1
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Liu HL, Nan H, Zhao WW, Wan XB, Fan XJ. Phase separation in DNA double-strand break response. Nucleus 2024; 15:2296243. [PMID: 38146123 PMCID: PMC10761171 DOI: 10.1080/19491034.2023.2296243] [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: 03/07/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023] Open
Abstract
DNA double-strand break (DSB) is the most dangerous type of DNA damage, which may lead to cell death or oncogenic mutations. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are two typical DSB repair mechanisms. Recently, many studies have revealed that liquid-liquid phase separation (LLPS) plays a pivotal role in DSB repair and response. Through LLPS, the crucial biomolecules are quickly recruited to damaged sites with a high concentration to ensure DNA repair is conducted quickly and efficiently, which facilitates DSB repair factors activating downstream proteins or transmitting signals. In addition, the dysregulation of the DSB repair factor's phase separation has been reported to promote the development of a variety of diseases. This review not only provides a comprehensive overview of the emerging roles of LLPS in the repair of DSB but also sheds light on the regulatory patterns of phase separation in relation to the DNA damage response (DDR).
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Affiliation(s)
- Huan-Lei Liu
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- College of Life Sciences, Northwest AF University, Yangling, Shaanxi, China
| | - Hao Nan
- College of Life Sciences, Northwest AF University, Yangling, Shaanxi, China
| | - Wan-Wen Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
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2
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Qin Y, Shi L. Lighting ATR/Chk1 by mesoscale TopBP1 condensates. Trends Cell Biol 2024:S0962-8924(24)00073-4. [PMID: 38714421 DOI: 10.1016/j.tcb.2024.04.002] [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: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Biomolecular condensation has gained considerable attention as a fundamental mechanism in cell signaling and various biological processes. A recent study by Egger et al. provides valuable insights into the constituents of topoisomerase IIβ binding protein 1 (TopBP1) condensates and sheds light on the mechanism of Chk1 activation by ataxia telangiectasia-mutated and Rad3-related (ATR) at the interface of these condensates.
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Affiliation(s)
- Yan Qin
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin 300070, China
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin 300070, China.
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3
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Sun X, Zhou Y, Wang Z, Peng M, Wei X, Xie Y, Wen C, Liu J, Ye M. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices. Int J Mol Sci 2024; 25:4127. [PMID: 38612940 PMCID: PMC11012904 DOI: 10.3390/ijms25074127] [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: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted.
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Affiliation(s)
- Xing Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Yangyang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Zhiyan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Yifang Xie
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Chengcai Wen
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
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4
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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5
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Bao K, Ma Y, Li Y, Shen X, Zhao J, Tian S, Zhang C, Liang C, Zhao Z, Yang Y, Zhang K, Yang N, Meng FL, Hao J, Yang J, Liu T, Yao Z, Ai D, Shi L. A di-acetyl-decorated chromatin signature couples liquid condensation to suppress DNA end synapsis. Mol Cell 2024; 84:1206-1223.e15. [PMID: 38423014 DOI: 10.1016/j.molcel.2024.02.002] [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: 12/27/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Appropriate DNA end synapsis, regulated by core components of the synaptic complex including KU70-KU80, LIG4, XRCC4, and XLF, is central to non-homologous end joining (NHEJ) repair of chromatinized DNA double-strand breaks (DSBs). However, it remains enigmatic whether chromatin modifications can influence the formation of NHEJ synaptic complex at DNA ends, and if so, how this is achieved. Here, we report that the mitotic deacetylase complex (MiDAC) serves as a key regulator of DNA end synapsis during NHEJ repair in mammalian cells. Mechanistically, MiDAC removes combinatorial acetyl marks on histone H2A (H2AK5acK9ac) around DSB-proximal chromatin, suppressing hyperaccumulation of bromodomain-containing protein BRD4 that would otherwise undergo liquid-liquid phase separation with KU80 and prevent the proper installation of LIG4-XRCC4-XLF onto DSB ends. This study provides mechanistic insight into the control of NHEJ synaptic complex assembly by a specific chromatin signature and highlights the critical role of H2A hypoacetylation in restraining unscheduled compartmentalization of DNA repair machinery.
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Affiliation(s)
- Kaiwen Bao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanhui Ma
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yuan Li
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xilin Shen
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiao Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chunyong Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Can Liang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ziyan Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, Beijing, China
| | - Kai Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Hao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhi Yao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ding Ai
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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6
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Fang Y, Bansal K, Mostafavi S, Benoist C, Mathis D. AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization. Nature 2024; 628:400-407. [PMID: 38480882 PMCID: PMC11091860 DOI: 10.1038/s41586-024-07169-7] [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: 02/14/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells1-4. The biological logic of AIRE's target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE's cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice5. Both approaches nominated Z-DNA and NFE2-MAF as putative positive influences on AIRE's target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene's promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.
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Affiliation(s)
- Yuan Fang
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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7
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Han S, Zhao S, Ren H, Jiao Q, Wu X, Hao X, Liu M, Han L, Han L. Novel lncRNA 803 related to Marek's disease inhibits apoptosis of DF-1 cells. Avian Pathol 2024:1-13. [PMID: 38323582 DOI: 10.1080/03079457.2024.2316817] [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: 08/16/2023] [Accepted: 02/02/2024] [Indexed: 02/08/2024]
Abstract
RESEARCH HIGHLIGHTS Differentially expressed lncRNAs in spleens of chickens infected with Marek's disease virus at different stages were identified for the first time.The effects of novel lncRNA 803 on p53 pathway and apoptosis of DF-1 cells were reported for the first time.
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Affiliation(s)
- Shuo Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Shuang Zhao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Haile Ren
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Qianqian Jiao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Xianjia Wu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Xinrui Hao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Mingchun Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Liping Han
- Department of Bioscience, Changchun Normal University, Changchun, People's Republic of China
| | - Limei Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
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8
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Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [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: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
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Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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9
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Chappidi N, Quail T, Doll S, Vogel LT, Aleksandrov R, Felekyan S, Kühnemuth R, Stoynov S, Seidel CAM, Brugués J, Jahnel M, Franzmann TM, Alberti S. PARP1-DNA co-condensation drives DNA repair site assembly to prevent disjunction of broken DNA ends. Cell 2024; 187:945-961.e18. [PMID: 38320550 DOI: 10.1016/j.cell.2024.01.015] [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: 05/09/2023] [Revised: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
DNA double-strand breaks (DSBs) are repaired at DSB sites. How DSB sites assemble and how broken DNA is prevented from separating is not understood. Here we uncover that the synapsis of broken DNA is mediated by the DSB sensor protein poly(ADP-ribose) (PAR) polymerase 1 (PARP1). Using bottom-up biochemistry, we reconstitute functional DSB sites and show that DSB sites form through co-condensation of PARP1 multimers with DNA. The co-condensates exert mechanical forces to keep DNA ends together and become enzymatically active for PAR synthesis. PARylation promotes release of PARP1 from DNA ends and the recruitment of effectors, such as Fused in Sarcoma, which stabilizes broken DNA ends against separation, revealing a finely orchestrated order of events that primes broken DNA for repair. We provide a comprehensive model for the hierarchical assembly of DSB condensates to explain DNA end synapsis and the recruitment of effector proteins for DNA damage repair.
