1
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Thu YM. Multifaceted roles of SUMO in DNA metabolism. Nucleus 2024; 15:2398450. [PMID: 39287196 PMCID: PMC11409511 DOI: 10.1080/19491034.2024.2398450] [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: 06/26/2024] [Revised: 08/16/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Sumoylation, a process in which SUMO (small ubiquitin like modifier) is conjugated to target proteins, emerges as a post-translational modification that mediates protein-protein interactions, protein complex assembly, and localization of target proteins. The coordinated actions of SUMO ligases, proteases, and SUMO-targeted ubiquitin ligases determine the net result of sumoylation. It is well established that sumoylation can somewhat promiscuously target proteins in groups as well as selectively target individual proteins. Through changing protein dynamics, sumoylation orchestrates multi-step processes in chromatin biology. Sumoylation influences various steps of mitosis, DNA replication, DNA damage repair, and pathways protecting chromosome integrity. This review highlights examples of SUMO-regulated nuclear processes to provide mechanistic views of sumoylation in DNA metabolism.
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Affiliation(s)
- Yee Mon Thu
- Department of Biology, Colby College, Waterville, ME, USA
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2
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Kendek A, Sandron A, Lambooij JP, Colmenares SU, Pociunaite SM, Gooijers I, de Groot L, Karpen GH, Janssen A. DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5. Nucleic Acids Res 2024:gkae775. [PMID: 39258543 DOI: 10.1093/nar/gkae775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/12/2024] Open
Abstract
Cells employ diverse strategies to repair double-strand breaks (DSBs), a dangerous form of DNA damage that threatens genome integrity. Eukaryotic nuclei consist of different chromatin environments, each displaying distinct molecular and biophysical properties that can significantly influence the DSB-repair process. DSBs arising in the compact and silenced heterochromatin domains have been found to move to the heterochromatin periphery in mouse and Drosophila to prevent aberrant recombination events. However, it is poorly understood how chromatin components, such as histone post-translational modifications, contribute to these DSB movements within heterochromatin. Using irradiation as well as locus-specific DSB induction in Drosophila tissues and cultured cells, we find enrichment of histone H3 lysine 9 acetylation (H3K9ac) at DSBs in heterochromatin but not euchromatin. We find this increase is mediated by the histone acetyltransferase dGcn5, which rapidly localizes to heterochromatic DSBs. Moreover, we demonstrate that in the absence of dGcn5, heterochromatic DSBs display impaired recruitment of the SUMO E3 ligase Nse2/Qjt and fail to relocate to the heterochromatin periphery to complete repair. In summary, our results reveal a previously unidentified role for dGcn5 and H3K9ac in heterochromatic DSB repair and underscore the importance of differential chromatin responses at heterochromatic and euchromatic DSBs to promote safe repair.
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Affiliation(s)
- Apfrida Kendek
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Arianna Sandron
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Jan-Paul Lambooij
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Serafin U Colmenares
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, Berkeley, California, USA
| | - Severina M Pociunaite
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Iris Gooijers
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Lars de Groot
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Gary H Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, Berkeley, California, USA
- Division of Biological Sciences and the Environment, Lawrence Berkeley National Laboratory, CA 94720, Berkeley, California, USA
| | - Aniek Janssen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
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3
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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.
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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
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4
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Su XA, Stopsack KH, Schmidt DR, Ma D, Li Z, Scheet PA, Penney KL, Lotan TL, Abida W, DeArment EG, Lu K, Janas T, Hu S, Vander Heiden MG, Loda M, Boselli M, Amon A, Mucci LA. RAD21 promotes oncogenesis and lethal progression of prostate cancer. Proc Natl Acad Sci U S A 2024; 121:e2405543121. [PMID: 39190349 PMCID: PMC11388324 DOI: 10.1073/pnas.2405543121] [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: 03/18/2024] [Accepted: 07/12/2024] [Indexed: 08/28/2024] Open
Abstract
Higher levels of aneuploidy, characterized by imbalanced chromosome numbers, are associated with lethal progression in prostate cancer. However, how aneuploidy contributes to prostate cancer aggressiveness remains poorly understood. In this study, we assessed in patients which genes on chromosome 8q, one of the most frequently gained chromosome arms in prostate tumors, were most strongly associated with long-term risk of cancer progression to metastases and death from prostate cancer (lethal disease) in 403 patients and found the strongest candidate was cohesin subunit gene, RAD21, with an odds ratio of 3.7 (95% CI 1.8, 7.6) comparing the highest vs. lowest tertiles of mRNA expression and adjusting for overall aneuploidy burden and Gleason score, both strong prognostic factors in primary prostate cancer. Studying prostate cancer driven by the TMPRSS2-ERG oncogenic fusion, found in about half of all prostate tumors, we found that increased RAD21 alleviated toxic oncogenic stress and DNA damage caused by oncogene expression. Data from both organoids and patients indicate that increased RAD21 thereby enables aggressive tumors to sustain tumor proliferation, and more broadly suggests one path through which tumors benefit from aneuploidy.
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Affiliation(s)
- Xiaofeng A Su
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD 20817
- Henry M Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817
- Genitourinary Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20817
| | - Konrad H Stopsack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Daniel R Schmidt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115
| | - Duanduan Ma
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Zhe Li
- Division of Genetics, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Paul A Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, TX 77030
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
- Division of Genetics, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21218
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY 10065
| | - Elise G DeArment
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD 20817
- Henry M Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817
| | - Kate Lu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Thomas Janas
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD 20817
- Henry M Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817
| | - Sofia Hu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Matthew G Vander Heiden
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Dana-Farber Cancer Institute, Boston, MA 02115
| | - Massimo Loda
- Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY 10065
| | - Monica Boselli
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- HHMI, Cambridge, MA 02139
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
- Discovery Science, American Cancer Society, Atlanta, GA 30144
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Palek M, Palkova N, Kleiblova P, Kleibl Z, Macurek L. RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin. Nucleic Acids Res 2024; 52:7687-7703. [PMID: 38884202 PMCID: PMC11260465 DOI: 10.1093/nar/gkae499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
RAD18 is an E3 ubiquitin ligase that prevents replication fork collapse by promoting DNA translesion synthesis and template switching. Besides this classical role, RAD18 has been implicated in homologous recombination; however, this function is incompletely understood. Here, we show that RAD18 is recruited to DNA lesions by monoubiquitination of histone H2A at K15 and counteracts accumulation of 53BP1. Super-resolution microscopy revealed that RAD18 localizes to the proximity of DNA double strand breaks and limits the distribution of 53BP1 to the peripheral chromatin nanodomains. Whereas auto-ubiquitination of RAD18 mediated by RAD6 inhibits its recruitment to DNA breaks, interaction with SLF1 promotes RAD18 accumulation at DNA breaks in the post-replicative chromatin by recognition of histone H4K20me0. Surprisingly, suppression of 53BP1 function by RAD18 is not involved in homologous recombination and rather leads to reduction of non-homologous end joining. Instead, we provide evidence that RAD18 promotes HR repair by recruiting the SMC5/6 complex to DNA breaks. Finally, we identified several new loss-of-function mutations in RAD18 in cancer patients suggesting that RAD18 could be involved in cancer development.
