1
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Downs JA, Gasser SM. Chromatin remodeling and spatial concerns in DNA double-strand break repair. Curr Opin Cell Biol 2024; 90:102405. [PMID: 39083951 DOI: 10.1016/j.ceb.2024.102405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024]
Abstract
The substrate for the repair of DNA damage in living cells is not DNA but chromatin. Chromatin bears a range of modifications, which in turn bind ligands that compact or open chromatin structure, and determine its spatial organization within the nucleus. In some cases, RNA in the form of RNA:DNA hybrids or R-loops modulates DNA accessibility. Each of these parameters can favor particular pathways of repair. Chromatin or nucleosome remodelers are key regulators of chromatin structure, and a number of remodeling complexes are implicated in DNA repair. We cover novel insights into the impact of chromatin structure, nuclear organization, R-loop formation, nuclear actin, and nucleosome remodelers in DNA double-strand break repair, focusing on factors that alter repair functional upon ablation.
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Affiliation(s)
- Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Susan M Gasser
- ISREC Foundation, and University of Lausanne, Agora Cancer Research Center, Rue du Bugnon 25a, 1005 Lausanne, Switzerland.
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2
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Danovski G, Panova G, Keister B, Georgiev G, Atemin A, Uzunova S, Stamatov R, Kanev PB, Aleksandrov R, Blagoev KB, Stoynov SS. Diffusion of activated ATM explains γH2AX and MDC1 spread beyond the DNA damage site. iScience 2024; 27:110826. [PMID: 39310780 PMCID: PMC11416226 DOI: 10.1016/j.isci.2024.110826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/12/2024] [Accepted: 08/22/2024] [Indexed: 09/25/2024] Open
Abstract
During DNA repair, ATM-induced H2AX histone phosphorylation and MDC1 recruitment spread megabases beyond the damage site. While loop extrusion has been suggested to drive this spread, the underlying mechanism remains unclear. Herein, we provide two lines of evidence that loop extrusion is not the only driver of damage-induced γH2AX spread. First, cohesin loader NIPBL and cohesin subunit RAD21 accumulate considerably later than the phosphorylation of H2AX and MDC1 recruitment at micro-IR-induced damage. Second, auxin-induced RAD21 depletion does not affect γH2AX/MDC1 spread following micro-irradiation or DSB induction by zeocin. To determine if diffusion of activated ATM could account for the observed behavior, we measured the exchange rate and diffusion constants of ATM and MDC1 within damaged and unperturbed chromatin. Using these measurements, we introduced a quantitative model in which the freely diffusing activated ATM phosphorylates H2AX. This model faithfully describes the dynamics of ATM and subsequent γH2AX/MDC1 spread at complex DNA lesions.
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Affiliation(s)
- Georgi Danovski
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | | | | | - Georgi Georgiev
- Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Boulevard, 1164 Sofia, Bulgaria
| | - Aleksandar Atemin
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | - Sonya Uzunova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | - Rumen Stamatov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | - Petar-Bogomil Kanev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | - Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
| | - Krastan B. Blagoev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
- National Science Foundation, Alexandria, VA 22230, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Stoyno S. Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str, 1113 Sofia, Bulgaria
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3
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Qu SJ, Zhu SY, Wang EY, Yan XL, Cao RF, Li HT, Jiang ZL. Environmental high temperature affects pre-implantation embryo development by impairing the DNA repair ability. J Therm Biol 2024; 125:103968. [PMID: 39312816 DOI: 10.1016/j.jtherbio.2024.103968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/25/2024] [Accepted: 08/26/2024] [Indexed: 09/25/2024]
Abstract
Environmental high temperature poses a significant threat to human health, however, limited information is available for understanding the relationship between the hot weather and infertility. This study aims to assess the adverse effect of the hot weather to early embryonic cells. Our results indicated that environmental high temperature exposure could cause the decline of early embryo quality and implantation ability. In detail, it led to early embryonic development retardation, embryo degeneration rate increased, the rate of blastocyst and hatching decreased, and reduced the number of implants. And the finding also the impairment of environmental high temperature on early embryonic cells may be due to oxidative damage of DNA caused by ROS, while BER repair ability is decreased, failing to repair oxidative damage of DNA in time, resulting in a large number of early embryonic apoptosis. The work underscored that pregnant women should stay away from high-temperature environments.
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Affiliation(s)
- Si-Jing Qu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shi-Yong Zhu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - En-Yan Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin-Lei Yan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Rong-Feng Cao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hua-Tao Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhong-Ling Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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4
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Yao W, Hu X, Wang X. Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases. Signal Transduct Target Ther 2024; 9:232. [PMID: 39278916 PMCID: PMC11403012 DOI: 10.1038/s41392-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 09/18/2024] Open
Abstract
Histone post-translational modifications (HPTMs), as one of the core mechanisms of epigenetic regulation, are garnering increasing attention due to their close association with the onset and progression of diseases and their potential as targeted therapeutic agents. Advances in high-throughput molecular tools and the abundance of bioinformatics data have led to the discovery of novel HPTMs which similarly affect gene expression, metabolism, and chromatin structure. Furthermore, a growing body of research has demonstrated that novel histone modifications also play crucial roles in the development and progression of various diseases, including various cancers, cardiovascular diseases, infectious diseases, psychiatric disorders, and reproductive system diseases. This review defines nine novel histone modifications: lactylation, citrullination, crotonylation, succinylation, SUMOylation, propionylation, butyrylation, 2-hydroxyisobutyrylation, and 2-hydroxybutyrylation. It comprehensively introduces the modification processes of these nine novel HPTMs, their roles in transcription, replication, DNA repair and recombination, metabolism, and chromatin structure, as well as their involvement in promoting the occurrence and development of various diseases and their clinical applications as therapeutic targets and potential biomarkers. Moreover, this review provides a detailed overview of novel HPTM inhibitors targeting various targets and their emerging strategies in the treatment of multiple diseases while offering insights into their future development prospects and challenges. Additionally, we briefly introduce novel epigenetic research techniques and their applications in the field of novel HPTM research.
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Affiliation(s)
- Weiyi Yao
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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5
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Wu Y, Adeel MM, Xia D, Sancar A, Li W. Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization. Nucleic Acids Res 2024:gkae755. [PMID: 39258558 DOI: 10.1093/nar/gkae755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Aflatoxin B1 (AFB1), a potent mycotoxin, is one of the environmental risk factors that cause liver cancer. In the liver, the bioactivated AFB1 intercalates into the DNA double helix to form a bulky DNA adduct which will lead to mutation if left unrepaired. Here, we adapted the tXR-seq method to measure the nucleotide excision repair of AFB1-induced DNA adducts at single-nucleotide resolution on a genome-wide scale, and compared it with repair data obtained from conventional UV-damage XR-seq. Our results showed that transcription-coupled repair plays a major role in the damage removal process. We further analyzed the distribution of nucleotide excision repair sites for AFB1-induced DNA adducts within the 3D human genome organization. Our analysis revealed a heterogeneous AFB1-dG repair across four different organization levels, including chromosome territories, A/B compartments, TADs, and chromatin loops. We found that chromosomes positioned closer to the nuclear center and regions within A compartments have higher levels of nucleotide excision repair. Notably, we observed high repair activity around both TAD boundaries and loop anchors. These findings provide insights into the complex interplay between AFB1-induced DNA damage repair, transcription, and 3D genome organization, shedding light on the mechanisms underlying AFB1-induced mutagenesis.