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Affiliation(s)
- Nagaraja Chappidi
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Doll
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ralf Kühnemuth
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jan Brugués
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Marcus Jahnel
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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10
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Nosella ML, Kim TH, Huang SK, Harkness RW, Goncalves M, Pan A, Tereshchenko M, Vahidi S, Rubinstein JL, Lee HO, Forman-Kay JD, Kay LE. Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates. Mol Cell 2024; 84:429-446.e17. [PMID: 38215753 DOI: 10.1016/j.molcel.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
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Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae Hun Kim
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuya Kate Huang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert W Harkness
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Monica Goncalves
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alisia Pan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Lewis E Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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11
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Fu Q, Zhang B, Chen X, Chu L. Liquid-liquid phase separation in Alzheimer's disease. J Mol Med (Berl) 2024; 102:167-181. [PMID: 38167731 DOI: 10.1007/s00109-023-02407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
The pathological aggregation and misfolding of tau and amyloid-β play a key role in Alzheimer's disease (AD). However, the underlying pathological mechanisms remain unclear. Emerging evidences indicate that liquid-liquid phase separation (LLPS) has great impacts on regulating human health and diseases, especially neurodegenerative diseases. A series of studies have revealed the significance of LLPS in AD. In this review, we summarize the latest progress of LLPS in AD, focusing on the impact of metal ions, small-molecule inhibitors, and proteinaceous partners on tau LLPS and aggregation, as well as toxic oligomerization, the role of LLPS on amyloid-β (Aβ) aggregation, and the cross-interactions between amyloidogenic proteins in AD. Eventually, the fundamental methods and techniques used in LLPS study are introduced. We expect to present readers a deeper understanding of the relationship between LLPS and AD.
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Affiliation(s)
- Qinggang Fu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Bixiang Zhang
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiaoping Chen
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liang Chu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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12
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Gopal AA, Fernandez B, Delano J, Weissleder R, Dubach JM. PARP trapping is governed by the PARP inhibitor dissociation rate constant. Cell Chem Biol 2024:S2451-9456(23)00476-2. [PMID: 38262416 DOI: 10.1016/j.chembiol.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 09/13/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a class of cancer drugs that enzymatically inhibit PARP activity at sites of DNA damage. Yet, PARPi function mainly by trapping PARP1 onto DNA with a wide range of potency among the clinically relevant inhibitors. How PARPi trap and why some are better trappers remain unknown. Here, we show trapping occurs primarily through a kinetic phenomenon at sites of DNA damage that correlates with PARPi koff. Our results suggest PARP trapping is not the physical stalling of PARP1 on DNA, rather the high probability of PARP re-binding damaged DNA in the absence of other DNA-binding protein recruitment. These results clarify how PARPi trap, shed new light on how PARPi function, and describe how PARPi properties correlate to trapping potency.
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Affiliation(s)
- Angelica A Gopal
- Institute for Innovation in Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Bianca Fernandez
- Institute for Innovation in Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Justin Delano
- Institute for Innovation in Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - J Matthew Dubach
- Institute for Innovation in Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.
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13
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Shah M, Sarkar D. HCC-Related lncRNAs: Roles and Mechanisms. Int J Mol Sci 2024; 25:597. [PMID: 38203767 PMCID: PMC10779127 DOI: 10.3390/ijms25010597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health threat, particularly in regions endemic to hepatitis B and C viruses, and because of the ongoing pandemic of obesity causing metabolic-dysfunction-related fatty liver disease (MAFLD), a precursor to HCC. The molecular intricacies of HCC, genetic and epigenetic alterations, and dysregulated signaling pathways facilitate personalized treatment strategies based on molecular profiling. Epigenetic regulation, encompassing DNA methyltion, histone modifications, and noncoding RNAs, functions as a critical layer influencing HCC development. Long noncoding RNAs (lncRNAs) are spotlighted for their diverse roles in gene regulation and their potential as diagnostic and therapeutic tools in cancer. In this review, we explore the pivotal role of lncRNAs in HCC, including MAFLD and viral hepatitis, the most prevalent risk factors for hepatocarcinogenesis. The dysregulation of lncRNAs is implicated in HCC progression by modulating chromatin regulation and transcription, sponging miRNAs, and influencing structural functions. The ongoing studies on lncRNAs contribute to a deeper comprehension of HCC pathogenesis and offer promising routes for precision medicine, highlighting the utility of lncRNAs as early biomarkers, prognostic indicators, and therapeutic targets.
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Affiliation(s)
- Mimansha Shah
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Massey Comprehensive Cancer Center, and VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
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14
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Hariprakash JM, Salviato E, La Mastra F, Sebestyén E, Tagliaferri I, Silva RS, Lucini F, Farina L, Cinquanta M, Rancati I, Riboni M, Minardi SP, Roz L, Gorini F, Lanzuolo C, Casola S, Ferrari F. Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. Cancer Res 2024; 84:133-153. [PMID: 37855660 PMCID: PMC10758689 DOI: 10.1158/0008-5472.can-23-1129] [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: 08/29/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue-specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer-target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. SIGNIFICANCE Mapping enhancer-target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.
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Affiliation(s)
| | - Elisa Salviato
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Endre Sebestyén
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Federica Lucini
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Lorenzo Farina
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Ilaria Rancati
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Luca Roz
- Fondazione IRCCS—Istituto Nazionale Tumori, Milan, Italy
| | - Francesca Gorini
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
| | - Chiara Lanzuolo
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Stefano Casola
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesco Ferrari
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” National Research Council (IGM-CNR), Pavia, Italy
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15
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Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
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Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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16
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Long Q, Sebesta M, Sedova K, Haluza V, Alagia A, Liu Z, Stefl R, Gullerova M. The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell Rep 2023; 42:113489. [PMID: 38039132 DOI: 10.1016/j.celrep.2023.113489] [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: 08/17/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Double-strand breaks (DSBs) are the most severe type of DNA damage. Previously, we demonstrated that RNA polymerase II (RNAPII) phosphorylated at the tyrosine 1 (Y1P) residue of its C-terminal domain (CTD) generates RNAs at DSBs. However, the regulation of transcription at DSBs remains enigmatic. Here, we show that the damage-activated tyrosine kinase c-Abl phosphorylates hSSB1, enabling its interaction with Y1P RNAPII at DSBs. Furthermore, the trimeric SOSS1 complex, consisting of hSSB1, INTS3, and c9orf80, binds to Y1P RNAPII in response to DNA damage in an R-loop-dependent manner. Specifically, hSSB1, as a part of the trimeric SOSS1 complex, exhibits a strong affinity for R-loops, even in the presence of replication protein A (RPA). Our in vitro and in vivo data reveal that the SOSS1 complex and RNAPII form dynamic liquid-like repair compartments at DSBs. Depletion of the SOSS1 complex impairs DNA repair, underscoring its biological role in the R-loop-dependent DNA damage response.