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Affiliation(s)
- Matous Palek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Natalie Palkova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
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Collins RRJ, Gee RRF, Sanchez MCH, Tozandehjani S, Bayat T, Breznik B, Lee AK, Peters ST, Connelly JP, Pruett-Miller SM, Roussel MF, Rakheja D, Tillman HS, Potts PR, Fon Tacer K. Melanoma antigens in pediatric medulloblastoma contribute to tumor heterogeneity and species-specificity of group 3 tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594201. [PMID: 38798351 PMCID: PMC11118370 DOI: 10.1101/2024.05.14.594201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Medulloblastoma (MB) is the most malignant childhood brain cancer. Group 3 MB subtype accounts for about 25% of MB diagnoses and is associated with the most unfavorable outcomes. Herein, we report that more than half of group 3 MB tumors express melanoma antigens (MAGEs), which are potential prognostic and therapeutic markers. MAGEs are tumor antigens, expressed in several types of adult cancers and associated with poorer prognosis and therapy resistance; however, their expression in pediatric cancers is mostly unknown. The aim of this study was to determine whether MAGEs are activated in pediatric MB. Methods To determine MAGE frequency in pediatric MB, we obtained formalin-fixed paraffin-embedded tissue (FFPE) samples of 34 patients, collected between 2008 - 2015, from the Children's Medical Center Dallas pathology archives and applied our validated reverse transcription quantitative PCR (RT-qPCR) assay to measure the relative expression of 23 MAGE cancer-testis antigen genes. To validate our data, we analyzed several published datasets from pediatric MB patients and patient-derived orthotopic xenografts, totaling 860 patients. We then examined how MAGE expression affects the growth and oncogenic potential of medulloblastoma cells by CRISPR-Cas9- and siRNA-mediated gene depletion. Results Our RT-qPCR analysis suggested that MAGEs were expressed in group 3/4 medulloblastoma. Further mining of bulk and single-cell RNA-sequencing datasets confirmed that 50-75% of group 3 tumors activate a subset of MAGE genes. Depletion of MAGEAs, B2, and Cs alter MB cell survival, viability, and clonogenic growth due to decreased proliferation and increased apoptosis. Conclusions These results indicate that targeting MAGEs in medulloblastoma may be a potential therapeutic option for group 3 medulloblastomas. Key Points Several Type I MAGE CTAs are expressed in >60% of group 3 MBs. Type I MAGEs affect MB cell proliferation and apoptosis. MAGEs are potential biomarkers and therapeutic targets for group 3 MBs. Importance of the Study This study is the first comprehensive analysis of all Type I MAGE CTAs ( MAGEA , -B , and -C subfamily members) in pediatric MBs. Our results show that more than 60% of group 3 MBs express MAGE genes, which are required for the viability and growth of cells in which they are expressed. Collectively, these data provide novel insights into the antigen landscape of pediatric MBs. The activation of MAGE genes in group 3 MBs presents potential stratifying and therapeutic options. Abstract Figure
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7
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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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8
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Gómez-González B, Aguilera A. Break-induced RNA-DNA hybrids (BIRDHs) in homologous recombination: friend or foe? EMBO Rep 2023; 24:e57801. [PMID: 37818834 DOI: 10.15252/embr.202357801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Double-strand breaks (DSBs) are the most harmful DNA lesions, with a strong impact on cell proliferation and genome integrity. Depending on cell cycle stage, DSBs are preferentially repaired by non-homologous end joining or homologous recombination (HR). In recent years, numerous reports have revealed that DSBs enhance DNA-RNA hybrid formation around the break site. We call these hybrids "break-induced RNA-DNA hybrids" (BIRDHs) to differentiate them from sporadic R-loops consisting of DNA-RNA hybrids and a displaced single-strand DNA occurring co-transcriptionally in intact DNA. Here, we review and discuss the most relevant data about BIRDHs, with a focus on two main questions raised: (i) whether BIRDHs form by de novo transcription after a DSB or by a pre-existing nascent RNA in DNA regions undergoing transcription and (ii) whether they have a positive role in HR or are just obstacles to HR accidentally generated as an intrinsic risk of transcription. We aim to provide a comprehensive view of the exciting and yet unresolved questions about the source and impact of BIRDHs in the cell.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
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9
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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10
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- 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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11
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Stefanova ME, Ing-Simmons E, Stefanov S, Flyamer I, Dorado Garcia H, Schöpflin R, Henssen AG, Vaquerizas JM, Mundlos S. Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters. Cells 2023; 12:2001. [PMID: 37566080 PMCID: PMC10417312 DOI: 10.3390/cells12152001] [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: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
In this study, we delve into the impact of genotoxic anticancer drug treatment on the chromatin structure of human cells, with a particular focus on the effects of doxorubicin. Using Hi-C, ChIP-seq, and RNA-seq, we explore the changes in chromatin architecture brought about by doxorubicin and ICRF193. Our results indicate that physiologically relevant doses of doxorubicin lead to a local reduction in Hi-C interactions in certain genomic regions that contain active promoters, with changes in chromatin architecture occurring independently of Top2 inhibition, cell cycle arrest, and differential gene expression. Inside the regions with decreased interactions, we detected redistribution of RAD21 around the peaks of H3K27 acetylation. Our study also revealed a common structural pattern in the regions with altered architecture, characterized by two large domains separated from each other. Additionally, doxorubicin was found to increase CTCF binding in H3K27 acetylated regions. Furthermore, we discovered that Top2-dependent chemotherapy causes changes in the distance decay of Hi-C contacts, which are driven by direct and indirect inhibitors. Our proposed model suggests that doxorubicin-induced DSBs cause cohesin redistribution, which leads to increased insulation on actively transcribed TAD boundaries. Our findings underscore the significant impact of genotoxic anticancer treatment on the chromatin structure of the human genome.
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Affiliation(s)
- Maria E. Stefanova
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Elizabeth Ing-Simmons
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; (E.I.-S.); (J.M.V.)
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Stefan Stefanov
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany;
- Department of Biology, Chemistry, and Pharmacology, Institute of Biochemistry, Freie Universität Berlin, 14163 Berlin, Germany
| | - Ilya Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland;
| | - Heathcliff Dorado Garcia
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany; (H.D.G.); (A.G.H.)
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany; (H.D.G.); (A.G.H.)
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Juan M. Vaquerizas
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; (E.I.-S.); (J.M.V.)
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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12
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Guo T, Liu M, Chen L, Liu Y, Li L, Li Y, Cao X, Mao Z, Wang W, Yang HQ. Photoexcited cryptochromes interact with ADA2b and SMC5 to promote the repair of DNA double-strand breaks in Arabidopsis. NATURE PLANTS 2023; 9:1280-1290. [PMID: 37488265 DOI: 10.1038/s41477-023-01461-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cryptochromes (CRYs) act as blue-light photoreceptors that regulate development and circadian rhythms in plants and animals and as navigating magnetoreceptors in migratory birds. DNA double-strand breaks (DSBs) are the most serious type of DNA damage and threaten genome stability in all organisms. Although CRYs have been shown to respond to DNA damage, whether and how they participate in DSB repair is not well understood. Here we report that Arabidopsis CRYs promote the repair of DSBs through direct interactions with ADA2b and SMC5 in a blue-light-dependent manner to enhance their interaction. Mutations in CRYs and in ADA2b lead to similar enhanced DNA damage accumulation. In response to DNA damage, CRYs are localized at DSBs, and the recruitment of SMC5 to DSBs is dependent on CRYs. These results suggest that CRY-enhanced ADA2b-SMC5 interaction promotes ADA2b-mediated recruitment of SMC5 to DSBs, leading to DSB repair.