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Affiliation(s)
- Yiran Wu
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Muhammad Muzammal Adeel
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Dian Xia
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Wentao Li
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
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6
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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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7
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Shokrollahi M, Stanic M, Hundal A, Chan JNY, Urman D, Jordan CA, Hakem A, Espin R, Hao J, Krishnan R, Maass PG, Dickson BC, Hande MP, Pujana MA, Hakem R, Mekhail K. DNA double-strand break-capturing nuclear envelope tubules drive DNA repair. Nat Struct Mol Biol 2024; 31:1319-1330. [PMID: 38632359 DOI: 10.1038/s41594-024-01286-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly(ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.
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Affiliation(s)
- Mitra Shokrollahi
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mia Stanic
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anisha Hundal
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Defne Urman
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chris A Jordan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anne Hakem
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Roderic Espin
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jun Hao
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Philipp G Maass
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Manoor P Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Miquel A Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Razqallah Hakem
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Temerty Centre for AI Research and Education in Medicine, University of Toronto, Toronto, Ontario, Canada.
- College of New Scholars, Artists and Scientists, Royal Society of Canada, Ottawa, Ontario, Canada.
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8
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Jann JC, Hergott CB, Winkler M, Liu Y, Braun B, Charles A, Copson KM, Barua S, Meggendorfer M, Nadarajah N, Shimony S, Winer ES, Wadleigh M, Stone RM, DeAngelo DJ, Garcia JS, Haferlach T, Lindsley RC, Luskin MR, Stahl M, Tothova Z. Subunit-specific analysis of cohesin-mutant myeloid malignancies reveals distinct ontogeny and outcomes. Leukemia 2024; 38:1992-2002. [PMID: 39033241 PMCID: PMC11347381 DOI: 10.1038/s41375-024-02347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
Mutations in the cohesin complex components (STAG2, RAD21, SMC1A, SMC3, and PDS5B) are recurrent genetic drivers in myelodysplastic neoplasm (MDS) and acute myeloid leukemia (AML). Whether the different cohesin subunit mutations share clinical characteristics and prognostic significance is not known. We analyzed 790 cohesin-mutant patients from the Dana-Farber Cancer Institute (DFCI) and the Munich Leukemia Laboratory (MLL), 390 of which had available outcome data, and identified subunit-specific clinical, prognostic, and genetic characteristics suggestive of distinct ontogenies. We found that STAG2 mutations are acquired at MDS stage and are associated with secondary AML, adverse prognosis, and co-occurrence of secondary AML-type mutations. In contrast, mutations in RAD21, SMC1A and SMC3 share features with de novo AML with better prognosis, and co-occurrence with de novo AML-type lesions. The findings show the heterogeneous nature of cohesin complex mutations, and inform clinical and prognostic classification, as well as distinct biology of the cohesin complex.
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Affiliation(s)
- Johann-Christoph Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Cancer Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Christopher B Hergott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Marisa Winkler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Element Iowa City (JMI Laboratories), North Liberty, IA, 52317, USA
| | - Yiwen Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Anne Charles
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kevin M Copson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shougat Barua
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute, Cambridge, MA, 02142, USA.
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9
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Wong LH, Tremethick DJ. Multifunctional histone variants in genome function. Nat Rev Genet 2024:10.1038/s41576-024-00759-1. [PMID: 39138293 DOI: 10.1038/s41576-024-00759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 08/15/2024]
Abstract
Histones are integral components of eukaryotic chromatin that have a pivotal role in the organization and function of the genome. The dynamic regulation of chromatin involves the incorporation of histone variants, which can dramatically alter its structural and functional properties. Contrary to an earlier view that limited individual histone variants to specific genomic functions, new insights have revealed that histone variants exert multifaceted roles involving all aspects of genome function, from governing patterns of gene expression at precise genomic loci to participating in genome replication, repair and maintenance. This conceptual change has led to a new understanding of the intricate interplay between chromatin and DNA-dependent processes and how this connection translates into normal and abnormal cellular functions.
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Affiliation(s)
- Lee H Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capial Territory, Australia.
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10
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Shi G, Pang Q, Lin Z, Zhang X, Huang K. Repetitive Sequence Stability in Embryonic Stem Cells. Int J Mol Sci 2024; 25:8819. [PMID: 39201503 PMCID: PMC11354519 DOI: 10.3390/ijms25168819] [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: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Repetitive sequences play an indispensable role in gene expression, transcriptional regulation, and chromosome arrangements through trans and cis regulation. In this review, focusing on recent advances, we summarize the epigenetic regulatory mechanisms of repetitive sequences in embryonic stem cells. We aim to bridge the knowledge gap by discussing DNA damage repair pathway choices on repetitive sequences and summarizing the significance of chromatin organization on repetitive sequences in response to DNA damage. By consolidating these insights, we underscore the critical relationship between the stability of repetitive sequences and early embryonic development, seeking to provide a deeper understanding of repetitive sequence stability and setting the stage for further research and potential therapeutic strategies in developmental biology and regenerative medicine.
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Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Qianwen Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Zhancheng Lin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Xinyi Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Kaimeng Huang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA;
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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11
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Chang LH, Noordermeer D. Permeable TAD boundaries and their impact on genome-associated functions. Bioessays 2024:e2400137. [PMID: 39093600 DOI: 10.1002/bies.202400137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.
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Affiliation(s)
- Li-Hsin Chang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Blood and Transplant Research Unit in Precision Cellular Therapeutics, National Institute of Health Research, Oxford, UK
| | - Daan Noordermeer
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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12
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Dabin J, Giacomini G, Petit E, Polo SE. New facets in the chromatin-based regulation of genome maintenance. DNA Repair (Amst) 2024; 140:103702. [PMID: 38878564 DOI: 10.1016/j.dnarep.2024.103702] [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: 04/09/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 07/13/2024]
Abstract
The maintenance of genome integrity by DNA damage response machineries is key to protect cells against pathological development. In cell nuclei, these genome maintenance machineries operate in the context of chromatin, where the DNA wraps around histone proteins. Here, we review recent findings illustrating how the chromatin substrate modulates genome maintenance mechanisms, focusing on the regulatory role of histone variants and post-translational modifications. In particular, we discuss how the pre-existing chromatin landscape impacts DNA damage formation and guides DNA repair pathway choice, and how DNA damage-induced chromatin alterations control DNA damage signaling and repair, and DNA damage segregation through cell divisions. We also highlight that pathological alterations of histone proteins may trigger genome instability by impairing chromosome segregation and DNA repair, thus defining new oncogenic mechanisms and opening up therapeutic options.