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Affiliation(s)
- Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic.
| | - Katerina Sedova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Vojtech Haluza
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Zhichao Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Richard Stefl
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic; National Center for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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17
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Gómez-González B, Aguilera A. Break-induced RNA-DNA hybrids (BIRDHs) in homologous recombination: friend or foe? EMBO Rep 2023; 24:e57801. [PMID: 37818834 DOI: 10.15252/embr.202357801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Double-strand breaks (DSBs) are the most harmful DNA lesions, with a strong impact on cell proliferation and genome integrity. Depending on cell cycle stage, DSBs are preferentially repaired by non-homologous end joining or homologous recombination (HR). In recent years, numerous reports have revealed that DSBs enhance DNA-RNA hybrid formation around the break site. We call these hybrids "break-induced RNA-DNA hybrids" (BIRDHs) to differentiate them from sporadic R-loops consisting of DNA-RNA hybrids and a displaced single-strand DNA occurring co-transcriptionally in intact DNA. Here, we review and discuss the most relevant data about BIRDHs, with a focus on two main questions raised: (i) whether BIRDHs form by de novo transcription after a DSB or by a pre-existing nascent RNA in DNA regions undergoing transcription and (ii) whether they have a positive role in HR or are just obstacles to HR accidentally generated as an intrinsic risk of transcription. We aim to provide a comprehensive view of the exciting and yet unresolved questions about the source and impact of BIRDHs in the cell.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Seville, Spain
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18
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Zheng S, Tian Q, Yuan Y, Sun S, Li T, Xia R, He R, Luo Y, Lin Q, Fu Z, Zhou Y, Chen R, Hu C. Extracellular vesicle-packaged circBIRC6 from cancer-associated fibroblasts induce platinum resistance via SUMOylation modulation in pancreatic cancer. J Exp Clin Cancer Res 2023; 42:324. [PMID: 38012734 PMCID: PMC10683239 DOI: 10.1186/s13046-023-02854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/07/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) play pivotal roles in chemoresistance of pancreatic ductal adenocarcinoma (PDAC). However, the underlying mechanisms are poorly understood. Revealing the cross-talk network between tumor stroma and pancreatic cancer and developing effective strategies against oxaliplatin resistance are highly desired in the clinic. METHODS High-throughput sequence was used to screened the key circRNAs transmitted by extracellular vesicles (EVs) from CAFs to pancreatic cancer cells. The associations between EV-packaged circBIRC6 and chemotherapy responsiveness were validated in a cohort of 82 cases of advanced PDAC patients. Then, the effects of EV-packaged circBIRC6 on CAF-induced oxaliplatin resistance were investigated by flow cytometry, colony formation, viability of pancreatic cancer organoids in vitro and by xenograft models in vivo. RNA pulldown, RNA immunoprecipitation, and sites mutation assays were used to reveal the underlying mechanism. RESULTS We identified a circRNA, circBIRC6, is significantly upregulated in CAF-derived EVs and is positively associated with oxaliplatin-based chemoresistance. In vitro and in vivo functional assays showed that CAF-derived EV-packaged circBIRC6 enhance oxaliplatin resistance of pancreatic cancer cells and organoids via regulating the non-homologous end joining (NHEJ) dependent DNA repair. Mechanistically, circBIRC6 directly binds with XRCC4 and enhanced the interaction of XRCC4 with SUMO1 at the lysine 115 residue, which facilitated XRCC4 chromatin localization. XRCC4K115R mutation dramatically abrogated the EV-packaged circBIRC6 induced effect. Moreover, combination of antisense oligonucleotide inhibitors against circBIRC6 with Olaparib dramatically suppressed chemoresistance in patient-derived xenograft models. CONCLUSIONS Our study revealed that EV-packaged circBIRC6 confer oxaliplatin resistance in PDAC by mediating SUMOylation of XRCC4, introducing a promising predictive and therapeutic target for PDAC on oxaliplatin resistance.
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Affiliation(s)
- Shangyou Zheng
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Qing Tian
- School of medicine, South China University of Technology, Guangzhou, 510006, Guangdong Province, China
| | - Yuan Yuan
- Guangdong cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
| | - Shuxin Sun
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Tingting Li
- School of medicine, South China University of Technology, Guangzhou, 510006, Guangdong Province, China
| | - Renpeng Xia
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Rihua He
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China
- Shantou University Medical College, Shantou, 515041, Guangdong province, China
| | - Yuming Luo
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Qing Lin
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Zhiqiang Fu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Yu Zhou
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China.
| | - Rufu Chen
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China.
- School of medicine, South China University of Technology, Guangzhou, 510006, Guangdong Province, China.
- Guangdong cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China.
| | - Chonghui Hu
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, 510080, Guangdong, China.
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19
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Wang YL, Zhao WW, Shi J, Wan XB, Zheng J, Fan XJ. Liquid-liquid phase separation in DNA double-strand breaks repair. Cell Death Dis 2023; 14:746. [PMID: 37968256 PMCID: PMC10651886 DOI: 10.1038/s41419-023-06267-0] [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: 12/26/2022] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
DNA double-strand breaks (DSBs) are the fatal type of DNA damage mostly induced by exposure genome to ionizing radiation or genotoxic chemicals. DSBs are mainly repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). To repair DSBs, a large amount of DNA repair factors was observed to be concentrated at the end of DSBs in a specific spatiotemporal manner to form a repair center. Recently, this repair center was characterized as a condensate derived from liquid-liquid phase separation (LLPS) of key DSBs repair factors. LLPS has been found to be the mechanism of membraneless organelles formation and plays key roles in a variety of biological processes. In this review, the recent advances and mechanisms of LLPS in the formation of DSBs repair-related condensates are summarized.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
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20
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Rosso I, Jones-Weinert C, Rossiello F, Cabrini M, Brambillasca S, Munoz-Sagredo L, Lavagnino Z, Martini E, Tedone E, Garre' M, Aguado J, Parazzoli D, Mione M, Shay JW, Mercurio C, d'Adda di Fagagna F. Alternative lengthening of telomeres (ALT) cells viability is dependent on C-rich telomeric RNAs. Nat Commun 2023; 14:7086. [PMID: 37925537 PMCID: PMC10625592 DOI: 10.1038/s41467-023-42831-0] [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: 03/24/2022] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism activated in ~10-15% of cancers, characterized by telomeric damage. Telomeric damage-induced long non-coding RNAs (dilncRNAs) are transcribed at dysfunctional telomeres and contribute to telomeric DNA damage response (DDR) activation and repair. Here we observed that telomeric dilncRNAs are preferentially elevated in ALT cells. Inhibition of C-rich (teloC) dilncRNAs with antisense oligonucleotides leads to DNA replication stress responses, increased genomic instability, and apoptosis induction selectively in ALT cells. Cell death is dependent on DNA replication and is increased by DNA replication stress. Mechanistically, teloC dilncRNA inhibition reduces RAD51 and 53BP1 recruitment to telomeres, boosts the engagement of BIR machinery, and increases C-circles and telomeric sister chromatid exchanges, without increasing telomeric non-S phase synthesis. These results indicate that teloC dilncRNA is necessary for a coordinated recruitment of DDR factors to ALT telomeres and it is essential for ALT cancer cells survival.