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Affiliation(s)
- Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Minqing Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ling Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yupeng Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Cao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
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13
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Farcy S, Hachour H, Bahi-Buisson N, Passemard S. Genetic Primary Microcephalies: When Centrosome Dysfunction Dictates Brain and Body Size. Cells 2023; 12:1807. [PMID: 37443841 PMCID: PMC10340463 DOI: 10.3390/cells12131807] [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: 04/06/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Primary microcephalies (PMs) are defects in brain growth that are detectable at or before birth and are responsible for neurodevelopmental disorders. Most are caused by biallelic or, more rarely, dominant mutations in one of the likely hundreds of genes encoding PM proteins, i.e., ubiquitous centrosome or microtubule-associated proteins required for the division of neural progenitor cells in the embryonic brain. Here, we provide an overview of the different types of PMs, i.e., isolated PMs with or without malformations of cortical development and PMs associated with short stature (microcephalic dwarfism) or sensorineural disorders. We present an overview of the genetic, developmental, neurological, and cognitive aspects characterizing the most representative PMs. The analysis of phenotypic similarities and differences among patients has led scientists to elucidate the roles of these PM proteins in humans. Phenotypic similarities indicate possible redundant functions of a few of these proteins, such as ASPM and WDR62, which play roles only in determining brain size and structure. However, the protein pericentrin (PCNT) is equally required for determining brain and body size. Other PM proteins perform both functions, albeit to different degrees. Finally, by comparing phenotypes, we considered the interrelationships among these proteins.
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Affiliation(s)
- Sarah Farcy
- UMR144, Institut Curie, 75005 Paris, France;
- Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Hassina Hachour
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
| | - Nadia Bahi-Buisson
- Service de Neurologie Pédiatrique, DMU MICADO, APHP, Hôpital Necker Enfants Malades, 75015 Paris, France;
- Université Paris Cité, Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Sandrine Passemard
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
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14
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Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. THE PLANT CELL 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
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Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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15
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Li C, Guo Y, Wang L, Yan S. The SMC5/6 complex recruits the PAF1 complex to facilitate DNA double-strand break repair in Arabidopsis. EMBO J 2023; 42:e112756. [PMID: 36815434 PMCID: PMC10068331 DOI: 10.15252/embj.2022112756] [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: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most toxic forms of DNA damage, which threatens genome stability. Homologous recombination is an error-free DSB repair pathway, in which the evolutionarily conserved SMC5/6 complex (SMC5/6) plays essential roles. The PAF1 complex (PAF1C) is well known to regulate transcription. Here we show that SMC5/6 recruits PAF1C to facilitate DSB repair in plants. In a genetic screen for DNA damage response mutants (DDRMs), we found that the Arabidopsis ddrm4 mutant is hypersensitive to DSB-inducing agents and is defective in homologous recombination. DDRM4 encodes PAF1, a core subunit of PAF1C. Further biochemical and genetic studies reveal that SMC5/6 recruits PAF1C to DSB sites, where PAF1C further recruits the E2 ubiquitin-conjugating enzymes UBC1/2, which interact with the E3 ubiquitin ligases HUB1/2 to mediate the monoubiquitination of histone H2B at DSBs. These results implicate SMC5/6-PAF1C-UBC1/2-HUB1/2 as a new axis for DSB repair through homologous recombination, revealing a new mechanism of SMC5/6 and uncovering a novel function of PAF1C.
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Affiliation(s)
- Cunliang Li
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuyu Guo
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Lili Wang
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Shunping Yan
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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16
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Pradhan B, Kanno T, Umeda Igarashi M, Loke MS, Baaske MD, Wong JSK, Jeppsson K, Björkegren C, Kim E. The Smc5/6 complex is a DNA loop-extruding motor. Nature 2023; 616:843-848. [PMID: 37076626 PMCID: PMC10132971 DOI: 10.1038/s41586-023-05963-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 03/16/2023] [Indexed: 04/21/2023]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes1. Whereas cohesin and condensin organize chromosomes by extrusion of DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown2. Using single-molecule imaging, we show that Smc5/6 forms DNA loops by extrusion. Upon ATP hydrolysis, Smc5/6 reels DNA symmetrically into loops at a force-dependent rate of one kilobase pair per second. Smc5/6 extrudes loops in the form of dimers, whereas monomeric Smc5/6 unidirectionally translocates along DNA. We also find that the subunits Nse5 and Nse6 (Nse5/6) act as negative regulators of loop extrusion. Nse5/6 inhibits loop-extrusion initiation by hindering Smc5/6 dimerization but has no influence on ongoing loop extrusion. Our findings reveal functions of Smc5/6 at the molecular level and establish DNA loop extrusion as a conserved mechanism among eukaryotic SMC complexes.
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Affiliation(s)
| | - Takaharu Kanno
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Miki Umeda Igarashi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Mun Siong Loke
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | | | - Kristian Jeppsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Camilla Björkegren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| | - Eugene Kim
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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17
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Sohn EJ, Goralsky JA, Shay JW, Min J. The Molecular Mechanisms and Therapeutic Prospects of Alternative Lengthening of Telomeres (ALT). Cancers (Basel) 2023; 15:cancers15071945. [PMID: 37046606 PMCID: PMC10093677 DOI: 10.3390/cancers15071945] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
As detailed by the end replication problem, the linear ends of a cell's chromosomes, known as telomeres, shorten with each successive round of replication until a cell enters into a state of growth arrest referred to as senescence. To maintain their immortal proliferation capacity, cancer cells must employ a telomere maintenance mechanism, such as telomerase activation or the Alternative Lengthening of Telomeres pathway (ALT). With only 10-15% of cancers utilizing the ALT mechanism, progress towards understanding its molecular components and associated hallmarks has only recently been made. This review analyzes the advances towards understanding the ALT pathway by: (1) detailing the mechanisms associated with engaging the ALT pathway as well as (2) identifying potential therapeutic targets of ALT that may lead to novel cancer therapeutic treatments. Collectively, these studies indicate that the ALT molecular mechanisms involve at least two distinct pathways induced by replication stress and damage at telomeres. We suggest exploiting tumor dependency on ALT is a promising field of study because it suggests new approaches to ALT-specific therapies for cancers with poorer prognosis. While substantial progress has been made in the ALT research field, additional progress will be required to realize these advances into clinical practices to treat ALT cancers and improve patient prognoses.
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Affiliation(s)
- Eric J Sohn
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia A Goralsky
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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18
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Kabirova E, Nurislamov A, Shadskiy A, Smirnov A, Popov A, Salnikov P, Battulin N, Fishman V. Function and Evolution of the Loop Extrusion Machinery in Animals. Int J Mol Sci 2023; 24:5017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Nurislamov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Shadskiy
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander Smirnov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Andrey Popov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Salnikov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Artificial Intelligence Research Institute (AIRI), 121108 Moscow, Russia
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19
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Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging. Cell Rep 2022; 41:111778. [PMID: 36476856 PMCID: PMC9756111 DOI: 10.1016/j.celrep.2022.111778] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/15/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.