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Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Giulia Giacomini
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Eliane Petit
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France.
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13
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He S, Huang Z, Liu Y, Ha T, Wu B. DNA break induces rapid transcription repression mediated by proteasome-dependent RNAPII removal. Cell Rep 2024; 43:114420. [PMID: 38954517 PMCID: PMC11337244 DOI: 10.1016/j.celrep.2024.114420] [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: 08/28/2023] [Revised: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
A DNA double-strand break (DSB) jeopardizes genome integrity and endangers cell viability. Actively transcribed genes are particularly detrimental if broken and need to be repressed. However, it remains elusive how fast the repression is initiated and how far it influences the neighboring genes on the chromosome. We adopt a recently developed, very fast CRISPR to generate a DSB at a specific genomic locus with precise timing, visualize transcription in live cells, and measure the RNA polymerase II (RNAPII) occupancy near the broken site. We observe that a single DSB represses the transcription of the damaged gene in minutes, which coincides with the recruitment of a damage repair protein. Transcription repression propagates bi-directionally along the chromosome from the DSB for hundreds of kilobases, and proteasome is evoked to remove RNAPII in this process. Our method builds a foundation to measure the rapid kinetic events around a single DSB and elucidate the molecular mechanism.
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Affiliation(s)
- Shuaixin He
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhiyuan Huang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yang Liu
- Department of Biochemistry, The University of Utah, Salt Lake City, UT 84112, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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14
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Zhang C, Liu J, Wu J, Ranjan K, Cui X, Wang X, Zhang D, Zhu S. Key molecular DNA damage responses of human cells to radiation. Front Cell Dev Biol 2024; 12:1422520. [PMID: 39050891 PMCID: PMC11266142 DOI: 10.3389/fcell.2024.1422520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Our understanding of the DNA damage responses of human cells to radiation has increased remarkably over the recent years although some notable signaling events remain to be discovered. Here we provide a brief account of the key molecular events of the responses to reflect the current understanding of the key underlying mechanisms involved.
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Affiliation(s)
- Chencheng Zhang
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
| | - Jibin Liu
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
| | - Jun Wu
- Nantong Tumor Hospital, Nantong, China
| | - Kamakshi Ranjan
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Xiaopeng Cui
- Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong, China
| | - Xingdan Wang
- Department of Radiotherapy, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Shudong Zhu
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
- Argus Pharmaceuticals, Changsha, China
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15
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Grothusen GP, Chang R, Cao Z, Zhou N, Mittal M, Datta A, Wulfridge P, Beer T, Wang B, Zheng N, Tang HY, Sarma K, Greenberg RA, Shi J, Busino L. DCAF15 control of cohesin dynamics sustains acute myeloid leukemia. Nat Commun 2024; 15:5604. [PMID: 38961054 PMCID: PMC11222469 DOI: 10.1038/s41467-024-49882-x] [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: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The CRL4-DCAF15 E3 ubiquitin ligase complex is targeted by the aryl-sulfonamide molecular glues, leading to neo-substrate recruitment, ubiquitination, and proteasomal degradation. However, the physiological function of DCAF15 remains unknown. Using a domain-focused genetic screening approach, we reveal DCAF15 as an acute myeloid leukemia (AML)-biased dependency. Loss of DCAF15 results in suppression of AML through compromised replication fork integrity and consequent accumulation of DNA damage. Accordingly, DCAF15 loss sensitizes AML to replication stress-inducing therapeutics. Mechanistically, we discover that DCAF15 directly interacts with the SMC1A protein of the cohesin complex and destabilizes the cohesin regulatory factors PDS5A and CDCA5. Loss of PDS5A and CDCA5 removal precludes cohesin acetylation on chromatin, resulting in uncontrolled chromatin loop extrusion, defective DNA replication, and apoptosis. Collectively, our findings uncover an endogenous, cell autonomous function of DCAF15 in sustaining AML proliferation through post-translational control of cohesin dynamics.
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Affiliation(s)
- Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renxu Chang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhendong Cao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Zhou
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Mittal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Datta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Wulfridge
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Thomas Beer
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Baiyun Wang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Bakr A, Corte GD, Veselinov O, Kelekçi S, Chen MJM, Lin YY, Sigismondo G, Iacovone M, Cross A, Syed R, Jeong Y, Sollier E, Liu CS, Lutsik P, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response. Nucleic Acids Res 2024; 52:5698-5719. [PMID: 38587186 PMCID: PMC11162808 DOI: 10.1093/nar/gkae233] [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: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Giuditta Della Corte
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Olivera Veselinov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Mei-Ju May Chen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Marika Iacovone
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Rabail Syed
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Chun- Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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17
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Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
The intricate landscape of cellular processes governing gene transcription, chromatin organization, and genome stability is a fascinating field of study. A key player in maintaining this delicate equilibrium is the cohesin complex, a molecular machine with multifaceted roles. This review presents an in-depth exploration of these intricate connections and their significant impact on various human diseases.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
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18
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Bergis-Ser C, Reji M, Latrasse D, Bergounioux C, Benhamed M, Raynaud C. Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity. NATURE PLANTS 2024; 10:857-873. [PMID: 38658791 DOI: 10.1038/s41477-024-01678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
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Affiliation(s)
- Clara Bergis-Ser
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Meega Reji
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, India
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
- Institut Universitaire de France, Orsay, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France.
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19
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Chen B, Ren C, Ouyang Z, Xu J, Xu K, Li Y, Guo H, Bai X, Tian M, Xu X, Wang Y, Li H, Bo X, Chen H. Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. Brief Bioinform 2024; 25:bbae306. [PMID: 38935071 PMCID: PMC11210073 DOI: 10.1093/bib/bbae306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/01/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.
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Affiliation(s)
- Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Chao Ren
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Kang Xu
- School of Software, Shandong University, Jinan 250101, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hejiang Guo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xuemei Bai
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Mengge Tian
- The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yuyang Wang
- College of Computer and Data Science, Fuzhou University, Fuzhou 350108, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
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20
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Wang J, Sadeghi CA, Frock RL. DNA-PKcs suppresses illegitimate chromosome rearrangements. Nucleic Acids Res 2024; 52:5048-5066. [PMID: 38412274 PMCID: PMC11109964 DOI: 10.1093/nar/gkae140] [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: 07/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in humans and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-exclusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.