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Affiliation(s)
- Ilaria Rosso
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Corey Jones-Weinert
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Matteo Cabrini
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Brambillasca
- IFOM ETS - The AIRC Institute of Molecular Oncology (Experimental Therapeutics Program), Milan, Italy
| | - Leonel Munoz-Sagredo
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- School of Medicine, Universidad de Valparaiso, Valparaiso, Chile
| | - Zeno Lavagnino
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Emanuele Martini
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Enzo Tedone
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Massimiliano Garre'
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- RCSI, Royal College of Surgeons in Ireland, Department of Chemistry, Dublin, Ireland
| | - Julio Aguado
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Dario Parazzoli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marina Mione
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ciro Mercurio
- IFOM ETS - The AIRC Institute of Molecular Oncology (Experimental Therapeutics Program), Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy.
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21
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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22
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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: 6] [Impact Index Per Article: 6.0] [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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23
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Zhang L, Xu J, Li M, Chen X. The role of long noncoding RNAs in liquid-liquid phase separation. Cell Signal 2023; 111:110848. [PMID: 37557974 DOI: 10.1016/j.cellsig.2023.110848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are among the most well-characterized noncoding RNAs, have attracted much attention due to their regulatory functions and potential therapeutic options in many types of disease. Liquid-liquid phase separation (LLPS), the formation of droplet condensates, is involved in various cellular processes, but the molecular interactions of lncRNAs in LLPS are unclear. In this review, we describe the research development on LLPS, including descriptions of various methods established to identify LLPS, summarize the physiological and pathological functions of LLPS, identify the molecular interactions of lncRNAs in LLPS, and present the potential applications of leveraging LLPS in the clinic. The aim of this review is to update the knowledge on the association between LLPS and lncRNAs, which might provide a new direction for the treatment of LLPS-mediated disease.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Jinjin Xu
- Department of Imaging Medicine, The People's Hospital of the Inner Mongolia Autonomous Region, Hohhot 010017, Inner Mongolia, China
| | - Muxuan Li
- The First Clinical Medical College of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiujuan Chen
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
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24
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Wysocki R, Rodrigues JI, Litwin I, Tamás MJ. Mechanisms of genotoxicity and proteotoxicity induced by the metalloids arsenic and antimony. Cell Mol Life Sci 2023; 80:342. [PMID: 37904059 PMCID: PMC10616229 DOI: 10.1007/s00018-023-04992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.
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Affiliation(s)
- Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Joana I Rodrigues
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden
| | - Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden.
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25
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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26
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Qin C, Wang YL, Zhou JY, Shi J, Zhao WW, Zhu YX, Bai SM, Feng LL, Bie SY, Zeng B, Zheng J, Zeng GD, Feng WX, Wan XB, Fan XJ. RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment. Nucleic Acids Res 2023; 51:9733-9747. [PMID: 37638744 PMCID: PMC10570032 DOI: 10.1093/nar/gkad686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
RAP80 has been characterized as a component of the BRCA1-A complex and is responsible for the recruitment of BRCA1 to DNA double-strand breaks (DSBs). However, we and others found that the recruitment of RAP80 and BRCA1 were not absolutely temporally synchronized, indicating that other mechanisms, apart from physical interaction, might be implicated. Recently, liquid-liquid phase separation (LLPS) has been characterized as a novel mechanism for the organization of key signaling molecules to drive their particular cellular functions. Here, we characterized that RAP80 LLPS at DSB was required for RAP80-mediated BRCA1 recruitment. Both cellular and in vitro experiments showed that RAP80 phase separated at DSB, which was ascribed to a highly disordered region (IDR) at its N-terminal. Meanwhile, the Lys63-linked poly-ubiquitin chains that quickly formed after DSBs occur, strongly enhanced RAP80 phase separation and were responsible for the induction of RAP80 condensation at the DSB site. Most importantly, abolishing the condensation of RAP80 significantly suppressed the formation of BRCA1 foci, encovering a pivotal role of RAP80 condensates in BRCA1 recruitment and radiosensitivity. Together, our study disclosed a new mechanism underlying RAP80-mediated BRCA1 recruitment, which provided new insight into the role of phase separation in DSB repair.
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Affiliation(s)
- Caolitao Qin
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jin-Ying Zhou
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Ya-Xi Zhu
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Li-Li Feng
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510655, P.R. China
| | - Shu-Ying Bie
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Bing Zeng
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Gastroenterology, Hernia and Abdominal Wall Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wei-Xing Feng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
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27
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Papadopoulos D, Uhl L, Ha SA, Eilers M. Beyond gene expression: how MYC relieves transcription stress. Trends Cancer 2023; 9:805-816. [PMID: 37422352 DOI: 10.1016/j.trecan.2023.06.008] [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: 04/23/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
MYC oncoproteins are key drivers of tumorigenesis. As transcription factors, MYC proteins regulate transcription by all three nuclear polymerases and gene expression. Accumulating evidence shows that MYC proteins are also crucial for enhancing the stress resilience of transcription. MYC proteins relieve torsional stress caused by active transcription, prevent collisions between the transcription and replication machineries, resolve R-loops, and repair DNA damage by participating in a range of protein complexes and forming multimeric structures at sites of genomic instability. We review the key complexes and multimerization properties of MYC proteins that allow them to mitigate transcription-associated DNA damage, and propose that the oncogenic functions of MYC extend beyond the modulation of gene expression.
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Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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28
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Xin D, Gai X, Ma Y, Li Z, Li Q, Yu X. Pre-rRNA Facilitates TopBP1-Mediated DNA Double-Strand Break Response. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206931. [PMID: 37582658 PMCID: PMC10558638 DOI: 10.1002/advs.202206931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/28/2023] [Indexed: 08/17/2023]
Abstract
In response to genotoxic stress-induced DNA damage, TopBP1 mediates ATR activation for signaling transduction and DNA damage repair. However, the detailed molecular mechanism remains elusive. Here, using unbiased protein affinity purification and RNA sequencing, it is found that TopBP1 is associated with pre-ribosomal RNA (pre-rRNA). Pre-rRNA co-localized with TopBP1 at DNA double-strand breaks (DSBs). Similar to pre-rRNA, ribosomal proteins also colocalize with TopBP1 at DSBs. The recruitment of TopBP1 to DSBs is suppressed when cells are transiently treated with RNA polymerase I inhibitor (Pol I-i) to suppress pre-rRNA biogenesis but not protein translation. Moreover, the BRCT4-5 of TopBP1 recognizes pre-rRNA and forms liquid-liquid phase separation (LLPS) with pre-rRNA, which may be the molecular basis of DSB-induced foci of TopBP1. Finally, Pol I-i treatment impairs TopBP1-associated cell cycle checkpoint activation and homologous recombination repair. Collectively, this study reveals that pre-rRNA plays a key role in the TopBP1-dependent DNA damage response.