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20
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NSMCE2, a novel super-enhancer-regulated gene, is linked to poor prognosis and therapy resistance in breast cancer. BMC Cancer 2022; 22:1056. [PMID: 36224576 PMCID: PMC9555101 DOI: 10.1186/s12885-022-10157-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/07/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite today's advances in the treatment of cancer, breast cancer-related mortality remains high, in part due to the lack of effective targeted therapies against breast tumor types that do not respond to standard treatments. Therefore, identifying additional breast cancer molecular targets is urgently needed. Super-enhancers are large regions of open chromatin involved in the overactivation of oncogenes. Thus, inhibition of super-enhancers has become a focus in clinical trials for its therapeutic potential. Here, we aimed to identify novel super-enhancer dysregulated genes highly associated with breast cancer patients' poor prognosis and negative response to treatment. METHODS Using existing datasets containing super-enhancer-associated genes identified in breast tumors and public databases comprising genomic and clinical information for breast cancer patients, we investigated whether highly expressed super-enhancer-associated genes correlate to breast cancer patients' poor prognosis and to patients' poor response to therapy. Our computational findings were experimentally confirmed in breast cancer cells by pharmacological SE disruption and gene silencing techniques. RESULTS We bioinformatically identified two novel super-enhancer-associated genes - NSMCE2 and MAL2 - highly upregulated in breast tumors, for which high RNA levels significantly and specifically correlate with breast cancer patients' poor prognosis. Through in-vitro pharmacological super-enhancer disruption assays, we confirmed that super-enhancers upregulate NSMCE2 and MAL2 transcriptionally, and, through bioinformatics, we found that high levels of NSMCE2 strongly associate with patients' poor response to chemotherapy, especially for patients diagnosed with aggressive triple negative and HER2 positive tumor types. Finally, we showed that decreasing NSMCE2 gene expression increases breast cancer cells' sensitivity to chemotherapy treatment. CONCLUSIONS Our results indicate that moderating the transcript levels of NSMCE2 could improve patients' response to standard chemotherapy consequently improving disease outcome. Our approach offers a new avenue to identify a signature of tumor specific genes that are not frequently mutated but dysregulated by super-enhancers. As a result, this strategy can lead to the discovery of potential and novel pharmacological targets for improving targeted therapy and the treatment of breast cancer.
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21
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Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, Ofir G, Hochhauser D, Stokar-Avihail A, Tal N, Sharir S, Voichek M, Erez Z, Ferrer JLM, Dar D, Kacen A, Amitai G, Sorek R. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 2022; 30:1556-1569.e5. [DOI: 10.1016/j.chom.2022.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/15/2022] [Accepted: 09/28/2022] [Indexed: 01/16/2023]
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22
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Jiang J, Ou X, Han D, He Z, Liu S, Mao N, Zhang Z, Peng CL, Lai J, Yang C. A diRNA-protein scaffold module mediates SMC5/6 recruitment in plant DNA repair. THE PLANT CELL 2022; 34:3899-3914. [PMID: 35775944 PMCID: PMC9516202 DOI: 10.1093/plcell/koac191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/21/2022] [Indexed: 06/06/2023]
Abstract
In eukaryotes, the STRUCTURAL MAINTENANCE OF CHROMOSOME 5/6 (SMC5/6) complex is critical to maintaining chromosomal structures around double-strand breaks (DSBs) in DNA damage repair. However, the recruitment mechanism of this conserved complex at DSBs remains unclear. In this study, using Arabidopsis thaliana as a model, we found that SMC5/6 localization at DSBs is dependent on the protein scaffold containing INVOLVED IN DE NOVO 2 (IDN2), CELL DIVISION CYCLE 5 (CDC5), and ALTERATION/DEFICIENCY IN ACTIVATION 2B (ADA2b), whose recruitment is further mediated by DNA-damage-induced RNAs (diRNAs) generated from DNA regions around DSBs. The physical interactions of protein components including SMC5-ADA2b, ADA2b-CDC5, and CDC5-IDN2 result in formation of the protein scaffold. Further analysis indicated that the DSB localization of IDN2 requires its RNA-binding activity and ARGONAUTE 2 (AGO2), indicating a role for the AGO2-diRNA complex in this process. Given that most of the components in the scaffold are conserved, the mechanism presented here, which connects SMC5/6 recruitment and small RNAs, will improve our understanding of DNA repair mechanisms in eukaryotes.
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Affiliation(s)
- Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaolin Ou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhipeng He
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Ning Mao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chang-Lian Peng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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Smc5/6 silences episomal transcription by a three-step function. Nat Struct Mol Biol 2022; 29:922-931. [PMID: 36097294 DOI: 10.1038/s41594-022-00829-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
In addition to its role in chromosome maintenance, the six-membered Smc5/6 complex functions as a restriction factor that binds to and transcriptionally silences viral and other episomal DNA. However, the underlying mechanism is unknown. Here, we show that transcriptional silencing by the human Smc5/6 complex is a three-step process. The first step is entrapment of the episomal DNA by a mechanism dependent on Smc5/6 ATPase activity and a function of its Nse4a subunit for which the Nse4b paralog cannot substitute. The second step results in Smc5/6 recruitment to promyelocytic leukemia nuclear bodies by SLF2 (the human ortholog of Nse6). The third step promotes silencing through a mechanism requiring Nse2 but not its SUMO ligase activity. By contrast, the related cohesin and condensin complexes fail to bind to or silence episomal DNA, indicating a property unique to Smc5/6.
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24
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Wu Z, Wang L, Wang X, Sun Y, Li H, Zhang Z, Ren C, Zhang X, Li S, Lu J, Xu L, Yue X, Hong Y, Li Q, Zhu H, Gong Y, Gao C, Hu H, Gao L, Liang X, Ma C. cccDNA Surrogate MC-HBV-Based Screen Identifies Cohesin Complex as a Novel HBV Restriction Factor. Cell Mol Gastroenterol Hepatol 2022; 14:1177-1198. [PMID: 35987451 PMCID: PMC9579331 DOI: 10.1016/j.jcmgh.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV), existing as a stable minichromosome in the hepatocyte, is responsible for persistent HBV infection. Maintenance and sustained replication of cccDNA require its interaction with both viral and host proteins. However, the cccDNA-interacting host factors that limit HBV replication remain elusive. METHODS Minicircle HBV (MC-HBV), a recombinant cccDNA, was constructed based on chimeric intron and minicircle DNA technology. By mass spectrometry based on pull-down with biotinylated MC-HBV, the cccDNA-hepatocyte interaction profile was mapped. HBV replication was assessed in different cell models that support cccDNA formation. RESULTS MC-HBV supports persistent HBV replication and mimics the cccDNA minichromosome. The MC-HBV-based screen identified cohesin complex as a cccDNA binding host factor, leading to reduced HBV replication. Mechanistically, with the help of CCCTC-binding factor (CTCF), which has specific binding sites on cccDNA, cohesin loads on cccDNA and reshapes cccDNA confirmation to prevent RNA polymerase II enrichment. Interestingly, HBV X protein transcriptionally reduces structural maintenance of chromosomes complex expression to partially relieve the inhibitory role of the cohesin complex on HBV replication. CONCLUSIONS Our data not only provide a feasible approach to explore cccDNA-binding factors, but also identify cohesin/CTCF complex as a critical host restriction factor for cccDNA-driven HBV replication. These findings provide a novel insight into cccDNA-host interaction and targeted therapeutic intervention for HBV infection.
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Affiliation(s)
- Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xin Wang
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Yang Sun
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Haoran Li
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Zhaoying Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Caiyue Ren
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohui Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Shuangjie Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Jinghui Lu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Leiqi Xu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Xuetian Yue
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Yue Hong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Qiang Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chengjiang Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Huili Hu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Chunhong Ma, PhD, Key Laboratory for Experimental Teratology of Ministry of Education and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012 China.
