1
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Jeon Y, Lu Y, Ferrari MM, Channagiri T, Xu P, Meers C, Zhang Y, Balachander S, Park VS, Marsili S, Pursell ZF, Jonoska N, Storici F. RNA-mediated double-strand break repair by end-joining mechanisms. Nat Commun 2024; 15:7935. [PMID: 39261460 PMCID: PMC11390984 DOI: 10.1038/s41467-024-51457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/07/2024] [Indexed: 09/13/2024] Open
Abstract
Double-strand breaks (DSBs) in DNA are challenging to repair. Cells employ at least three DSB-repair mechanisms, with a preference for non-homologous end joining (NHEJ) over homologous recombination (HR) and microhomology-mediated end joining (MMEJ). While most eukaryotic DNA is transcribed into RNA, providing complementary genetic information, much remains unknown about the direct impact of RNA on DSB-repair outcomes and its role in DSB-repair via end joining. Here, we show that both sense and antisense-transcript RNAs impact DSB repair in a sequence-specific manner in wild-type human and yeast cells. Depending on its sequence complementarity with the broken DNA ends, a transcript RNA can promote repair of a DSB or a double-strand gap in its DNA gene via NHEJ or MMEJ, independently from DNA synthesis. The results demonstrate a role of transcript RNA in directing the way DSBs are repaired in DNA, suggesting that RNA may directly modulate genome stability and evolution.
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Affiliation(s)
- Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Fredrick, MD, USA
| | - Yilin Lu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Margherita Maria Ferrari
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| | - Tejasvi Channagiri
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Columbia University Irving Medical Center, New York, NY, USA
| | - Yiqi Zhang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Program for Lung and Vascular Biology, Section for Injury Repair and Regeneration Research, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Division of Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory University, Atlanta, GA, USA
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA.
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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2
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Sagi T, Sadato D, Takayasu K, Sasanuma H, Kanoh Y, Masai H. RNA-DNA hybrids on protein coding genes are stabilized by loss of RNase H and are associated with DNA damages during S-phase in fission yeast. Genes Cells 2024. [PMID: 39252397 DOI: 10.1111/gtc.13157] [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: 07/13/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024]
Abstract
RNA-DNA hybrid is a part of the R-loop which is an important non-standard nucleic acid structure. RNA-DNA hybrid/R-loop causes genomic instability by inducing DNA damages or inhibiting DNA replication. It also plays biologically important roles in regulation of transcription, replication, recombination and repair. Here, we have employed catalytically inactive human RNase H1 mutant (D145N) to visualize RNA-DNA hybrids and map their genomic locations in fission yeast cells. The RNA-DNA hybrids appear as multiple nuclear foci in rnh1∆rnh201∆ cells lacking cellular RNase H activity, but not in the wild-type. The majority of RNA-DNA hybrid loci are detected at the protein coding regions and tRNA. In rnh1∆rnh201∆ cells, cells with multiple Rad52 foci increase during S-phase and about 20% of the RNA-DNA hybrids overlap with Rad52 loci. During S-phase, more robust association of Rad52 with RNA-DNA hybrids was observed in the protein coding region than in M-phase. These results suggest that persistent RNA-DNA hybrids in the protein coding region in rnh1∆rnh201∆ cells generate DNA damages during S-phase, potentially through collision with DNA replication forks.