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Affiliation(s)
- Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne A Sadeghi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard L Frock
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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21
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Biot M, Toth A, Brun C, Guichard L, de Massy B, Grey C. Principles of chromosome organization for meiotic recombination. Mol Cell 2024; 84:1826-1841.e5. [PMID: 38657614 DOI: 10.1016/j.molcel.2024.04.001] [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: 11/15/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identify three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form; binding sites of the insulator protein CTCF; and H3K4me3-enriched sites. We demonstrate that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1, and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.
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Affiliation(s)
- Mathilde Biot
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Attila Toth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Dresden, Germany
| | - Christine Brun
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Leon Guichard
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Bernard de Massy
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Corinne Grey
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
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22
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Jin P, Duan X, Li L, Zhou P, Zou C, Xie K. Cellular senescence in cancer: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2024; 5:e542. [PMID: 38660685 PMCID: PMC11042538 DOI: 10.1002/mco2.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024] Open
Abstract
Aging exhibits several hallmarks in common with cancer, such as cellular senescence, dysbiosis, inflammation, genomic instability, and epigenetic changes. In recent decades, research into the role of cellular senescence on tumor progression has received widespread attention. While how senescence limits the course of cancer is well established, senescence has also been found to promote certain malignant phenotypes. The tumor-promoting effect of senescence is mainly elicited by a senescence-associated secretory phenotype, which facilitates the interaction of senescent tumor cells with their surroundings. Targeting senescent cells therefore offers a promising technique for cancer therapy. Drugs that pharmacologically restore the normal function of senescent cells or eliminate them would assist in reestablishing homeostasis of cell signaling. Here, we describe cell senescence, its occurrence, phenotype, and impact on tumor biology. A "one-two-punch" therapeutic strategy in which cancer cell senescence is first induced, followed by the use of senotherapeutics for eliminating the senescent cells is introduced. The advances in the application of senotherapeutics for targeting senescent cells to assist cancer treatment are outlined, with an emphasis on drug categories, and the strategies for their screening, design, and efficient targeting. This work will foster a thorough comprehension and encourage additional research within this field.
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Affiliation(s)
- Ping Jin
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Xirui Duan
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Lei Li
- Department of Anorectal SurgeryHospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese MedicineChengduChina
| | - Ping Zhou
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Cheng‐Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Ke Xie
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
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23
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Min J, Gautier J. Chromatin compartments at DNA double-stranded breaks. Cell Res 2024; 34:337-338. [PMID: 38097773 PMCID: PMC11061130 DOI: 10.1038/s41422-023-00912-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Affiliation(s)
- Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeon, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeon, New York, NY, USA.
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24
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Raimer Young HM, Hou PC, Bartosik AR, Atkin ND, Wang L, Wang Z, Ratan A, Zang C, Wang YH. DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity. Nucleic Acids Res 2024; 52:3837-3855. [PMID: 38452213 DOI: 10.1093/nar/gkae164] [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: 08/15/2023] [Revised: 02/03/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.
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Affiliation(s)
- Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Pei-Chi Hou
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Anna R Bartosik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
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25
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Qu H, Wang Y, Yan Q, Fan C, Zhang X, Wang D, Guo C, Chen P, Shi L, Liao Q, Zhou M, Wang F, Zeng Z, Xiang B, Xiong W. CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair. J Exp Clin Cancer Res 2024; 43:122. [PMID: 38654320 PMCID: PMC11036759 DOI: 10.1186/s13046-024-03049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Radiation therapy stands to be one of the primary approaches in the clinical treatment of malignant tumors. Nasopharyngeal Carcinoma, a malignancy predominantly treated with radiation therapy, provides an invaluable model for investigating the mechanisms underlying radiation therapy resistance in cancer. While some reports have suggested the involvement of circRNAs in modulating resistance to radiation therapy, the underpinning mechanisms remain unclear. METHODS RT-qPCR and in situ hybridization were used to detect the expression level of circCDYL2 in nasopharyngeal carcinoma tissue samples. The effect of circCDYL2 on radiotherapy resistance in nasopharyngeal carcinoma was demonstrated by in vitro and in vivo functional experiments. The HR-GFP reporter assay determined that circCDYL2 affected homologous recombination repair. RNA pull down, RIP, western blotting, IF, and polysome profiling assays were used to verify that circCDYL2 promoted the translation of RAD51 by binding to EIF3D protein. RESULTS We have identified circCDYL2 as highly expressed in nasopharyngeal carcinoma tissues, and it was closely associated with poor prognosis. In vitro and in vivo experiments demonstrate that circCDYL2 plays a pivotal role in promoting radiotherapy resistance in nasopharyngeal carcinoma. Our investigation unveils a specific mechanism by which circCDYL2, acting as a scaffold molecule, recruits eukaryotic translation initiation factor 3 subunit D protein (EIF3D) to the 5'-UTR of RAD51 mRNA, a crucial component of the DNA damage repair pathway to facilitate the initiation of RAD51 translation and enhance homologous recombination repair capability, and ultimately leads to radiotherapy resistance in nasopharyngeal carcinoma. CONCLUSIONS These findings establish a novel role of the circCDYL2/EIF3D/RAD51 axis in nasopharyngeal carcinoma radiotherapy resistance. Our work not only sheds light on the underlying molecular mechanism but also highlights the potential of circCDYL2 as a therapeutic sensitization target and a promising prognostic molecular marker for nasopharyngeal carcinoma.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Xiangyan Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Lei Shi
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
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26
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Schneck C, Smrek J, Likos CN, Zöttl A. Supercoiled ring polymers under shear flow. NANOSCALE 2024. [PMID: 38639709 DOI: 10.1039/d3nr04258h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu et al., Commun. Mater. 2020, 1, 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.
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Affiliation(s)
- Christoph Schneck
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Andreas Zöttl
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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27
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Nie H, Kong X, Song X, Guo X, Li Z, Fan C, Zhai B, Yang X, Wang Y. Roles of histone post-translational modifications in meiosis†. Biol Reprod 2024; 110:648-659. [PMID: 38224305 DOI: 10.1093/biolre/ioae011] [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: 09/11/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024] Open
Abstract
Histone post-translational modifications, such as phosphorylation, methylation, acetylation, and ubiquitination, play vital roles in various chromatin-based cellular processes. Meiosis is crucial for organisms that depend on sexual reproduction to produce haploid gametes, during which chromatin undergoes intricate conformational changes. An increasing body of evidence is clarifying the essential roles of histone post-translational modifications during meiotic divisions. In this review, we concentrate on the post-translational modifications of H2A, H2B, H3, and H4, as well as the linker histone H1, that are required for meiosis, and summarize recent progress in understanding how these modifications influence diverse meiotic events. Finally, challenges and exciting open questions for future research in this field are discussed. Summary Sentence Diverse histone post-translational modifications exert important effects on the meiotic cell cycle and these "histone codes" in meiosis might lead to the development of novel therapeutic strategies against reproductive diseases.