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Affiliation(s)
- Di Xin
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic DiseaseThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310003China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Xiaochen Gai
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Yidi Ma
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Zexing Li
- School of Life SciencesTianjin UniversityTianjin300072China
| | - Qilin Li
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Xiaochun Yu
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
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Chen J, Shi J, Zheng J, Wang Y, Wan X. Liquid-liquid phase separation in DNA double-strand break repair. Cancer Biol Med 2023; 20:j.issn.2095-3941.2023.0252. [PMID: 37731219 PMCID: PMC10546095 DOI: 10.20892/j.issn.2095-3941.2023.0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Affiliation(s)
- Jia Chen
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Yunlong Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xiangbo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
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Wang T, Shi S, Shi Y, Jiang P, Hu G, Ye Q, Shi Z, Yu K, Wang C, Fan G, Zhao S, Ma H, Chang ACY, Li Z, Bian Q, Lin CP. Chemical-induced phase transition and global conformational reorganization of chromatin. Nat Commun 2023; 14:5556. [PMID: 37689690 PMCID: PMC10492836 DOI: 10.1038/s41467-023-41340-4] [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: 01/27/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Chemicals or drugs can accumulate within biomolecular condensates formed through phase separation in cells. Here, we use super-resolution imaging to search for chemicals that induce phase transition within chromatin at the microscale. This microscopic screening approach reveals that adriamycin (doxorubicin) - a widely used anticancer drug that is known to interact with chromatin - specifically induces visible local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments systematically and quantitatively demonstrate that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces phase transition of H1, forming fibrous aggregates in vitro. These results reveal a phase separation-driven mechanism for a chemotherapeutic drug.
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Affiliation(s)
- Tengfei Wang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Shuxiang Shi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- Lingang Laboratory, 200031, Shanghai, China
| | - Yuanyuan Shi
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Peipei Jiang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qinying Ye
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Zhan Shi
- School of Physical Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Kexin Yu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- iHuman Institute, ShanghaiTech University, 201010, Shanghai, China
| | - Chenguang Wang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Cardiology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoping Fan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- iHuman Institute, ShanghaiTech University, 201010, Shanghai, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Alex C Y Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Cardiology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Li
- School of Physical Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qian Bian
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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Wei M, Huang X, Liao L, Tian Y, Zheng X. SENP1 Decreases RNF168 Phase Separation to Promote DNA Damage Repair and Drug Resistance in Colon Cancer. Cancer Res 2023; 83:2908-2923. [PMID: 37350666 DOI: 10.1158/0008-5472.can-22-4017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/26/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
The DNA damage response (DDR) is essential for the maintenance of genomic stability. Protein posttranslational modifications play pivotal roles in regulating the DDR process. Here, we found that SUMOylated RNF168 undergoes liquid-liquid phase separation (LLPS), which restricts the recruitment of RNF168 to DNA damage sites, reduces RNF168-catalyzed H2A ubiquitination, restrains 53BP1 in nuclear condensates, and ultimately impairs nonhomologous DNA end joining repair efficiency. Sentrin/SUMO-specific protease 1 (SENP1) was identified as a specific deSUMOylase of RNF168, and it was highly expressed in colorectal adenocarcinoma. In response to DNA damage, SENP1 decreased RNF168 SUMOylation and prevented RNF168 from forming nuclear condensates, thus promoting damage repair efficiency and cancer cell resistance to DNA damaging agents. Moreover, high SENP1 expression correlated with poor prognosis in patients with cancer, and SENP1 depletion sensitized cancer cells to chemotherapy. In summary, these findings reveal DDR is suppressed by SUMOylation-induced LLPS of RNF168 and suggest that SENP1 is a potential target for cancer therapy. SIGNIFICANCE Sentrin/SUMO-specific protease 1 decreases RNF168 SUMOylation and liquid-liquid phase separation to promote DNA damage repair, safeguarding genomic integrity and driving chemotherapy resistance.
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Affiliation(s)
- Min Wei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xinping Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Liming Liao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Yonglu Tian
- School of Psychological and Cognitive Sciences, Peking University, Beijing, China
- IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
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32
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Yin C, Sun A, Guo T, Mao X, Fang Y. Arabidopsis lamin-like proteins CRWN1 and CRWN2 interact with SUPPRESSOR OF NPR1-1 INDUCIBLE 1 and RAD51D to prevent DNA damage. THE PLANT CELL 2023; 35:3345-3362. [PMID: 37335899 PMCID: PMC10473219 DOI: 10.1093/plcell/koad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/21/2023]
Abstract
Plants cope with various recurring stress conditions that often induce DNA damage, ultimately affecting plant genome integrity, growth, and productivity. The CROWDED NUCLEI (CRWN) family comprises lamin-like proteins with multiple functions, such as regulating gene expression, genome organization, and DNA damage repair in Arabidopsis (Arabidopsis thaliana). However, the mechanisms and consequences of CRWNs in DNA damage repair are largely unknown. Here, we reveal that CRWNs maintain genome stability by forming repairing nuclear bodies at DNA double-strand breaks. We demonstrate that CRWN1 and CRWN2 physically associate with the DNA damage repair proteins RAD51D and SUPPRESSOR OF NPR1-1 Inducible 1 (SNI1) and act in the same genetic pathway to mediate this process. Moreover, CRWN1 and CRWN2 partially localize at γ-H2AX foci upon DNA damage. Notably, CRWN1 and CRWN2 undergo liquid-liquid phase separation to form highly dynamic droplet-like structures with RAD51D and SNI1 to promote the DNA damage response (DDR). Collectively, our data shed light on the function of plant lamin-like proteins in the DDR and maintenance of genome stability.
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Affiliation(s)
- Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuegao Mao
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Wang J, Muste Sadurni M, Saponaro M. RNAPII response to transcription-blocking DNA lesions in mammalian cells. FEBS J 2023; 290:4382-4394. [PMID: 35731652 PMCID: PMC10952651 DOI: 10.1111/febs.16561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 09/21/2023]
Abstract
RNA polymerase II moves along genes to decode genetic information stored in the mammalian genome into messenger RNA and different forms of non-coding RNA. However, the transcription process is frequently challenged by DNA lesions caused by exogenous and endogenous insults, among which helix-distorting DNA lesions and double-stranded DNA breaks are particularly harmful for cell survival. In response to such DNA damage, RNA polymerase II transcription is regulated both locally and globally by multi-layer mechanisms, whereas transcription-blocking lesions are repaired before transcription can recover. Failure in DNA damage repair will cause genome instability and cell death. Although recent studies have expanded our understanding of RNA polymerase II regulation confronting DNA lesions, it is still not always clear what the direct contribution of RNA polymerase II is in the DNA damage repair processes. In this review, we focus on how RNA polymerase II and transcription are both repressed by transcription stalling lesions such as DNA-adducts and double strand breaks, as well as how they are actively regulated to support the cellular response to DNA damage and favour the repair of lesions.