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Wu Y, Zhang H, Chen J, Shi Z, Li M, Zhao Y, Shi H, Shi D, Guo L, Feng L. Stromal Antigen 2 Deficiency Induces Interferon Responses and Restricts Porcine Deltacoronavirus Infection. Viruses 2022; 14:1783. [PMID: 36016405 PMCID: PMC9414771 DOI: 10.3390/v14081783] [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: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/20/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) is a recently discovered enteropathogenic coronavirus and has caused significant economic impacts on the pork industry. Although studies have partly uncovered the molecular mechanism of PDCoV-host interaction, it requires further research. In this study, we explored the roles of Stromal Antigen 2 (STAG2) in PDCoV infection. We found that STAG2-deficient cells inhibited infection with vesicular stomatitis virus (VSV) and PDCoV, whereas restoration of STAG2 expression in STAG2-depleted (STAG2-/-) IPEC-J2 cells line restored PDCoV infection, suggesting that STAG2 is involved in the PDCoV replication. Furthermore, we found that STAG2 deficiency results in robust interferon (IFN) expression. Subsequently, we found that STAG2 deficiency results in the activation of JAK-STAT signaling and the expression of IFN stimulated gene (ISG), which establish an antiviral state. Taken together, the depletion of STAG2 activates the JAK-STAT signaling and induces the expression of ISG, thereby inhibiting PDCoV replication. Our study provides new insights and potential therapeutic targets for unraveling the mechanism of PDCoV replication.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Longjun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
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26
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Hepatitis B virus-associated hepatocellular carcinoma with Smc5/6 complex deficiency is susceptible to PARP inhibitors. Biochem Biophys Res Commun 2022; 607:89-95. [DOI: 10.1016/j.bbrc.2022.03.137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022]
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27
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Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022; 17:1486-1517. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Abstract
Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.
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28
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Yang F, Pecinka A. Multiple Roles of SMC5/6 Complex during Plant Sexual Reproduction. Int J Mol Sci 2022; 23:ijms23094503. [PMID: 35562893 PMCID: PMC9099584 DOI: 10.3390/ijms23094503] [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: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Chromatin-based processes are essential for cellular functions. Structural maintenance of chromosomes (SMCs) are evolutionarily conserved molecular machines that organize chromosomes throughout the cell cycle, mediate chromosome compaction, promote DNA repair, or control sister chromatid attachment. The SMC5/6 complex is known for its pivotal role during the maintenance of genome stability. However, a dozen recent plant studies expanded the repertoire of SMC5/6 complex functions to the entire plant sexual reproductive phase. The SMC5/6 complex is essential in meiosis, where its activity must be precisely regulated to allow for normal meiocyte development. Initially, it is attenuated by the recombinase RAD51 to allow for efficient strand invasion by the meiosis-specific recombinase DMC1. At later stages, it is essential for the normal ratio of interfering and non-interfering crossovers, detoxifying aberrant joint molecules, preventing chromosome fragmentation, and ensuring normal chromosome/sister chromatid segregation. The latter meiotic defects lead to the production of diploid male gametes in Arabidopsis SMC5/6 complex mutants, increased seed abortion, and production of triploid offspring. The SMC5/6 complex is directly involved in controlling normal embryo and endosperm cell divisions, and pioneer studies show that the SMC5/6 complex is also important for seed development and normal plant growth in cereals.
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Affiliation(s)
- Fen Yang
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
- Correspondence:
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29
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Di Nardo M, Pallotta MM, Musio A. The multifaceted roles of cohesin in cancer. J Exp Clin Cancer Res 2022; 41:96. [PMID: 35287703 PMCID: PMC8919599 DOI: 10.1186/s13046-022-02321-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
The cohesin complex controls faithful chromosome segregation by pairing sister chromatids after DNA replication until mitosis. In addition, it is crucial for hierarchal three-dimensional organization of the genome, transcription regulation and maintaining DNA integrity. The core complex subunits SMC1A, SMC3, STAG1/2, and RAD21 as well as its modulators, have been found to be recurrently mutated in human cancers. The mechanisms by which cohesin mutations trigger cancer development and disease progression are still poorly understood. Since cohesin is involved in a range of chromosome-related processes, the outcome of cohesin mutations in cancer is complex. Herein, we discuss recent discoveries regarding cohesin that provide new insight into its role in tumorigenesis.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Maria M. Pallotta
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
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30
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Choi EH, Yoon S, Koh YE, Hong TK, Do JT, Lee BK, Hahn Y, Kim KP. Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes. Genome Biol 2022; 23:70. [PMID: 35241136 PMCID: PMC8892811 DOI: 10.1186/s13059-022-02632-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cohesin is a chromosome-associated SMC-kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether meiosis-specific cohesin complexes are functionally active in mitotic chromosomes. RESULTS Through high-resolution 3D-structured illumination microscopy (3D-SIM) and functional analyses, we report multiple biological processes associated with the meiosis-specific cohesin components, α-kleisin REC8 and STAG3, and the distinct loss of function of meiotic cohesin during the cell cycle of embryonic stem cells (ESCs). First, we show that STAG3 is required for the efficient localization of REC8 to the nucleus by interacting with REC8. REC8-STAG3-containing cohesin regulates topological properties of chromosomes and maintains sister chromatid cohesion. Second, REC8-cohesin has additional sister chromatid cohesion roles in concert with mitotic RAD21-cohesin on ESC chromosomes. SIM imaging of REC8 and RAD21 co-staining revealed that the two types of α-kleisin subunits exhibited distinct loading patterns along ESC chromosomes. Third, knockdown of REC8 or RAD21-cohesin not only leads to higher rates of premature sister chromatid separation and delayed replication fork progression, which can cause proliferation and developmental defects, but also enhances chromosome compaction by hyperloading of retinoblastoma protein-condensin complexes from the prophase onward. CONCLUSIONS Our findings indicate that the delicate balance between mitotic and meiotic cohesins may regulate ESC-specific chromosomal organization and the mitotic program.
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Affiliation(s)
- Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Young Eun Koh
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Tae Kyung Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University of Albany-State University of New York, Rensselaer, NY, USA
| | - Yoonsoo Hahn
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea.
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31
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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Phipps J, Dubrana K. DNA Repair in Space and Time: Safeguarding the Genome with the Cohesin Complex. Genes (Basel) 2022; 13:198. [PMID: 35205243 PMCID: PMC8872453 DOI: 10.3390/genes13020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a deleterious form of DNA damage, which must be robustly addressed to ensure genome stability. Defective repair can result in chromosome loss, point mutations, loss of heterozygosity or chromosomal rearrangements, which could lead to oncogenesis or cell death. We explore the requirements for the successful repair of DNA DSBs by non-homologous end joining and homology-directed repair (HDR) mechanisms in relation to genome folding and dynamics. On the occurrence of a DSB, local and global chromatin composition and dynamics, as well as 3D genome organization and break localization within the nuclear space, influence how repair proceeds. The cohesin complex is increasingly implicated as a key regulator of the genome, influencing chromatin composition and dynamics, and crucially genome organization through folding chromosomes by an active loop extrusion mechanism, and maintaining sister chromatid cohesion. Here, we consider how this complex is now emerging as a key player in the DNA damage response, influencing repair pathway choice and efficiency.