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Affiliation(s)
- Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xueyu Kong
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Song
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Guo
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Zhanyu Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Cunxian Fan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Binyuan Zhai
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiao Yang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Ying Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
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28
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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29
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Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R. Sister chromatid cohesion halts DNA loop expansion. Mol Cell 2024; 84:1139-1148.e5. [PMID: 38452765 DOI: 10.1016/j.molcel.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are folded into DNA loops mediated by structural maintenance of chromosomes (SMC) complexes such as cohesin, condensin, and Smc5/6. This organization regulates different DNA-related processes along the cell cycle, such as transcription, recombination, segregation, and DNA repair. During the G2 stage, SMC-mediated DNA loops coexist with cohesin complexes involved in sister chromatid cohesion (SCC). However, the articulation between the establishment of SCC and the formation of SMC-mediated DNA loops along the chromatin remains unknown. Here, we show that SCC is indeed a barrier to cohesin-mediated DNA loop expansion along G2/M Saccharomyces cerevisiae chromosomes.
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Affiliation(s)
- Nathalie Bastié
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Christophe Chapard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Axel Cournac
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Sanae Nejmi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
| | - Henri Mboumba
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Gadal
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Frederic Beckouët
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France.
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30
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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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31
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Kim J, Wang H, Ercan S. Cohesin mediated loop extrusion from active enhancers form chromatin jets in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558239. [PMID: 37786717 PMCID: PMC10541618 DOI: 10.1101/2023.09.18.558239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
In mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication between cis-regulatory elements. However, many organisms, including S. cerevisiae , C. elegans , and A. thaliana lack CTCF. Here, we use C. elegans as a model to investigate the function of cohesin in 3D genome organization in an animal without CTCF. We use auxin-inducible degradation to acutely deplete SMC-3 or its negative regulator WAPL-1 from somatic cells. Using Hi-C data, we identify a cohesin-dependent 3D genome organization feature called chromatin jets (aka fountains). These are population average reflections of DNA loops that are ∼20-40 kb in scale and often cover a few transcribed genes. The jets emerge from NIPBL occupied segments, and the trajectory of the jets coincides with cohesin binding. Cohesin translocation from jet origins depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C results support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. The location of putative loading sites coincide with active enhancers and the strength of chromatin jet pattern correlates with transcription. Hi-C analyses upon WAPL-1 depletion reveal unequal loop extrusion processivity on each side and stalling due to cohesin molecules colliding. Compared to mammalian systems, average processivity of C. elegans cohesin is ∼10-fold shorter and NIPBL binding does not depend on cohesin. We conclude that the processivity of cohesin scales with genome size; and regardless of CTCF presence, preferential loading of cohesin at enhancers is a conserved mechanism of genome organization that regulates the interaction of gene regulatory elements in 3D.
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Prasad A, Kanakkanthara A. An ATM D-compartmentalization in DNA damage response. Trends Cell Biol 2024; 34:173-175. [PMID: 38160123 PMCID: PMC10939911 DOI: 10.1016/j.tcb.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
How chromatin configuration impacts DNA repair is an emerging question. A recent study by Arnould et al. shows that ATM orchestrates a new chromatin compartment (D compartment) following DNA double-strand breaks and establishes that this compartment enhances cellular response to such breaks but also introduces a risk to genome integrity.
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Affiliation(s)
- Anjali Prasad
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Arun Kanakkanthara
- Department of Oncology, Mayo Clinic, Rochester, MN, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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33
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Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
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Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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34
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Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024; 25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [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] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
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Affiliation(s)
- Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lorenzo Boninsegna
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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35
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Poignant F, Pariset E, Plante I, Ponomarev AL, Evain T, Viger L, Slaba TC, Blattnig SR, Costes SV. DNA break clustering as a predictor of cell death across various radiation qualities: influence of cell size, cell asymmetry, and beam orientation. Integr Biol (Camb) 2024; 16:zyae015. [PMID: 39299711 DOI: 10.1093/intbio/zyae015] [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: 02/08/2024] [Revised: 08/23/2024] [Indexed: 09/22/2024]
Abstract
Cosmic radiation, composed of high charge and energy (HZE) particles, causes cellular DNA damage that can result in cell death or mutation that can evolve into cancer. In this work, a cell death model is applied to several cell lines exposed to HZE ions spanning a broad range of linear energy transfer (LET) values. We hypothesize that chromatin movement leads to the clustering of multiple double strand breaks (DSB) within one radiation-induced foci (RIF). The survival probability of a cell population is determined by averaging the survival probabilities of individual cells, which is function of the number of pairwise DSB interactions within RIF. The simulation code RITCARD was used to compute DSB. Two clustering approaches were applied to determine the number of RIF per cell. RITCARD outputs were combined with experimental data from four normal human cell lines to derive the model parameters and expand its predictions in response to ions with LET ranging from ~0.2 keV/μm to ~3000 keV/μm. Spherical and ellipsoidal nuclear shapes and two ion beam orientations were modeled to assess the impact of geometrical properties on cell death. The calculated average number of RIF per cell reproduces the saturation trend for high doses and high-LET values that is usually experimentally observed. The cell survival model generates the recognizable bell shape of LET dependence for the relative biological effectiveness (RBE). At low LET, smaller nuclei have lower survival due to increased DNA density and DSB clustering. At high LET, nuclei with a smaller irradiation area-either because of a smaller size or a change in beam orientation-have a higher survival rate due to a change in the distribution of DSB/RIF per cell. If confirmed experimentally, the geometric characteristics of cells would become a significant factor in predicting radiation-induced biological effects. Insight Box: High-charge and energy (HZE) ions are characterized by dense linear energy transfer (LET) that induce unique spatial distributions of DNA damage in cell nuclei that result in a greater biological effect than sparsely ionizing radiation like X-rays. HZE ions are a prominent component of galactic cosmic ray exposure during human spaceflight and specific ions are being used for radiotherapy. Here, we model DNA damage clustering at sub-micrometer scale to predict cell survival. The model is in good agreement with experimental data for a broad range of LET. Notably, the model indicates that nuclear geometry and ion beam orientation affect DNA damage clustering, which reveals their possible role in mediating cell radiosensitivity.