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Affiliation(s)
- Jianming Wang
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Martina Muste Sadurni
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
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Xu C, Kim A, Corbin JM, Wang GG. Onco-condensates: formation, multi-component organization, and biological functions. Trends Cancer 2023; 9:738-751. [PMID: 37349246 PMCID: PMC10524369 DOI: 10.1016/j.trecan.2023.05.006] [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: 03/28/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
Numerous cellular processes occur in the context of condensates, a type of large, membrane-less biomolecular assembly generated through phase separation. These condensates function as a hub of diversified cellular events by concentrating the required components. Cancer frequently coopts biomolecular condensation mechanisms to promote survival and/or proliferation. Onco-condensates, which refer to those that have causal roles or are critically involved in tumorigenicity, operate to abnormally elevate biological output of a proliferative process, or to suppress a tumor-suppressive pathway, thereby promoting oncogenesis. Here, we summarize advances regarding how multi-component onco-condensates are established and organized to promote oncogenesis, with those related to chromatin and transcription deregulation used as showcases. A better understanding should enable development of new means of targeting onco-condensates as potential therapeutics.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joshua M Corbin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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35
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Liu Z, Qin Z, Liu Y, Xia X, He L, Chen N, Hu X, Peng X. Liquid‒liquid phase separation: roles and implications in future cancer treatment. Int J Biol Sci 2023; 19:4139-4156. [PMID: 37705755 PMCID: PMC10496506 DOI: 10.7150/ijbs.81521] [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: 12/04/2022] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
Liquid‒liquid phase separation (LLPS) is a phenomenon driven by weak interactions between biomolecules, such as proteins and nucleic acids, that leads to the formation of distinct liquid-like condensates. Through LLPS, membraneless condensates are formed, selectively concentrating specific proteins while excluding other molecules to maintain normal cellular functions. Emerging evidence shows that cancer-related mutations cause aberrant condensate assembly, resulting in disrupted signal transduction, impaired DNA repair, and abnormal chromatin organization and eventually contributing to tumorigenesis. The objective of this review is to summarize recent advancements in understanding the potential implications of LLPS in the contexts of cancer progression and therapeutic interventions. By interfering with LLPS, it may be possible to restore normal cellular processes and inhibit tumor progression. The underlying mechanisms and potential drug targets associated with LLPS in cancer are discussed, shedding light on promising opportunities for novel therapeutic interventions.
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Affiliation(s)
- Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zijian Qin
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingtong Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu 610041, Sichuan, China
| | - Xi Xia
- Shanghai ETERN Biopharma Co., Ltd., Shanghai, China
| | - Ling He
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Na Chen
- School of Pharmacy, Chengdu Medical College, Xindu Avenue No 783, Chengdu, 610500, Sichuan Province, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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Guareschi S, Ravasi M, Baldessari D, Pozzi S, Zaffino T, Melazzini M, Ambrosini A. The positive impact on translational research of Fondazione italiana di ricerca per la Sclerosi Laterale Amiotrofica (AriSLA), a non-profit foundation focused on amyotrophic lateral sclerosis. Convergence of ex-ante evaluation and ex-post outcomes when goals are set upfront. Front Res Metr Anal 2023; 8:1067981. [PMID: 37601533 PMCID: PMC10436489 DOI: 10.3389/frma.2023.1067981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
Charities investing on rare disease research greatly contribute to generate ground-breaking knowledge with the clear goal of finding a cure for their condition of interest. Although the amount of their investments may be relatively small compared to major funders, the advocacy groups' clear mission promotes innovative research and aggregates highly motivated and mission-oriented scientists. Here, we illustrate the case of Fondazione italiana di ricerca per la Sclerosi Laterale Amiotrofica (AriSLA), the main Italian funding agency entirely dedicated to amyotrophic lateral sclerosis research. An international benchmark analysis of publications derived from AriSLA-funded projects indicated that their mean relative citation ratio values (iCite dashboard, National Institutes of Health, U.S.) were very high, suggesting a strong influence on the referring international scientific community. An interesting trend of research toward translation based on the "triangle of biomedicine" and paper citations (iCite) was also observed. Qualitative analysis on researchers' accomplishments was convergent with the bibliometric data, indicating a high level of performance of several working groups, lines of research that speak of progression toward clinical translation, and one study that has progressed from the investigation of cellular mechanisms to a Phase 2 international clinical trial. The key elements of the success of the AriSLA investment lie in: (i) the clear definition of the objectives (research with potential impact on patients, no matter how far), (ii) a rigorous peer-review process entrusted to an international panel of experts, (iii) diversification of the portfolio with ad hoc selection criteria, which also contributed to bringing new experts and younger scientists to the field, and (iv) a close interaction of AriSLA stakeholders with scientists, who developed a strong sense of belonging. Periodic review of the portfolio of investments is a vital practice for funding agencies. Sharing information between funding agencies about their own policies and research assessment methods and outcomes help guide the international debate on funding strategies and research directions to be undertaken, particularly in the field of rare diseases, where synergy is a relevant enabling factor.
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Affiliation(s)
| | | | | | | | | | | | - Anna Ambrosini
- Fondazione AriSLA ETS, Milan, Italy
- Fondazione Telethon ETS, Milan, Italy
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37
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Tabe-Bordbar S, Sinha S. Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention. BMC Genomics 2023; 24:395. [PMID: 37442953 DOI: 10.1186/s12864-023-09498-9] [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: 03/15/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Many long non-coding RNAs, known to be involved in transcriptional regulation, are enriched in the nucleus and interact with chromatin. However, their mechanisms of chromatin interaction and the served cellular functions are poorly understood. We sought to characterize the mechanisms of lncRNA nuclear retention by systematically mapping the sequence and chromatin features that distinguish lncRNA-interacting genomic segments. RESULTS We found DNA 5-mer frequencies to be predictive of chromatin interactions for all lncRNAs, suggesting sequence-specificity as a global theme in the interactome. Sequence features representing protein-DNA and protein-RNA binding motifs revealed potential mechanisms for specific lncRNAs. Complementary to these global themes, transcription-related features and DNA-RNA triplex formation potential were noted to be highly predictive for two mutually exclusive sets of lncRNAs. DNA methylation was also noted to be a significant predictor, but only when combined with other epigenomic features. CONCLUSIONS Taken together, our statistical findings suggest that a group of lncRNAs interacts with transcriptionally inactive chromatin through triplex formation, whereas another group interacts with transcriptionally active regions and is involved in DNA Damage Response (DDR) through formation of R-loops. Curiously, we observed a strong pattern of enrichment of 5-mers in four potentially interacting entities: lncRNA-bound DNA tiles, lncRNAs, miRNA seed sequences, and repeat elements. This finding points to a broad sequence-based network of interactions that may underlie regulation of fundamental cellular functions. Overall, this study reveals diverse sequence and chromatin features related to lncRNA-chromatin interactions, suggesting potential mechanisms of nuclear retention and regulatory function.
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Affiliation(s)
- Shayan Tabe-Bordbar
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Saurabh Sinha
- Department of Biomedical Engineering, Georgia Institute of Technology, UAW 3108, 313 Ferst Drive NW, Atlanta, GA, 30332, USA.
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38
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Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, Ferrage F. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548668. [PMID: 37503201 PMCID: PMC10369993 DOI: 10.1101/2023.07.12.548668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70/80 heterodimer (Ku), XRCC4 in complex with DNA Ligase 4 (X4L4), and XLF form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) have recently been obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here, we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at atomic resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs led to the formation of XLF and X4L4 condensates in vitro which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome editing strategies.
