1
|
Diman A, Panis G, Castrogiovanni C, Prados J, Baechler B, Strubin M. Human Smc5/6 recognises transcription-generated positive DNA supercoils. Nat Commun 2024; 15:7805. [PMID: 39242537 PMCID: PMC11379904 DOI: 10.1038/s41467-024-50646-w] [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: 05/17/2023] [Accepted: 07/18/2024] [Indexed: 09/09/2024] Open
Abstract
Beyond its essential roles in ensuring faithful chromosome segregation and genomic stability, the human Smc5/6 complex acts as an antiviral factor. It binds to and impedes the transcription of extrachromosomal DNA templates; an ability which is lost upon integration of the DNA into the chromosome. How the complex distinguishes among different DNA templates is unknown. Here we show that, in human cells, Smc5/6 preferentially binds to circular rather than linear extrachromosomal DNA. We further demonstrate that the transcriptional process, per se, and particularly the accumulation of DNA secondary structures known to be substrates for topoisomerases, is responsible for Smc5/6 recruitment. More specifically, we find that in vivo Smc5/6 binds to positively supercoiled DNA. Those findings, in conjunction with our genome-wide Smc5/6 binding analysis showing that Smc5/6 localizes at few but highly transcribed chromosome loci, not only unveil a previously unforeseen role of Smc5/6 in DNA topology management during transcription but highlight the significance of sensing DNA topology as an antiviral defense mechanism.
Collapse
Affiliation(s)
- Aurélie Diman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland.
- Geneva Centre for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Geneva 4, Switzerland.
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
- Geneva Centre for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
| | - Cédric Castrogiovanni
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
| | - Julien Prados
- Bioinformatics Support Platform, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
| | - Bastien Baechler
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
- Geneva Centre for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
| | - Michel Strubin
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
- Geneva Centre for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
| |
Collapse
|
2
|
Irvin EM, Wang H. Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA. Curr Opin Struct Biol 2024; 87:102863. [PMID: 38879921 DOI: 10.1016/j.sbi.2024.102863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
Defining the molecular mechanisms by which genome maintenance proteins dynamically associate with and process DNA is essential to understand the potential avenues by which these stabilizing mechanisms are disrupted. Single-molecule fluorescence imaging (SMFI) of protein dynamics on extended DNA has greatly expanded our ability to accomplish this, as it captures singular biomolecular interactions - in all their complexity and diversity - without relying on ensemble-averaging of bulk protein activity as most traditional biochemical techniques must do. In this review, we discuss how SMFI studies with extended DNA have substantially contributed to genome stability research over the past two years.
Collapse
Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
3
|
Palek M, Palkova N, Kleiblova P, Kleibl Z, Macurek L. RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin. Nucleic Acids Res 2024; 52:7687-7703. [PMID: 38884202 PMCID: PMC11260465 DOI: 10.1093/nar/gkae499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
RAD18 is an E3 ubiquitin ligase that prevents replication fork collapse by promoting DNA translesion synthesis and template switching. Besides this classical role, RAD18 has been implicated in homologous recombination; however, this function is incompletely understood. Here, we show that RAD18 is recruited to DNA lesions by monoubiquitination of histone H2A at K15 and counteracts accumulation of 53BP1. Super-resolution microscopy revealed that RAD18 localizes to the proximity of DNA double strand breaks and limits the distribution of 53BP1 to the peripheral chromatin nanodomains. Whereas auto-ubiquitination of RAD18 mediated by RAD6 inhibits its recruitment to DNA breaks, interaction with SLF1 promotes RAD18 accumulation at DNA breaks in the post-replicative chromatin by recognition of histone H4K20me0. Surprisingly, suppression of 53BP1 function by RAD18 is not involved in homologous recombination and rather leads to reduction of non-homologous end joining. Instead, we provide evidence that RAD18 promotes HR repair by recruiting the SMC5/6 complex to DNA breaks. Finally, we identified several new loss-of-function mutations in RAD18 in cancer patients suggesting that RAD18 could be involved in cancer development.
Collapse
Affiliation(s)
- Matous Palek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Natalie Palkova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
| |
Collapse
|
4
|
Brahmachari S, Tripathi S, Onuchic JN, Levine H. Nucleosomes play a dual role in regulating transcription dynamics. Proc Natl Acad Sci U S A 2024; 121:e2319772121. [PMID: 38968124 PMCID: PMC11252751 DOI: 10.1073/pnas.2319772121] [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: 11/10/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024] Open
Abstract
Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional stiffness of chromatin compared to bare DNA and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design.
Collapse
Affiliation(s)
| | - Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX77005
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Biosciences, Rice University, Houston, TX77005
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
| |
Collapse
|
5
|
Tan W, Park JV, Venugopal H, Lou JQ, Dias PS, Baldoni PL, Dite T, Moon KW, Keenan CR, Gurzau AD, Leis A, Yousef J, Vaibhav V, Dagley LF, Ang CS, Corso L, Davidovich C, Vervoort SJ, Smyth GK, Blewitt ME, Allan RS, Hinde E, D'Arcy S, Ryu JK, Shakeel S. MORC2 phosphorylation fine tunes its DNA compaction activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600912. [PMID: 38979330 PMCID: PMC11230365 DOI: 10.1101/2024.06.27.600912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Variants in the poorly characterised oncoprotein, MORC2, a chromatin remodelling ATPase, lead to defects in epigenetic regulation and DNA damage response. The C-terminal domain (CTD) of MORC2, frequently phosphorylated in DNA damage, promotes cancer progression, but its role in chromatin remodelling remains unclear. Here, we report a molecular characterisation of full-length, phosphorylated MORC2, demonstrating its preference for binding open chromatin and functioning as a DNA sliding clamp. We identified a phosphate interacting motif within the CTD that dictates ATP hydrolysis rate and cooperative DNA binding. The DNA binding impacts several structural domains within the ATPase region. We provide the first visual proof that MORC2 induces chromatin remodelling through ATP hydrolysis-dependent DNA compaction, regulated by its phosphorylation state. These findings highlight phosphorylation of MORC2 CTD as a key modulator of chromatin remodelling, presenting it as a potential therapeutic target.
Collapse
|
6
|
Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
Collapse
Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| |
Collapse
|
7
|
Haarhuis JHI, Rowland BD. Plot twists and cutting corners with atypical SMCs. Mol Cell 2024; 84:814-815. [PMID: 38458170 DOI: 10.1016/j.molcel.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
In this issue of Molecular Cell, two papers provide insight into atypical structural maintenance of chromosomes protein complexes (SMCs). Jeppsson et al.1 link Smc5/6 to supercoiled DNA, and Roisné-Hamelin et al.2 show how Wadjet SMC bends and cleaves invading DNAs.
Collapse
Affiliation(s)
- Judith H I Haarhuis
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
| |
Collapse
|