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Affiliation(s)
- Floriane Poignant
- Analytical Mechanics Associates Inc., 21 Enterprise Parkway, Hampton, VA 23666, United States
| | - Eloise Pariset
- NASA Ames Research Center, MS:288/2, Mountain View, CA 94035, United States
- Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, United States
| | - Ianik Plante
- KBR, 2400 NASA Parkway, Houston, TX 77058, United States
| | | | - Trevor Evain
- Life Sciences Division, Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94720, United States
| | - Louise Viger
- Life Sciences Division, Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94720, United States
| | - Tony C Slaba
- NASA Langley Research Center, 1 Nasa Drive, Hampton, VA 23666, United States
| | - Steve R Blattnig
- NASA Langley Research Center, 1 Nasa Drive, Hampton, VA 23666, United States
| | - Sylvain V Costes
- NASA Ames Research Center, MS:288/2, Mountain View, CA 94035, United States
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Chen Y, Wu J, Zhai L, Zhang T, Yin H, Gao H, Zhao F, Wang Z, Yang X, Jin M, Huang B, Ding X, Li R, Yang J, He Y, Wang Q, Wang W, Kloeber JA, Li Y, Hao B, Zhang Y, Wang J, Tan M, Li K, Wang P, Lou Z, Yuan J. Metabolic regulation of homologous recombination repair by MRE11 lactylation. Cell 2024; 187:294-311.e21. [PMID: 38128537 DOI: 10.1016/j.cell.2023.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 08/09/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
Lactylation is a lactate-induced post-translational modification best known for its roles in epigenetic regulation. Herein, we demonstrate that MRE11, a crucial homologous recombination (HR) protein, is lactylated at K673 by the CBP acetyltransferase in response to DNA damage and dependent on ATM phosphorylation of the latter. MRE11 lactylation promotes its binding to DNA, facilitating DNA end resection and HR. Inhibition of CBP or LDH downregulated MRE11 lactylation, impaired HR, and enhanced chemosensitivity of tumor cells in patient-derived xenograft and organoid models. A cell-penetrating peptide that specifically blocks MRE11 lactylation inhibited HR and sensitized cancer cells to cisplatin and PARPi. These findings unveil lactylation as a key regulator of HR, providing fresh insights into the ways in which cellular metabolism is linked to DSB repair. They also imply that the Warburg effect can confer chemoresistance through enhancing HR and suggest a potential therapeutic strategy of targeting MRE11 lactylation to mitigate the effects.
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Affiliation(s)
- Yuping Chen
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jinhuan Wu
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hui Yin
- Department of Thoracic Surgery, The First Affiliated Hospital of Shaoyang University, Shaoyang 422001, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhe Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaoning Yang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mingpeng Jin
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Bingsong Huang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xin Ding
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Rui Li
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jie Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yiming He
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Qianwen Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Yunxuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Zhang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Shanghai 200072, China
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China.
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37
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Fajish G, Challa K, Salim S, Vp A, Mwaniki S, Zhang R, Fujita Y, Ito M, Nishant KT, Shinohara A. DNA double-strand breaks regulate the cleavage-independent release of Rec8-cohesin during yeast meiosis. Genes Cells 2024; 29:86-98. [PMID: 37968127 DOI: 10.1111/gtc.13081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
The mitotic cohesin complex necessary for sister chromatid cohesion and chromatin loop formation shows local and global association to chromosomes in response to DNA double-strand breaks (DSBs). Here, by genome-wide binding analysis of the meiotic cohesin with Rec8, we found that the Rec8-localization profile along chromosomes is altered from middle to late meiotic prophase I with cleavage-independent dissociation. Each Rec8-binding site on the chromosome axis follows a unique alternation pattern with dissociation and probably association. Centromeres showed altered Rec8 binding in late prophase I relative to mid-prophase I, implying chromosome remodeling of the regions. Rec8 dissociation ratio per chromosome is correlated well with meiotic DSB density. Indeed, the spo11 mutant deficient in meiotic DSB formation did not change the distribution of Rec8 along chromosomes in late meiotic prophase I. These suggest the presence of a meiosis-specific regulatory pathway for the global binding of Rec8-cohesin in response to DSBs.
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Affiliation(s)
- Ghanim Fajish
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kiran Challa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Sagar Salim
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Ajith Vp
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Stephen Mwaniki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Ruihao Zhang
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masaru Ito
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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38
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Mao LW, Jiang QY, Meng N, Xiao L, Zhang Q, Chen YX, Liu LJ, Wang L. Sirt6 promotes DNA damage repair in osteoarthritis chondrocytes by activating the Keap1/Nrf2/HO-1 signaling pathway. Cell Cycle 2024; 23:205-217. [PMID: 38389322 PMCID: PMC11037281 DOI: 10.1080/15384101.2024.2316493] [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: 10/17/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The aim of this study was to explore the effect and mechanism of Sirt6 on DNA damage repair in OA chondrocytes. Cartilage tissues were collected from OA patients with knee arthroplasty and traumatic amputation patients without OA. Besides, 7-week-old male C57BL/6 mice were randomly divided into Control and OA groups; CHON-001 cells of corresponding groups were treated with 10 ng/ml interleukin (IL)-1β, respectively. Subsequently, Sirt6 or siNrf2 was over-expressed in CHON-001 cells to observe the effect of Sirt6 on DNA damage and senescence of chondrocytes by IL-1β through the nuclear factor E2-related factor 2 (Nrf2) signaling pathway. The expression level of Sirt6 in human and mouse OA cartilage tissues was significantly decreased. However, 24 h of treatment with IL-1β significantly decreased the expression of Sirt6 in chondrocytes, induced DNA damage, and promoted cellular senescence. In addition, over-expression of Sirt6 promoted DNA damage repair and inhibited cellular senescence in IL-1β-induced chondrocytes. Moreover, the overexpression of Sirt6 activated the Keap1/Nrf2/HO-1 signaling pathway in chondrocytes, while knockdown of Nrf2 expression inhibited the DNA damage repair and anti-senescence effects of Sirt6 on IL-1β-treated chondrocytes. Sirt6 may reduce DNA damage and cellular senescence in OA chondrocytes induced by IL-1β through activating the Keap1/Nrf2/HO-1 signaling pathway.