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Affiliation(s)
- Duc-Duy Vu
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Manon Brenière
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Philippe Pelupessy
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ziqing Wang
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ludovic Carlier
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Guillaume Bouvignies
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, 160 Convent Avenue, New York, NY 10029, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Martin Blackledge
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Zoher Gueroui
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Fabien Ferrage
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
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39
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Alghoul E, Basbous J, Constantinou A. Compartmentalization of the DNA damage response: Mechanisms and functions. DNA Repair (Amst) 2023; 128:103524. [PMID: 37320957 DOI: 10.1016/j.dnarep.2023.103524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Cells have evolved an arsenal of molecular mechanisms to respond to continuous alterations in the primary structure of DNA. At the cellular level, DNA damage response proteins accumulate at sites of DNA damage and organize into nuclear foci. As recounted by Errol Friedberg, pioneering work on DNA repair in the 1930 s was stimulated by collaborations between physicists and geneticists. In recent years, the introduction of ideas from physics on self-organizing compartments has taken the field of cell biology by storm. Percolation and phase separation theories are increasingly used to model the self-assembly of compartments, called biomolecular condensates, that selectively concentrate molecules without a surrounding membrane. In this review, we discuss these concepts in the context of the DNA damage response. We discuss how studies of DNA repair foci as condensates can link molecular mechanisms with cell physiological functions, provide new insights into regulatory mechanisms, and open new perspectives for targeting DNA damage responses for therapeutic purposes.
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Affiliation(s)
- Emile Alghoul
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
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40
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Li C, Li Z, Wu Z, Lu H. Phase separation in gene transcription control. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1052-1063. [PMID: 37265348 PMCID: PMC10415188 DOI: 10.3724/abbs.2023099] [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: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phase separation provides a general mechanism for the formation of biomolecular condensates, and it plays a vital role in regulating diverse cellular processes, including gene expression. Although the role of transcription factors and coactivators in regulating transcription has long been understood, how phase separation is involved in this process is just beginning to be explored. In this review, we highlight recent advance in elucidating the molecular mechanisms and functions of transcriptional condensates in gene expression control. We discuss the different condensates formed at each stage of the transcription cycle and how they are dynamically regulated in response to diverse cellular and extracellular cues that cause rapid changes in gene expression. Furthermore, we present new findings regarding the dysregulation of transcription condensates and their implications in human diseases.
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Affiliation(s)
- Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhuo Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhibing Wu
- Department of OncologyAffiliated Zhejiang HospitalZhejiang University School of MedicineHangzhou310058China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
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41
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Dall'Agnese G, Dall'Agnese A, Banani SF, Codrich M, Malfatti MC, Antoniali G, Tell G. Role of condensates in modulating DNA repair pathways and its implication for chemoresistance. J Biol Chem 2023:104800. [PMID: 37164156 DOI: 10.1016/j.jbc.2023.104800] [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: 11/22/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
For cells, it is important to repair DNA damage, such as double strand and single strand DNA breaks, because unrepaired DNA can compromise genetic integrity, potentially leading to cell death or cancer. Cells have multiple DNA damage repair pathways that have been the subject of detailed genetic, biochemical, and structural studies. Recently, the scientific community has started to gain evidence that the repair of DNA double strand breaks may occur within biomolecular condensates and that condensates may also contribute to DNA damage through concentrating genotoxic agents used to treat various cancers. Here, we summarize key features of biomolecular condensates and note where they have been implicated in the repair of DNA double strand breaks. We also describe evidence suggesting that condensates may be involved in the repair of other types of DNA damage, including single strand DNA breaks, nucleotide modifications (e.g., mismatch and oxidized bases) and bulky lesions, among others. Finally, we discuss old and new mysteries that could now be addressed considering the properties of condensates, including chemoresistance mechanisms.
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Affiliation(s)
- Giuseppe Dall'Agnese
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | - Salman F Banani
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy.
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42
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Hu M, Hu Y, Wu T. A multifunctional monolithic interfacial sensor based on gold nanoparticle. Talanta 2023; 259:124546. [PMID: 37062087 DOI: 10.1016/j.talanta.2023.124546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
The spatial and temporal uneven distribution of complex biochemical reactions creates the diversity of biological systems. And the microenvironment confers fine regulation of these reactions, a stunning example of which is liquid-liquid phase separation (LLPS). LLPS can form a separate compartment without the physical separation formed by conventional membrane structures, and the reactions within the interface have specific reaction dynamics. Inspired by this, we report an interfacial sensor based on gold nanoparticles showing that interfacial factors have similar properties operating in natural biological environments and sensors. It repels molecules outside the interface and adjusts the DNA conformation within the interface to produce unique dynamics. The sensor adopts a modular design, allowing functional modules assembled on a single nanoparticle to avoid complex designs. We demonstrate the functionality of logical operations, using apurinic/apyrimidinic endonuclease 1 and micro RNA as inputs, showing that the sensor has the ability and potential to become a multifunctional platform with clear interface nature.
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Affiliation(s)
- Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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43
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Gioia U, Tavella S, Martínez-Orellana P, Cicio G, Colliva A, Ceccon M, Cabrini M, Henriques AC, Fumagalli V, Paldino A, Presot E, Rajasekharan S, Iacomino N, Pisati F, Matti V, Sepe S, Conte MI, Barozzi S, Lavagnino Z, Carletti T, Volpe MC, Cavalcante P, Iannacone M, Rampazzo C, Bussani R, Tripodo C, Zacchigna S, Marcello A, d'Adda di Fagagna F. SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence. Nat Cell Biol 2023; 25:550-564. [PMID: 36894671 PMCID: PMC10104783 DOI: 10.1038/s41556-023-01096-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/25/2023] [Indexed: 03/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response. Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair. Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs' biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence.
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Affiliation(s)
- Ubaldo Gioia
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Sara Tavella
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Giada Cicio
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- University of Palermo, Palermo, Italy
| | - Andrea Colliva
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Marta Ceccon
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Matteo Cabrini
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ana C Henriques
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Alessia Paldino
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- University of Trieste, Trieste, Italy
| | | | - Sreejith Rajasekharan
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Nicola Iacomino
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | - Valentina Matti
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Sara Sepe
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Matilde I Conte
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Sara Barozzi
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Zeno Lavagnino
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Tea Carletti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | - Matteo Iannacone
- IRCCS San Raffaele Scientific Institute & University, Milan, Italy
| | | | | | - Claudio Tripodo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- University of Palermo, Palermo, Italy
| | - Serena Zacchigna
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- University of Trieste, Trieste, Italy
| | - Alessandro Marcello
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics (IGM), National Research Institute (CNR), Pavia, Italy.