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Affiliation(s)
- Tomoko Sagi
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Daichi Sadato
- Clinical Research and Trials Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Kazuto Takayasu
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Biosciences, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Hiroyuki Sasanuma
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yutaka Kanoh
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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3
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Li Y, Liu C, Jia X, Bi L, Ren Z, Zhao Y, Zhang X, Guo L, Bao Y, Liu C, Li W, Sun B. RPA transforms RNase H1 to a bidirectional exoribonuclease for processive RNA-DNA hybrid cleavage. Nat Commun 2024; 15:7464. [PMID: 39198528 PMCID: PMC11358518 DOI: 10.1038/s41467-024-51984-5] [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: 01/04/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024] Open
Abstract
RNase H1 has been acknowledged as an endoribonuclease specializing in the internal degradation of the RNA moiety within RNA-DNA hybrids, and its ribonuclease activity is indispensable in multifaceted aspects of nucleic acid metabolism. However, the molecular mechanism underlying RNase H1-mediated hybrid cleavage remains inadequately elucidated. Herein, using single-molecule approaches, we probe the dynamics of the hybrid cleavage by Saccharomyces cerevisiae RNase H1. Remarkably, a single RNase H1 enzyme displays 3'-to-5' exoribonuclease activity. The directional RNA degradation proceeds processively and yet discretely, wherein unwinding approximately 6-bp hybrids as a prerequisite for two consecutive 3-nt RNA excisions limits the overall rate within each catalytic cycle. Moreover, Replication Protein A (RPA) reinforces RNase H1's 3'-to-5' nucleolytic rate and processivity and stimulates its 5'-to-3' exoribonuclease activity. This stimulation is primarily realized through the pre-separation of the hybrids and consequently transfers RNase H1 to a bidirectional exoribonuclease, further potentiating its cleavage efficiency. These findings unveil unprecedented characteristics of an RNase and provide a dynamic view of RPA-enhanced processive hybrid cleavage by RNase H1.
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Affiliation(s)
- Yanan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinshuo Jia
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhiyun Ren
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yanling Bao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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4
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Secchi M, Garbelli A, Riva V, Deidda G, Santonicola C, Formica TM, Sabbioneda S, Crespan E, Maga G. Synergistic action of human RNaseH2 and the RNA helicase-nuclease DDX3X in processing R-loops. Nucleic Acids Res 2024:gkae731. [PMID: 39189461 DOI: 10.1093/nar/gkae731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 07/18/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
R-loops are three-stranded RNA-DNA hybrid structures that play important regulatory roles, but excessive or deregulated R-loops formation can trigger DNA damage and genome instability. Digestion of R-loops is mainly relying on the action of two specialized ribonucleases: RNaseH1 and RNaseH2. RNaseH2 is the main enzyme carrying out the removal of misincorporated rNMPs during DNA replication or repair, through the Ribonucleotide Excision Repair (RER) pathway. We have recently shown that the human RNA helicase DDX3X possessed RNaseH2-like activity, being able to substitute RNaseH2 in reconstituted RER reactions. Here, using synthetic R-loop mimicking substrates, we could show that human DDX3X alone was able to both displace and degrade the ssRNA strand hybridized to DNA. Moreover, DDX3X was found to physically interact with human RNaseH2. Such interaction suppressed the nuclease and helicase activities of DDX3X, but stimulated severalfold the catalytic activity of the trimeric RNaseH2, but not of RNaseH1. Finally, silencing of DDX3X in human cells caused accumulation of RNA-DNA hybrids and phosphorylated RPA foci. These results support a role of DDX3X as a scaffolding protein and auxiliary factor for RNaseH2 during R-loop degradation.
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Affiliation(s)
- Massimiliano Secchi
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Valentina Riva
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Graziano Deidda
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Carolina Santonicola
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Teresa Maria Formica
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
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5
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Bugallo A, Segurado M. Unraveling the complexity of asymmetric DNA replication: Advancements in ribonucleotide mapping techniques and beyond. Genomics 2024; 116:110908. [PMID: 39106913 DOI: 10.1016/j.ygeno.2024.110908] [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] [Revised: 07/18/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
DNA replication is a fundamental process for cell proliferation, governed by intricate mechanisms involving leading and lagging strand synthesis. In eukaryotes, canonical DNA replication occurs during the S phase of the cell cycle, facilitated by various components of the replicative machinery at sites known as replication origins. Leading and lagging strands exhibit distinct replication dynamics, with leading strand replication being relatively straightforward compared to the complex synthesis of lagging strands involving Okazaki fragment maturation. Central to DNA synthesis are DNA polymerases, with Polα, Polε, and Polδ playing pivotal roles, each specializing in specific tasks during replication. Notably, leading and lagging strands are replicated by different polymerases, contributing to the division of labor in DNA replication. Understanding the enzymology of asymmetric DNA replication has been challenging, with methods relying on ribonucleotide incorporation and next-generation sequencing techniques offering comprehensive insights. These methodologies, such as HydEn-seq, PU-seq, ribose-seq, and emRiboSeq, offer insights into polymerase activity and strand synthesis, aiding in understanding DNA replication dynamics. Recent advancements include novel conditional mutants for ribonucleotide excision repair, enzymatic cleavage alternatives, and unified pipelines for data analysis. Further developments in adapting techniques to different organisms, studying non-canonical polymerases, and exploring new sequencing platforms hold promise for expanding our understanding of DNA replication dynamics. Integrating strand-specific information into single-cell studies could offer novel insights into enzymology, opening avenues for future research and applications in repair and replication biology.