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Affiliation(s)
- Ling-Wei Mao
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Qin-Yi Jiang
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Nan Meng
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Li Xiao
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Qi Zhang
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yong-Xin Chen
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lin-Juan Liu
- Department of Stomatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lei Wang
- Department of Orthopedics, The Affiliated People’s Hospital with Jiangsu University, Zhenjiang, China
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39
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Jin Z, Shao Z, Yang S, Guo A, Han Y, Wu Y, Zhao Y, Wu Y, Shen J, Zhang M, Zhan X, Diao W, Ying S, Zhang C, Li W, Shen H, Chen Z, Yan F. Airway epithelial cGAS inhibits LPS-induced acute lung injury through CREB signaling. Cell Death Dis 2023; 14:844. [PMID: 38114479 PMCID: PMC10730695 DOI: 10.1038/s41419-023-06364-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Increased levels of cytosolic DNA in lung tissues play an important role in acute lung injury. However, the detailed mechanisms involved remain elusive. Here, we found that cyclic GMP-AMP synthase (cGAS, a cytosolic DNA sensor) expression was increased in airway epithelium in response to increased cytosolic DNA. Conditional deletion of airway epithelial cGAS exacerbated acute lung injury in mice, cGAS knockdown augmented LPS-induced production of interleukin (IL)-6 and IL-8. Mechanically, deletion of cGAS augmented expression of phosphorylated CREB (cAMP response element-binding protein), and cGAS directly interacted with CREB via its C-terminal domain. Furthermore, CREB knockdown rescued the LPS-induced excessive inflammatory response caused by cGAS deletion. Our study demonstrates that airway epithelial cGAS plays a protective role in acute lung injury and confirms a non-canonical cGAS-CREB pathway that regulates the inflammatory responses in airway epithelium to mediate LPS-induced acute lung injury.
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Affiliation(s)
- Zhangchu Jin
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhehua Shao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Shiyi Yang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Anyi Guo
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yinling Han
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yinfang Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yun Zhao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yanping Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Jiaxin Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Min Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xueqin Zhan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310009, Zhejiang, China
| | - Wenqi Diao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Songmin Ying
- International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, 322000, China
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, 310009, China
| | - Chao Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
- Department of Anatomy, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
- State Key Lab of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China.
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Fugui Yan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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40
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Chahar S, Ben Zouari Y, Salari H, Kobi D, Maroquenne M, Erb C, Molitor AM, Mossler A, Karasu N, Jost D, Sexton T. Transcription induces context-dependent remodeling of chromatin architecture during differentiation. PLoS Biol 2023; 21:e3002424. [PMID: 38048351 PMCID: PMC10721200 DOI: 10.1371/journal.pbio.3002424] [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: 04/13/2023] [Revised: 12/14/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Metazoan chromosomes are organized into discrete spatial domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between domain organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow chromatin architecture changes during development, we used Capture Hi-C to interrogate the domains around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and subdomains were formed around some activated genes without changes in CTCF binding. The ectopic induction of some genes was sufficient to recapitulate domain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex chromosome folding patterns that can be important in certain genomic contexts.
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Affiliation(s)
- Sanjay Chahar
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Yousra Ben Zouari
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Dominique Kobi
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Manon Maroquenne
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Cathie Erb
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Anne M. Molitor
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Audrey Mossler
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Nezih Karasu
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Tom Sexton
- University of Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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42
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Arnould C, Rocher V, Saur F, Bader AS, Muzzopappa F, Collins S, Lesage E, Le Bozec B, Puget N, Clouaire T, Mangeat T, Mourad R, Ahituv N, Noordermeer D, Erdel F, Bushell M, Marnef A, Legube G. Chromatin compartmentalization regulates the response to DNA damage. Nature 2023; 623:183-192. [PMID: 37853125 PMCID: PMC10620078 DOI: 10.1038/s41586-023-06635-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 09/12/2023] [Indexed: 10/20/2023]
Abstract
The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated1,2, the contribution of chromosome folding to these processes remains unclear3. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1. This compartment forms by a mechanism that is consistent with polymer-polymer phase separation rather than liquid-liquid phase separation. The D compartment arises mostly in G1 phase, is independent of cohesin and is enhanced after pharmacological inhibition of DNA-dependent protein kinase (DNA-PK) or R-loop accumulation. Importantly, R-loop-enriched DNA-damage-responsive genes physically localize to the D compartment, and this contributes to their optimal activation, providing a function for DSB clustering in the DNA damage response. However, DSB-induced chromosome reorganization comes at the expense of an increased rate of translocations, also observed in cancer genomes. Overall, we characterize how DSB-induced compartmentalization orchestrates the DNA damage response and highlight the critical impact of chromosome architecture in genomic instability.
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Affiliation(s)
- Coline Arnould
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vincent Rocher
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Florian Saur
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Fernando Muzzopappa
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Sarah Collins
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Emma Lesage
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Benjamin Le Bozec
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Nadine Puget
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Thomas Clouaire
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Thomas Mangeat
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Raphael Mourad
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Fabian Erdel
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Martin Bushell
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Aline Marnef
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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43
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Barghouth PG, Melemenidis S, Montay-Gruel P, Ollivier J, Viswanathan V, Jorge PG, Soto LA, Lau BC, Sadeghi C, Edlabadkar A, Zhang R, Ru N, Baulch JE, Manjappa R, Wang J, Le Bouteiller M, Surucu M, Yu A, Bush K, Skinner L, Maxim PG, Loo BW, Limoli CL, Vozenin MC, Frock RL. FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates. Radiother Oncol 2023; 188:109906. [PMID: 37690668 PMCID: PMC10591966 DOI: 10.1016/j.radonc.2023.109906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND AND PURPOSE The impact of radiotherapy (RT) at ultra high vs conventional dose rate (FLASH vs CONV) on the generation and repair of DNA double strand breaks (DSBs) is an important question that remains to be investigated. Here, we tested the hypothesis as to whether FLASH-RT generates decreased chromosomal translocations compared to CONV-RT. MATERIALS AND METHODS We used two FLASH validated electron beams and high-throughput rejoin and genome-wide translocation sequencing (HTGTS-JoinT-seq), employing S. aureus and S. pyogenes Cas9 "bait" DNA double strand breaks (DSBs) in HEK239T cells, to measure differences in bait-proximal repair and their genome-wide translocations to "prey" DSBs generated after various irradiation doses, dose rates and oxygen tensions (normoxic, 21% O2; physiological, 4% O2; hypoxic, 2% and 0.5% O2). Electron irradiation was delivered using a FLASH capable Varian Trilogy and the eRT6/Oriatron at CONV (0.08-0.13 Gy/s) and FLASH (1x102-5x106 Gy/s) dose rates. Related experiments using clonogenic survival and γH2AX foci in the 293T and the U87 glioblastoma lines were also performed to discern FLASH-RT vs CONV-RT DSB effects. RESULTS Normoxic and physioxic irradiation of HEK293T cells increased translocations at the cost of decreasing bait-proximal repair but were indistinguishable between CONV-RT and FLASH-RT. Although no apparent increase in chromosome translocations was observed with hypoxia-induced apoptosis, the combined decrease in oxygen tension with IR dose-rate modulation did not reveal significant differences in the level of translocations nor in their junction structures. Furthermore, RT dose rate modality on U87 cells did not change γH2AX foci numbers at 1- and 24-hours post-irradiation nor did this affect 293T clonogenic survival. CONCLUSION Irrespective of oxygen tension, FLASH-RT produces translocations and junction structures at levels and proportions that are indistinguishable from CONV-RT.
