and Rad21-NTD are hotspots, since 80 mutations (approx. 27%) were mapped in these locations. Properties of these substitutions indicate that they destabilize the interaction between the Psm3 head and Rad21-NTD. Thus, they may facilitate sister chromatid separation in a cleavage-independent way through cohesin structural re-arrangement.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Ryuta Kanai
- Institute of Quantitative Biosciences, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Li Wang
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
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41
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Bürmann F, Funke LFH, Chin JW, Löwe J. Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites. Mol Cell 2021; 81:4891-4906.e8. [PMID: 34739874 PMCID: PMC8669397 DOI: 10.1016/j.molcel.2021.10.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
| | - Louise F H Funke
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jason W Chin
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
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42
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Houlard M, Cutts EE, Shamim MS, Godwin J, Weisz D, Presser Aiden A, Lieberman Aiden E, Schermelleh L, Vannini A, Nasmyth K. MCPH1 inhibits Condensin II during interphase by regulating its SMC2-Kleisin interface. eLife 2021; 10:e73348. [PMID: 34850681 PMCID: PMC8673838 DOI: 10.7554/elife.73348] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Dramatic change in chromosomal DNA morphology between interphase and mitosis is a defining features of the eukaryotic cell cycle. Two types of enzymes, namely cohesin and condensin confer the topology of chromosomal DNA by extruding DNA loops. While condensin normally configures chromosomes exclusively during mitosis, cohesin does so during interphase. The processivity of cohesin's loop extrusion during interphase is limited by a regulatory factor called WAPL, which induces cohesin to dissociate from chromosomes via a mechanism that requires dissociation of its kleisin from the neck of SMC3. We show here that a related mechanism may be responsible for blocking condensin II from acting during interphase. Cells derived from patients affected by microcephaly caused by mutations in the MCPH1 gene undergo premature chromosome condensation. We show that deletion of Mcph1 in mouse embryonic stem cells unleashes an activity of condensin II that triggers formation of compact chromosomes in G1 and G2 phases, accompanied by enhanced mixing of A and B chromatin compartments, and this occurs even in the absence of CDK1 activity. Crucially, inhibition of condensin II by MCPH1 depends on the binding of a short linear motif within MCPH1 to condensin II's NCAPG2 subunit. MCPH1's ability to block condensin II's association with chromatin is abrogated by the fusion of SMC2 with NCAPH2, hence may work by a mechanism similar to cohesin. Remarkably, in the absence of both WAPL and MCPH1, cohesin and condensin II transform chromosomal DNAs of G2 cells into chromosomes with a solenoidal axis.
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Affiliation(s)
- Martin Houlard
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Muhammad S Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Medical Scientist Training Program, Baylor College of Medicine, Department of Bioengineering, Rice UniversityHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Jonathan Godwin
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Aviva Presser Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | | | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
- Human TechnopoleMilanItaly
| | - Kim Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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43
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Abstract
Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions.
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Affiliation(s)
- Rajarshi P Ghosh
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
| | - Barbara J Meyer
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
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44
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Smc5/6, an atypical SMC complex with two RING-type subunits. Biochem Soc Trans 2021; 48:2159-2171. [PMID: 32964921 DOI: 10.1042/bst20200389] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023]
Abstract
The Smc5/6 complex plays essential roles in chromosome segregation and repair, by promoting disjunction of sister chromatids. The core of the complex is constituted by an heterodimer of Structural Maintenance of Chromosomes (SMC) proteins that use ATP hydrolysis to dynamically associate with and organize chromosomes. In addition, the Smc5/6 complex contains six non-SMC subunits. Remarkably, and differently to other SMC complexes, the Nse1 and Nse2 subunits contain RING-type domains typically found in E3 ligases, pointing to the capacity to regulate other proteins and complexes through ubiquitin-like modifiers. Nse2 codes for a C-terminal SP-RING domain with SUMO ligase activity, assisting Smc5/6 functions in chromosome segregation through sumoylation of several chromosome-associated proteins. Nse1 codes for a C-terminal NH-RING domain and, although it has been proposed to have ubiquitin ligase activity, no Smc5/6-dependent ubiquitylation target has been described to date. Here, we review the function of the two RING domains of the Smc5/6 complex in the broader context of SMC complexes as global chromosome organizers of the genome.