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Affiliation(s)
| | - Karine Dubrana
- UMR Stabilité Génétique Cellules Souches et Radiations, INSERM, iRCM/IBFJ CEA, Université de Paris and Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France;
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Sekiba K, Otsuka M, Funato K, Miyakawa Y, Tanaka E, Seimiya T, Yamagami M, Tsutsumi T, Okushin K, Miyakawa K, Ryo A, Koike K. HBx-induced degradation of Smc5/6 complex impairs homologous recombination-mediated repair of damaged DNA. J Hepatol 2022; 76:53-62. [PMID: 34478763 DOI: 10.1016/j.jhep.2021.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/25/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS HBV causes hepatocellular carcinoma (HCC). While it was recently shown that the ability of HBV X protein (HBx) to impair the Smc5/6 (structural maintenance of chromosome 5/6) complex is important for viral transcription, HBx is also a potent driver of HCC. However, the mechanism by which HBx expression induces hepatocarcinogenesis is unclear. METHODS Degradation of the Smc5/6 complex and accumulation of DNA damage were observed in both in vivo and in vitro HBV infection models. Rescue experiments were performed using nitazoxanide (NTZ), which inhibits degradation of the Smc5/6 complex by HBx. RESULTS HBx-triggered degradation of the Smc5/6 complex causes impaired homologous recombination (HR) repair of DNA double-strand breaks (DSBs), leading to cellular transformation. We found that DNA damage accumulated in the liver tissue of HBV-infected humanized chimeric mice, HBx-transgenic mice, and human tissues. HBx suppressed the HR repair of DSBs, including that induced by the CRISPR-Cas9 system, in an Smc5/6-dependent manner, which was rescued by restoring the Smc5/6 complex. NTZ restored HR repair in, and colony formation by, HBx-expressing cells. CONCLUSIONS Degradation of the Smc5/6 complex by HBx increases viral transcription and promotes cellular transformation by impairing HR repair of DSBs. LAY SUMMARY The hepatitis B virus expresses a regulatory protein called HBV X protein (or HBx). This protein degrades the Smc5/6 complex in human hepatocytes, which is essential for viral replication. We found that this process also plays a key role in the accumulation of DNA damage, which contributes to HBx-mediated tumorigenesis.
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Affiliation(s)
- Kazuma Sekiba
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Kazuyoshi Funato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yu Miyakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Eri Tanaka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takahiro Seimiya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Mari Yamagami
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuya Okushin
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Infection Control and Prevention, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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3D Genome Organization: Causes and Consequences for DNA Damage and Repair. Genes (Basel) 2021; 13:genes13010007. [PMID: 35052348 PMCID: PMC8775012 DOI: 10.3390/genes13010007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 01/02/2023] Open
Abstract
The inability to repair damaged DNA severely compromises the integrity of any organism. In eukaryotes, the DNA damage response (DDR) operates within chromatin, a tightly organized DNA–histone complex in a non-random manner within the nucleus. Chromatin thus orchestrates various cellular processes, including repair. Here, we examine the chromatin landscape before, during, and after the DNA damage, focusing on double strand breaks (DSBs). We study how chromatin is modified during the repair process, not only around the damaged region (in cis), but also genome-wide (in trans). Recent evidence has highlighted a complex landscape in which different chromatin parameters (stiffness, compaction, loops) are transiently modified, defining “codes” for each specific stage of the DDR. We illustrate a novel aspect of DDR where chromatin modifications contribute to the movement of DSB-damaged chromatin, as well as undamaged chromatin, ensuring the mobilization of DSBs, their clustering, and their repair processes.
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35
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Stupp D, Sharon E, Bloch I, Zitnik M, Zuk O, Tabach Y. Co-evolution based machine-learning for predicting functional interactions between human genes. Nat Commun 2021; 12:6454. [PMID: 34753957 PMCID: PMC8578642 DOI: 10.1038/s41467-021-26792-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/09/2021] [Indexed: 12/20/2022] Open
Abstract
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary questions. Here, we develop a machine-learning approach for utilizing phylogenetic profiles across 1154 eukaryotic species. This method integrates co-evolution across eukaryotic clades to predict functional interactions between human genes and the context for these interactions. We benchmark our approach showing a 14% performance increase (auROC) compared to previous methods. Using this approach, we predict functional annotations for less studied genes. We focus on DNA repair and verify that 9 of the top 50 predicted genes have been identified elsewhere, with others previously prioritized by high-throughput screens. Overall, our approach enables better annotation of function and functional interactions and facilitates the understanding of evolutionary processes underlying co-evolution. The manuscript is accompanied by a webserver available at: https://mlpp.cs.huji.ac.il. With the rise in number of eukaryotic species being fully sequenced, large scale phylogenetic profiling can give insights on gene function, Here, the authors describe a machine-learning approach that integrates co-evolution across eukaryotic clades to predict gene function and functional interactions among human genes.
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Affiliation(s)
- Doron Stupp
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Elad Sharon
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard University, Boston, MA, 02115, USA
| | - Or Zuk
- Department of Statistics and Data Science, The Hebrew University of Jerusalem, Jerusalem, 9190501, Israel.
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel.
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Sebastian R, Aladjem MI, Oberdoerffer P. Encounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity. Front Genet 2021; 12:746380. [PMID: 34745220 PMCID: PMC8566435 DOI: 10.3389/fgene.2021.746380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Almost 25 years ago, the phosphorylation of a chromatin component, histone H2AX, was discovered as an integral part of the DNA damage response in eukaryotes. Much has been learned since then about the control of DNA repair in the context of chromatin. Recent technical and computational advances in imaging, biophysics and deep sequencing have led to unprecedented insight into nuclear organization, highlighting the impact of three-dimensional (3D) chromatin structure and nuclear topology on DNA repair. In this review, we will describe how DNA repair processes have adjusted to and in many cases adopted these organizational features to ensure accurate lesion repair. We focus on new findings that highlight the importance of chromatin context, topologically associated domains, phase separation and DNA break mobility for the establishment of repair-conducive nuclear environments. Finally, we address the consequences of aberrant 3D genome maintenance for genome instability and disease.
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Affiliation(s)
- Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Philipp Oberdoerffer
- Division of Cancer Biology, National Cancer Institute, NIH, Rockville, MD, United States
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STING protects breast cancer cells from intrinsic and genotoxic-induced DNA instability via a non-canonical, cell-autonomous pathway. Oncogene 2021; 40:6627-6640. [PMID: 34625708 DOI: 10.1038/s41388-021-02037-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 09/13/2021] [Accepted: 09/23/2021] [Indexed: 01/13/2023]
Abstract
STING (Stimulator of Interferon Genes) is an endoplasmic reticulum-anchored adaptor of the innate immunity best known to trigger pro-inflammatory cytokine expression in response to pathogen infection. In cancer, this canonical pathway can be activated by intrinsic or drug-induced genomic instability, potentiating antitumor immune responses. Here we report that STING downregulation decreases cell survival and increases sensitivity to genotoxic treatment in a panel of breast cancer cell lines in a cell-autonomous manner. STING silencing impaired DNA Damage Response (53BP1) foci formation and increased DNA break accumulation. These newly identified properties were found to be independent of STING partner cGAS and of its canonical pro-inflammatory pathway. STING was shown to partially localize at the inner nuclear membrane in a variety of breast cancer cell models and clinical tumor samples. Interactomics analysis of nuclear STING identified several proteins of the DNA Damage Response, including the three proteins of the DNA-PK complex, further supporting a role of STING in the regulation of genomic stability. In breast and ovarian cancer patients that received adjuvant chemotherapy, high STING expression is associated with increased risk of relapse. In summary, this study highlights an alternative, non-canonical tumor-promoting role of STING that opposes its well-documented function in tumor immunosurveillance.