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Affiliation(s)
- Alberto Bugallo
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
| | - Mónica Segurado
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain; Departamento de Microbiología y Genética (USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain.
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6
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Sang A, Zhuo S, Bochanis A, Manautou JE, Bahal R, Zhong XB, Rasmussen TP. Mechanisms of Action of the US Food and Drug Administration-Approved Antisense Oligonucleotide Drugs. BioDrugs 2024; 38:511-526. [PMID: 38914784 DOI: 10.1007/s40259-024-00665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
Antisense oligonucleotides (ASOs) are single stranded nucleic acids that target RNA. The US Food and Drug Administration has approved ASOs for several diseases. ASOs utilize three principal modes of action (MOA). The first MOA is initiated by base-pairing between the ASO and its target mRNA, followed by RNase H-dependent mRNA degradation. The second MOA is triggered by ASOs that occlude splice acceptor sites in pre-mRNAs leading to skipping of a mutation-bearing exon. The third MOA involves ASOs that sterically hinder mRNA function, often inhibiting translation. ASOs contain a variety of modifications to the sugar-phosphate backbone and bases that stabilize the ASO or render them resistant to RNase activity. RNase H-dependent ASOs include inotersen and eplontersen (for hereditary transthyretin amyloidosis), fomiversen (for opportunistic cytomegalovirus infection), mipomersen (for familial hypercholesterolemia), and tofersen [for amyotrophic lateral sclerosis (ALS)]. Splice modulating ASOs include nursinersen (for spinal muscular atrophy) and eteplirsen, golodirsen, viltolarsen, and casimersen (all for the treatment of Duchenne muscular dystrophy). In addition, a designer ASO, milasen, was used to treat a single individual afflicted with Batten disease. Since ASO design relies principally upon knowledge of mRNA sequence, the bench to bedside pipeline for ASOs is expedient compared with protein-directed drugs. [Graphical abstract available.].
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Affiliation(s)
- Angela Sang
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Selena Zhuo
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Adara Bochanis
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - José E Manautou
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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7
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Wen C, Cao L, Wang S, Xu W, Yu Y, Zhao S, Yang F, Chen ZJ, Zhao S, Yang Y, Qin Y. MCM8 interacts with DDX5 to promote R-loop resolution. EMBO J 2024; 43:3044-3071. [PMID: 38858601 PMCID: PMC11251167 DOI: 10.1038/s44318-024-00134-0] [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: 08/12/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
MCM8 has emerged as a core gene in reproductive aging and is crucial for meiotic homologous recombination repair. It also safeguards genome stability by coordinating the replication stress response during mitosis, but its function in mitotic germ cells remains elusive. Here we found that disabling MCM8 in mice resulted in proliferation defects of primordial germ cells (PGCs) and ultimately impaired fertility. We further demonstrated that MCM8 interacted with two known helicases DDX5 and DHX9, and loss of MCM8 led to R-loop accumulation by reducing the retention of these helicases at R-loops, thus inducing genome instability. Cells expressing premature ovarian insufficiency-causative mutants of MCM8 with decreased interaction with DDX5 displayed increased R-loop levels. These results show MCM8 interacts with R-loop-resolving factors to prevent R-loop-induced DNA damage, which may contribute to the maintenance of genome integrity of PGCs and reproductive reserve establishment. Our findings thus reveal an essential role for MCM8 in PGC development and improve our understanding of reproductive aging caused by genome instability in mitotic germ cells.