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45
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Anchimiuk A, Lioy VS, Bock FP, Minnen A, Boccard F, Gruber S. A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis. eLife 2021; 10:65467. [PMID: 34346312 PMCID: PMC8357415 DOI: 10.7554/elife.65467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
SMC complexes are widely conserved ATP-powered DNA-loop-extrusion motors indispensable for organizing and faithfully segregating chromosomes. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength, and the distribution of Smc loading sites, the residency time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.
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Affiliation(s)
- Anna Anchimiuk
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Florian Patrick Bock
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anita Minnen
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Frederic Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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46
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Taschner M, Basquin J, Steigenberger B, Schäfer IB, Soh Y, Basquin C, Lorentzen E, Räschle M, Scheltema RA, Gruber S. Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. EMBO J 2021; 40:e107807. [PMID: 34191293 PMCID: PMC8327961 DOI: 10.15252/embj.2021107807] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex. We found that the Nse5/6 sub-complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross-linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross-linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non-productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
| | | | - Barbara Steigenberger
- Max Planck Institute of BiochemistryMartinsriedGermany
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Netherlands Proteomics CentreUtrechtThe Netherlands
| | | | - Young‐Min Soh
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
| | | | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Markus Räschle
- Molecular GeneticsUniversity of KaiserslauternKaiserslauternGermany
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Netherlands Proteomics CentreUtrechtThe Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
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47
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Higashi TL, Pobegalov G, Tang M, Molodtsov MI, Uhlmann F. A Brownian ratchet model for DNA loop extrusion by the cohesin complex. eLife 2021; 10:e67530. [PMID: 34309513 PMCID: PMC8313234 DOI: 10.7554/elife.67530] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin's heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Minzhe Tang
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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48
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Petela NJ, Gonzalez Llamazares A, Dixon S, Hu B, Lee BG, Metson J, Seo H, Ferrer-Harding A, Voulgaris M, Gligoris T, Collier J, Oh BH, Löwe J, Nasmyth KA. Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes. eLife 2021; 10:e67268. [PMID: 34259632 PMCID: PMC8279761 DOI: 10.7554/elife.67268] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/21/2021] [Indexed: 01/01/2023] Open
Abstract
Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement of cohesin's Smc1 and Smc3 head domains. Scc2's replacement by Pds5 abrogates cohesin's ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1's ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin's coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1's hinge that alters how Scc2 and Pds5 interact with Smc1's hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin's hinge, which in turn requires coiled coil folding.
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Affiliation(s)
- Naomi J Petela
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | | | - Sarah Dixon
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Bin Hu
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Byung-Gil Lee
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Jean Metson
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Heekyo Seo
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
| | | | | | - Thomas Gligoris
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - James Collier
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
| | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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49
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SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization. Biochem J 2021; 478:2555-2569. [PMID: 34109974 PMCID: PMC8286825 DOI: 10.1042/bcj20210278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an epigenetic regulator that mediates gene expression silencing at targeted sites across the genome. Our current understanding of SMCHD1's molecular mechanism, and how substitutions within SMCHD1 lead to the diseases, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS), are only emerging. Recent structural studies of its two component domains - the N-terminal ATPase and C-terminal SMC hinge - suggest that dimerization of each domain plays a central role in SMCHD1 function. Here, using biophysical techniques, we demonstrate that the SMCHD1 ATPase undergoes dimerization in a process that is dependent on both the N-terminal UBL (Ubiquitin-like) domain and ATP binding. We show that neither the dimerization event, nor the presence of a C-terminal extension past the transducer domain, affect SMCHD1's in vitro catalytic activity as the rate of ATP turnover remains comparable to the monomeric protein. We further examined the functional importance of the N-terminal UBL domain in cells, revealing that its targeted deletion disrupts the localization of full-length SMCHD1 to chromatin. These findings implicate UBL-mediated SMCHD1 dimerization as a crucial step for chromatin interaction, and thereby for promoting SMCHD1-mediated gene silencing.
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50
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Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol 2021; 22:445-464. [PMID: 33767413 DOI: 10.1038/s41580-021-00349-7] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/02/2023]
Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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