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44
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Refaat AM, Nakata M, Husain A, Kosako H, Honjo T, Begum NA. HNRNPU facilitates antibody class-switch recombination through C-NHEJ promotion and R-loop suppression. Cell Rep 2023; 42:112284. [PMID: 36943867 DOI: 10.1016/j.celrep.2023.112284] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/23/2022] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
B cells generate functionally different classes of antibodies through class-switch recombination (CSR), which requires classical non-homologous end joining (C-NHEJ) to join the DNA breaks at the donor and acceptor switch (S) regions. We show that the RNA-binding protein HNRNPU promotes C-NHEJ-mediated S-S joining through the 53BP1-shieldin DNA-repair complex. Notably, HNRNPU binds to the S region RNA/DNA G-quadruplexes, contributing to regulating R-loop and single-stranded DNA (ssDNA) accumulation. HNRNPU is an intrinsically disordered protein that interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Strikingly, recruitment of HNRNPU and the C-NHEJ factors is highly sensitive to liquid-liquid phase separation inhibitors, suggestive of DNA-repair condensate formation. We propose that HNRNPU facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which otherwise would cause persistent DNA breaks and aberrant DNA repair, leading to genomic instability.
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Affiliation(s)
- Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Hidetaka Kosako
- Division of Cell Signaling, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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45
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Jiang P, Cai R, Lugo-Martinez J, Guo Y. A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation. Brief Bioinform 2023; 24:7031681. [PMID: 36754843 DOI: 10.1093/bib/bbad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 01/01/2023] [Indexed: 02/10/2023] Open
Abstract
Scaffold proteins drive liquid-liquid phase separation (LLPS) to form biomolecular condensates and organize various biochemical reactions in cells. Dysregulation of scaffolds can lead to aberrant condensate assembly and various complex diseases. However, bioinformatics predictors dedicated to scaffolds are still lacking and their development suffers from an extreme imbalance between limited experimentally identified scaffolds and unlabeled candidates. Here, using the joint distribution of hybrid multimodal features, we implemented a positive unlabeled (PU) learning-based framework named PULPS that combined ProbTagging and penalty logistic regression (PLR) to profile the propensity of scaffolds. PULPS achieved the best AUC of 0.8353 and showed an area under the lift curve (AUL) of 0.8339 as an estimation of true performance. Upon reviewing recent experimentally verified scaffolds, we performed a partial recovery with 2.85% increase in AUL from 0.8339 to 0.8577. In comparison, PULPS showed a 45.7% improvement in AUL compared with PLR, whereas 8.2% superiority over other existing tools. Our study first proved that PU learning is more suitable for scaffold prediction and demonstrated the widespread existence of phase separation states. This profile also uncovered potential scaffolds that co-drive LLPS in the human proteome and generated candidates for further experiments. PULPS is free for academic research at http://pulps.zbiolab.cn.
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Affiliation(s)
- Peiran Jiang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Ruoxi Cai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jose Lugo-Martinez
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Yaping Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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46
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A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Mol Cell 2023; 83:681-697.e7. [PMID: 36736317 DOI: 10.1016/j.molcel.2023.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 11/04/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023]
Abstract
Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.
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47
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González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW. Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun 2023; 14:1135. [PMID: 36854718 PMCID: PMC9975218 DOI: 10.1038/s41467-023-36391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.
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Affiliation(s)
- Lidice González
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Marlene Oeffinger
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada.
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48
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RNA:DNA hybrids from Okazaki fragments contribute to establish the Ku-mediated barrier to replication-fork degradation. Mol Cell 2023; 83:1061-1074.e6. [PMID: 36868227 DOI: 10.1016/j.molcel.2023.02.008] [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: 12/14/2021] [Revised: 12/09/2022] [Accepted: 02/04/2023] [Indexed: 03/05/2023]
Abstract
Nonhomologous end-joining (NHEJ) factors act in replication-fork protection, restart, and repair. Here, we identified a mechanism related to RNA:DNA hybrids to establish the NHEJ factor Ku-mediated barrier to nascent strand degradation in fission yeast. RNase H activities promote nascent strand degradation and replication restart, with a prominent role of RNase H2 in processing RNA:DNA hybrids to overcome the Ku barrier to nascent strand degradation. RNase H2 cooperates with the MRN-Ctp1 axis to sustain cell resistance to replication stress in a Ku-dependent manner. Mechanistically, the need of RNaseH2 in nascent strand degradation requires the primase activity that allows establishing the Ku barrier to Exo1, whereas impairing Okazaki fragment maturation reinforces the Ku barrier. Finally, replication stress induces Ku foci in a primase-dependent manner and favors Ku binding to RNA:DNA hybrids. We propose a function for the RNA:DNA hybrid originating from Okazaki fragments in controlling the Ku barrier specifying nuclease requirement to engage fork resection.
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49
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MDC1 maintains active elongation complexes of RNA polymerase II. Cell Rep 2023; 42:111979. [PMID: 36640322 DOI: 10.1016/j.celrep.2022.111979] [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: 12/14/2021] [Revised: 10/04/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The role of MDC1 in the DNA damage response has been extensively studied; however, its impact on other cellular processes is not well understood. Here, we describe the role of MDC1 in transcription as a regulator of RNA polymerase II (RNAPII). Depletion of MDC1 causes a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein-encoding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to changes in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.
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50
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Fluorescence and phosphorescence lifetime imaging reveals a significant cell nuclear viscosity and refractive index changes upon DNA damage. Sci Rep 2023; 13:422. [PMID: 36624137 PMCID: PMC9829731 DOI: 10.1038/s41598-022-26880-x] [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: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Cytoplasmic viscosity is a crucial parameter in determining rates of diffusion-limited reactions. Changes in viscosity are associated with several diseases, whilst nuclear viscosity determines gene integrity, regulation and expression. Yet how drugs including DNA-damaging agents affect viscosity is unknown. We demonstrate the use of a platinum complex, Pt[L]Cl, that localizes efficiently mostly in the nucleus as a probe for nuclear viscosity. The phosphorescence lifetime of Pt[L]Cl is sensitive to viscosity and provides an excellent tool to investigate the impact of DNA damage. We show using Fluorescence Lifetime Imaging (FLIM) that the lifetime of both green and red fluorescent proteins (FP) are also sensitive to changes in cellular viscosity and refractive index. However, Pt[L]Cl proved to be a more sensitive viscosity probe, by virtue of microsecond phosphorescence lifetime versus nanosecond fluorescence lifetime of FP, hence greater sensitivity to bimolecular reactions. DNA damage was inflicted by either a two-photon excitation, one-photon excitation microbeam and X-rays. DNA damage of live cells causes significant increase in the lifetime of either Pt[L]Cl (HeLa cells, 12.5-14.1 µs) or intracellularly expressed mCherry (HEK293 cells, 1.54-1.67 ns), but a decrease in fluorescence lifetime of GFP from 2.65 to 2.29 ns (in V15B cells). These values represent a viscosity change from 8.59 to 20.56 cP as well as significant changes in the refractive index (RI), according to independent calibration. Interestingly DNA damage localized to a submicron region following a laser microbeam induction showed a whole cell viscosity change, with those in the nucleus being greater than the cytoplasm. We also found evidence of a by-stander effect, whereby adjacent un-irradiated cells also showed nuclear viscosity change. Finally, an increase in viscosity following DNA damage was also observed in bacterial cells with an over-expressed mNeonGreen FP, evidenced by the change in its lifetime from 2.8 to 2.4 ns.
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