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Cahill T, Cope H, Bass JJ, Overbey EG, Gilbert R, da Silveira WA, Paul AM, Mishra T, Herranz R, Reinsch SS, Costes SV, Hardiman G, Szewczyk NJ, Tahimic CGT. Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight. Int J Mol Sci 2021; 22:ijms22179470. [PMID: 34502375 PMCID: PMC8430797 DOI: 10.3390/ijms22179470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Bioinformatics approaches have proven useful in understanding biological responses to spaceflight. Spaceflight experiments remain resource intensive and rare. One outstanding issue is how to maximize scientific output from a limited number of omics datasets from traditional animal models including nematodes, fruitfly, and rodents. The utility of omics data from invertebrate models in anticipating mammalian responses to spaceflight has not been fully explored. Hence, we performed comparative analyses of transcriptomes of soleus and extensor digitorum longus (EDL) in mice that underwent 37 days of spaceflight. Results indicate shared stress responses and altered circadian rhythm. EDL showed more robust growth signals and Pde2a downregulation, possibly underlying its resistance to atrophy versus soleus. Spaceflight and hindlimb unloading mice shared differential regulation of proliferation, circadian, and neuronal signaling. Shared gene regulation in muscles of humans on bedrest and space flown rodents suggest targets for mitigating muscle atrophy in space and on Earth. Spaceflight responses of C. elegans were more similar to EDL. Discrete life stages of D. melanogaster have distinct utility in anticipating EDL and soleus responses. In summary, spaceflight leads to shared and discrete molecular responses between muscle types and invertebrate models may augment mechanistic knowledge gained from rodent spaceflight and ground-based studies.
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Affiliation(s)
- Thomas Cahill
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
| | - Henry Cope
- Nottingham Biomedical Research Centre (BRC), School of Computer Science, University of Nottingham, Nottingham NG7 2QL, UK;
| | - Joseph J. Bass
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research (NIHR), Nottingham Biomedical Research Centre (BRC), University of Nottingham, Nottingham NG7 2QL, UK; (J.J.B.); (N.J.S.)
| | - Eliah G. Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Rachel Gilbert
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Universities Space Research Association, Columbia, MD 21046, USA
| | - Willian Abraham da Silveira
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
- Department of Biological Sciences, School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent ST4 2DF, UK
| | - Amber M. Paul
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL 32114, USA
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA;
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas–CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Sigrid S. Reinsch
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Nathaniel J. Szewczyk
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research (NIHR), Nottingham Biomedical Research Centre (BRC), University of Nottingham, Nottingham NG7 2QL, UK; (J.J.B.); (N.J.S.)
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Candice G. T. Tahimic
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
- Correspondence:
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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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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Psakhye I, Branzei D. SMC complexes are guarded by the SUMO protease Ulp2 against SUMO-chain-mediated turnover. Cell Rep 2021; 36:109485. [PMID: 34348159 DOI: 10.1016/j.celrep.2021.109485] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 01/01/2023] Open
Abstract
Structural maintenance of chromosomes (SMCs) complexes, cohesin, condensin, and Smc5/6, are essential for viability and participate in multiple processes, including sister chromatid cohesion, chromosome condensation, and DNA repair. Here we show that SUMO chains target all three SMC complexes and are antagonized by the SUMO protease Ulp2 to prevent their turnover. We uncover that the essential role of the cohesin-associated subunit Pds5 is to counteract SUMO chains jointly with Ulp2. Importantly, fusion of Ulp2 to kleisin Scc1 supports viability of PDS5 null cells and protects cohesin from proteasomal degradation mediated by the SUMO-targeted ubiquitin ligase Slx5/Slx8. The lethality of PDS5-deleted cells can also be bypassed by simultaneous loss of the proliferating cell nuclear antigen (PCNA) unloader, Elg1, and the cohesin releaser, Wpl1, but only when Ulp2 is functional. Condensin and Smc5/6 complex are similarly guarded by Ulp2 against unscheduled SUMO chain assembly, which we propose to time the availability of SMC complexes on chromatin.
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Affiliation(s)
- Ivan Psakhye
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy.
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Unique Features of Hepatitis B Virus-Related Hepatocellular Carcinoma in Pathogenesis and Clinical Significance. Cancers (Basel) 2021; 13:cancers13102454. [PMID: 34070067 PMCID: PMC8158142 DOI: 10.3390/cancers13102454] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hepatitis B virus (HBV) infection is the major risk factor for hepatocellular carcinoma (HCC). Understanding the unique features for HBV-induced HCC can shed new light on the unmet needs in its early diagnosis and effective therapy. During decades of chronic hepatitis B, hepatocytes undergoing repeated damage and regeneration accumulate genetic changes predisposing to HCC development. In addition to traditional mutations in viral and cellular oncogenes, HBV integration into the cell chromosomes is an alternative genetic change contributing to hepatocarcinogenesis. A striking male dominance in HBV-related HCC further highlights an interaction between androgen sex hormone and viral factors, which contributes to the gender difference via stimulating viral replication and activation of oncogenes preferentially in male patients. Meanwhile, a novel circulating tumor biomarker generated by HBV integration shows great potential for the early diagnosis of HCC. These unique HBV-induced hepatocarcinogenic mechanisms provide new insights for the future development of superior diagnosis and treatment strategies. Abstract Hepatitis B virus (HBV) infection is one of the important risk factors for hepatocellular carcinoma (HCC) worldwide, accounting for around 50% of cases. Chronic hepatitis B infection generates an inflammatory microenvironment, in which hepatocytes undergoing repeated cycles of damage and regeneration accumulate genetic mutations predisposing them to cancer. A striking male dominance in HBV-related HCC highlights the influence of sex hormones which interact with viral factors to influence carcinogenesis. HBV is also considered an oncogenic virus since its X and surface mutant proteins showed tumorigenic activity in mouse models. The other unique mechanism is the insertional mutagenesis by integration of HBV genome into hepatocyte chromosomes to activate oncogenes. HCC survival largely depends on tumor stages at diagnosis and effective treatment. However, early diagnosis by the conventional protein biomarkers achieves limited success. A new biomarker, the circulating virus–host chimera DNA from HBV integration sites in HCC, provides a liquid biopsy approach for monitoring the tumor load in the majority of HBV–HCC patients. To maximize the efficacy of new immunotherapies or molecular target therapies, it requires better classification of HCC based on the tumor microenvironment and specific carcinogenic pathways. An in-depth study may benefit both the diagnosis and treatment of HBV-related HCC.
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Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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Su XA, Ma D, Parsons JV, Replogle JM, Amatruda JF, Whittaker CA, Stegmaier K, Amon A. RAD21 is a driver of chromosome 8 gain in Ewing sarcoma to mitigate replication stress. Genes Dev 2021; 35:556-572. [PMID: 33766983 PMCID: PMC8015718 DOI: 10.1101/gad.345454.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/25/2021] [Indexed: 01/08/2023]
Abstract
In this study, Su et al. investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Using an evolution approach, they show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21, and deleting one copy of RAD21 in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. Aneuploidy, defined as whole-chromosome gain or loss, causes cellular stress but, paradoxically, is a frequent occurrence in cancers. Here, we investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Expression of the EWS-FLI1 fusion in primary cells causes replication stress that can result in cellular senescence. Using an evolution approach, we show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21. Low-level ectopic expression of RAD21 is sufficient to dampen replication stress and improve proliferation in EWS-FLI1-expressing cells. Conversely, deleting one copy in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. We propose that RAD21 promotes tumorigenesis through single gene copy gain. Such genes may explain some recurrent aneuploidies in cancer.