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Affiliation(s)
- Paul G Barghouth
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stavros Melemenidis
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre Montay-Gruel
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland; Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Jonathan Ollivier
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Vignesh Viswanathan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrik G Jorge
- Institute of Radiation Physics/CHUV, Lausanne University Hospital, Switzerland
| | - Luis A Soto
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brianna C Lau
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne Sadeghi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anushka Edlabadkar
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard Zhang
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Ning Ru
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Janet E Baulch
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Rakesh Manjappa
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinghui Wang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marie Le Bouteiller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Murat Surucu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amy Yu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karl Bush
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lawrie Skinner
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter G Maxim
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles L Limoli
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Marie-Catherine Vozenin
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Richard L Frock
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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44
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van Schie JJM, de Lint K, Molenaar TM, Moronta Gines M, Balk J, Rooimans M, Roohollahi K, Pai G, Borghuis L, Ramadhin A, Corazza F, Dorsman J, Wendt K, Wolthuis RF, de Lange J. CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin. Nucleic Acids Res 2023; 51:9594-9609. [PMID: 37702151 PMCID: PMC10570055 DOI: 10.1093/nar/gkad756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.
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Affiliation(s)
- Janne J M van Schie
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Klaas de Lint
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Thom M Molenaar
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | | | - Jesper A Balk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Khashayar Roohollahi
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Govind M Pai
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Lauri Borghuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Anisha R Ramadhin
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Francesco Corazza
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Josephine C Dorsman
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Kerstin S Wendt
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Job de Lange
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
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45
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Alonso-Gil D, Losada A. NIPBL and cohesin: new take on a classic tale. Trends Cell Biol 2023; 33:860-871. [PMID: 37062615 DOI: 10.1016/j.tcb.2023.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
Cohesin folds the genome in dynamic chromatin loops and holds the sister chromatids together. NIPBLScc2 is currently considered the cohesin loader, a role that may need reevaluation. NIPBL activates the cohesin ATPase, which is required for topological entrapment of sister DNAs and to fuel DNA loop extrusion, but is not required for chromatin association. Mechanistic dissection of these processes suggests that both NIPBL and the cohesin STAG subunit bind DNA. NIPBL also regulates conformational switches of the complex. Interactions of NIPBL with chromatin factors, including remodelers, replication proteins, and the transcriptional machinery, affect cohesin loading and distribution. Here, we discuss recent research addressing how NIPBL modulates cohesin activities and how its mutation causes a developmental disorder, Cornelia de Lange Syndrome (CdLS).
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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46
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Wu Y, Adeel MM, Sancar A, Li W. Nucleotide Excision Repair of Aflatoxin-induced DNA Damage within the 3D Human Genome Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559858. [PMID: 37808841 PMCID: PMC10557652 DOI: 10.1101/2023.09.27.559858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aflatoxin B1 (AFB1), a potent mycotoxin, is one of the two primary risk factors that cause liver cancer. In the liver, the bioactivated AFB1 intercalates into the DNA double helix to form a bulky DNA adduct which will lead to mutation if left unrepaired. We have adapted the tXR-seq method to measure the nucleotide excision repair of AFB1-induced DNA adducts. We have found that transcription-coupled repair plays a major role in the damage removal process and the released excision products have a distinctive length distribution pattern. We further analyzed the impact of 3D genome organization on the repair of AFB1-induced DNA adducts. We have revealed that chromosomes close to the nuclear center and A compartments undergo expedited repair processes. Notably, we observed an accelerated repair around both TAD boundaries and loop anchors. These findings provide insights into the complex interplay between repair, transcription, and 3D genome organization, shedding light on the mechanisms underlying AFB1-induced liver cancer.
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Affiliation(s)
- Yiran Wu
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
| | - Muhammad Muzammal Adeel
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Wentao Li
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
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47
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Dileep V, Boix CA, Mathys H, Marco A, Welch GM, Meharena HS, Loon A, Jeloka R, Peng Z, Bennett DA, Kellis M, Tsai LH. Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration. Cell 2023; 186:4404-4421.e20. [PMID: 37774679 PMCID: PMC10697236 DOI: 10.1016/j.cell.2023.08.038] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/02/2023] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.
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Affiliation(s)
- Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gwyneth M Welch
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anjanet Loon
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ritika Jeloka
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhuyu Peng
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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48
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Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Nat Commun 2023; 14:5615. [PMID: 37699887 PMCID: PMC10497529 DOI: 10.1038/s41467-023-41265-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
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Affiliation(s)
- Li-Hsin Chang
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, and National Institute of Health Research, Blood and Transplant Research Unit in Precision Cellular Therapeutics, OX3 9DS, Oxford, UK
| | - Sourav Ghosh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Pathology and Laboratory Medicine, Western University, N6A3K7, London, ON, Canada
| | - Andrea Papale
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
| | - Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Vincent Piras
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Joanne Edouard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mallory Poncelet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nathan Lecouvreur
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sébastien Bloyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Holcman
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
- Churchill College, University of Cambridge, CB3 0DS, Cambridge, UK
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Heyza JR, Mikhova M, Schmidt JC. Live cell single-molecule imaging to study DNA repair in human cells. DNA Repair (Amst) 2023; 129:103540. [PMID: 37467632 PMCID: PMC10530516 DOI: 10.1016/j.dnarep.2023.103540] [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: 03/31/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
The genetic material in human cells is continuously exposed to a wide variety of insults that can induce different DNA lesions. To maintain genomic stability and prevent potentially deleterious genetic changes caused by DNA damage, mammalian cells have evolved a number of pathways that repair specific types of DNA damage. These DNA repair pathways vary in their accuracy, some providing high-fidelity repair while others are error-prone and are only activated as a last resort. Adding additional complexity to cellular mechanisms of DNA repair is the DNA damage response which is a sophisticated a signaling network that coordinates repair outcomes, cell-cycle checkpoint activation, and cell fate decisions. As a result of the sheer complexity of the various DNA repair pathways and the DNA damage response there are large gaps in our understanding of the molecular mechanisms underlying DNA damage repair in human cells. A key unaddressed question is how the dynamic recruitment of DNA repair factors contributes to repair kinetics and repair pathway choice in human cells. Methodological advances in live cell single-molecule imaging over the last decade now allow researchers to directly observe and analyze the dynamics of DNA repair proteins in living cells with high spatiotemporal resolution. Live cell single-molecule imaging combined with single-particle tracking can provide direct insight into the biochemical reactions that control DNA repair and has the power to identify previously unobservable processes in living cells. This review summarizes the main considerations for experimental design and execution for live cell single-molecule imaging experiments and describes how they can be used to define the molecular mechanisms of DNA damage repair in mammalian cells.
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Affiliation(s)
- Joshua R Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Mariia Mikhova
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA.
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50
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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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