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Affiliation(s)
- Xiaofeng A Su
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James V Parsons
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - John M Replogle
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James F Amatruda
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Charles A Whittaker
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Arnould C, Rocher V, Finoux AL, Clouaire T, Li K, Zhou F, Caron P, Mangeot PE, Ricci EP, Mourad R, Haber JE, Noordermeer D, Legube G. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 2021; 590:660-665. [PMID: 33597753 PMCID: PMC7116834 DOI: 10.1038/s41586-021-03193-z] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022]
Abstract
The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci1. It is unclear how these foci are rapidly assembled to establish a 'repair-prone' environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX-53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.
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Affiliation(s)
- Coline Arnould
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Vincent Rocher
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Anne-Laure Finoux
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Thomas Clouaire
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Kevin Li
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Felix Zhou
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Pierre Caron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Philippe E Mangeot
- CIRI - International Center for Infectiology Research, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, INSERM U1293, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Raphaël Mourad
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Gaëlle Legube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France.
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Wang J, Zhao H, Yu J, Xu X, Jing H, Li N, Tang Y, Wang S, Li Y, Cai J, Jin J. MiR-320b/RAD21 axis affects hepatocellular carcinoma radiosensitivity to ionizing radiation treatment through DNA damage repair signaling. Cancer Sci 2020; 112:575-588. [PMID: 33251678 PMCID: PMC7894001 DOI: 10.1111/cas.14751] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies in the world and is associated with high mortality. Ionizing radiation (IR)-based therapy causes DNA damage, exerting a curative effect; however, DNA damage repair signaling pathways lead to HCC resistance to IR-based therapy. RAD21 is a component of the cohesion complex, crucial for chromosome segregation and DNA damage repair, while it is still unclear whether RAD21 is implicated in DNA damage and influences IR sensitivity in HCC. The current research explores the effect and upstream regulatory mechanism of RAD21 on IR sensitivity in HCC. In the present study, RAD21 mRNA and protein expression were increased within HCC tissue samples, particularly within IR-insensitive HCC tissues. The overexpression of RAD21 partially attenuated the roles of IR in HCC by promoting the viability and suppressing the apoptosis of HCC cells. RAD21 overexpression reduced the culture medium 8-hydroxy-2-deoxyguanosine concentration and decreased the protein levels of γH2AX and ATM, suggesting that RAD21 overexpression attenuated IR treatment-induced DNA damage to HCC cells. miR-320b targeted RAD21 3'-UTR to inhibit RAD21 expression. In HCC tissues, particularly in IR-insensitive HCC tissues, miR-320b expression was significantly downregulated. miR-320b inhibition also attenuated IR treatment-induced DNA damage to HCC cells; more importantly, RAD21 silencing significantly attenuated the effects of miR-320b inhibition on IR treatment-induced DNA damage, suggesting that miR-320b plays a role through targeting RAD21. In conclusion, an miR-320b/RAD21 axis modulating HCC sensitivity to IR treatment through acting on IR-induced DNA damage was demonstrated. The miR-320b/RAD21 axis could be a novel therapeutic target for further study of HCC sensitivity to IR treatment.
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Affiliation(s)
- Jianyang Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Yu
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xin Xu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Jing
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Tang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shulian Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yexiong Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Jin
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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47
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Gutierrez-Escribano P, Hormeño S, Madariaga-Marcos J, Solé-Soler R, O'Reilly FJ, Morris K, Aicart-Ramos C, Aramayo R, Montoya A, Kramer H, Rappsilber J, Torres-Rosell J, Moreno-Herrero F, Aragon L. Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction. Mol Cell 2020; 80:1039-1054.e6. [PMID: 33301732 PMCID: PMC7758880 DOI: 10.1016/j.molcel.2020.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
Eukaryotic SMC complexes, cohesin, condensin, and Smc5/6, use ATP hydrolysis to power a plethora of functions requiring organization and restructuring of eukaryotic chromosomes in interphase and during mitosis. The Smc5/6 mechanism of action and its activity on DNA are largely unknown. Here we purified the budding yeast Smc5/6 holocomplex and characterized its core biochemical and biophysical activities. Purified Smc5/6 exhibits DNA-dependent ATP hydrolysis and SUMO E3 ligase activity. We show that Smc5/6 binds DNA topologically with affinity for supercoiled and catenated DNA templates. Employing single-molecule assays to analyze the functional and dynamic characteristics of Smc5/6 bound to DNA, we show that Smc5/6 locks DNA plectonemes and can compact DNA in an ATP-dependent manner. These results demonstrate that the Smc5/6 complex recognizes DNA tertiary structures involving juxtaposed helices and might modulate DNA topology by plectoneme stabilization and local compaction.
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Affiliation(s)
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roger Solé-Soler
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kyle Morris
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ricardo Aramayo
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jordi Torres-Rosell
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Luis Aragon
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK.
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48
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The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Mol Cell 2020; 80:1025-1038.e5. [PMID: 33301731 DOI: 10.1016/j.molcel.2020.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
The structural organization of chromosomes is a crucial feature that defines the functional state of genes and genomes. The extent of structural changes experienced by genomes of eukaryotic cells can be dramatic and spans several orders of magnitude. At the core of these changes lies a unique group of ATPases-the SMC proteins-that act as major effectors of chromosome behavior in cells. The Smc5/6 proteins play essential roles in the maintenance of genome stability, yet their mode of action is not fully understood. Here we show that the human Smc5/6 complex recognizes unusual DNA configurations and uses the energy of ATP hydrolysis to promote their compaction. Structural analyses reveal subunit interfaces responsible for the functionality of the Smc5/6 complex and how mutations in these regions may lead to chromosome breakage syndromes in humans. Collectively, our results suggest that the Smc5/6 complex promotes genome stability as a DNA micro-compaction machine.
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49
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Idilli AI, Pazzi C, dal Pozzolo F, Roccuzzo M, Mione MC. Rad21 Haploinsufficiency Prevents ALT-Associated Phenotypes in Zebrafish Brain Tumors. Genes (Basel) 2020; 11:E1442. [PMID: 33266037 PMCID: PMC7760354 DOI: 10.3390/genes11121442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/17/2023] Open
Abstract
Cohesin is a protein complex consisting of four core subunits responsible for sister chromatid cohesion in mitosis and meiosis, and for 3D genome organization and gene expression through the establishment of long distance interactions regulating transcriptional activity in the interphase. Both roles are important for telomere integrity, but the role of cohesin in telomere maintenance mechanisms in highly replicating cancer cells in vivo is poorly studied. Here we used a zebrafish model of brain tumor, which uses alternative lengthening of telomeres (ALT) as primary telomere maintenance mechanism to test whether haploinsufficiency for Rad21, a member of the cohesin ring, affects ALT development. We found that a reduction in Rad21 levels prevents ALT-associated phenotypes in zebrafish brain tumors and triggers an increase in tert expression. Despite the rescue of ALT phenotypes, tumor cells in rad21+/- fish exhibit an increase in DNA damage foci, probably due to a reduction in double-strand breaks repair efficiency.
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Affiliation(s)
- Aurora Irene Idilli
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Cecilia Pazzi
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Francesca dal Pozzolo
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Michela Roccuzzo
- Advanced Imaging Facility, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy;
| | - Maria Caterina Mione
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
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50
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Florke Gee RR, Chen H, Lee AK, Daly CA, Wilander BA, Fon Tacer K, Potts PR. Emerging roles of the MAGE protein family in stress response pathways. J Biol Chem 2020; 295:16121-16155. [PMID: 32921631 PMCID: PMC7681028 DOI: 10.1074/jbc.rev120.008029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.
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Affiliation(s)
- Rebecca R Florke Gee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Helen Chen
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna K Lee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christina A Daly
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Benjamin A Wilander
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA.
| | - Patrick Ryan Potts
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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