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Affiliation(s)
- Canxin Wen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Lili Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Shuhan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Weiwei Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Yongze Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Simin Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Fan Yang
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shidou Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yajuan Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yingying Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
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8
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Verma I, Chhatlani K, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae. iScience 2024; 27:110012. [PMID: 38868188 PMCID: PMC11166700 DOI: 10.1016/j.isci.2024.110012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.
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Affiliation(s)
- Deepali L. Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L. Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ishika Verma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kirti Chhatlani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zeel H. Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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9
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [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: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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10
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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11
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Piguet B, Houseley J. Transcription as source of genetic heterogeneity in budding yeast. Yeast 2024; 41:171-185. [PMID: 38196235 DOI: 10.1002/yea.3926] [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: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.
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12
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Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [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: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
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Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
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13
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Wang Z, Qu M, Chang S, Dai X, You C. Human RNA-binding protein HNRNPD interacts with and regulates the repair of deoxyribouridine in DNA. Int J Biol Macromol 2024; 262:129951. [PMID: 38325695 DOI: 10.1016/j.ijbiomac.2024.129951] [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: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Deoxyribouridine (dU) is an abnormal nucleoside in DNA and plays vital roles in multiple biological and physiological processes. Here, we conducted a mass spectrometry-based screen for dU-binding proteins and found that the heterogeneous nuclear ribonucleoprotein D (HNRNPD) could preferentially bind to dU-containing DNA. We also discovered that HNRNPD engages in the 5-Fluorouracil (5FU)-induced DNA damage response and can modulate the repair of dU in DNA in vitro and in human cells. Moreover, using a shuttle vector- and next-generation sequencing-based method, we unveiled the crucial role of HNRNPD in promoting the replicative bypass of dU in human cells. Taken together, these findings suggested that HNRNPD is a novel dU-bearing DNA-binding protein capable of regulating the removal of dU in DNA, and provided new insights into the molecular mechanisms of dU-associated diseases.
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Affiliation(s)
- Ziyu Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Minghui Qu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Sijia Chang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaoxia Dai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Changjun You
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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14
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Wu W, Wu W, Zhou Y, Yang Q, Zhuang S, Zhong C, Li W, Li A, Zhao W, Yin X, Zu X, Chak-Lui Wong C, Yin D, Hu K, Cai M. The dePARylase NUDT16 promotes radiation resistance of cancer cells by blocking SETD3 for degradation via reversing its ADP-ribosylation. J Biol Chem 2024; 300:105671. [PMID: 38272222 PMCID: PMC10926213 DOI: 10.1016/j.jbc.2024.105671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a critical posttranslational modification that plays a vital role in maintaining genomic stability via a variety of molecular mechanisms, including activation of replication stress and the DNA damage response. The nudix hydrolase NUDT16 was recently identified as a phosphodiesterase that is responsible for removing ADP-ribose units and that plays an important role in DNA repair. However, the roles of NUDT16 in coordinating replication stress and cell cycle progression remain elusive. Here, we report that SETD3, which is a member of the SET-domain containing protein (SETD) family, is a novel substrate for NUDT16, that its protein levels fluctuate during cell cycle progression, and that its stability is strictly regulated by NUDT16-mediated dePARylation. Moreover, our data indicated that the E3 ligase CHFR is responsible for the recognition and degradation of endogenous SETD3 in a PARP1-mediated PARylation-dependent manner. Mechanistically, we revealed that SETD3 associates with BRCA2 and promotes its recruitment to stalled replication fork and DNA damage sites upon replication stress or DNA double-strand breaks, respectively. Importantly, depletion of SETD3 in NUDT16-deficient cells did not further exacerbate DNA breaks or enhance the sensitivity of cancer cells to IR exposure, suggesting that the NUDT16-SETD3 pathway may play critical roles in the induction of tolerance to radiotherapy. Collectively, these data showed that NUDT16 functions as a key upstream regulator of SETD3 protein stability by reversing the ADP-ribosylation of SETD3, and NUDT16 participates in the resolution of replication stress and facilitates HR repair.
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Affiliation(s)
- Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiao Yang
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjia Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Aixin Li
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wanzhen Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaomin Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Carmen Chak-Lui Wong
- Li Ka Shing Faculty of Medicine, Department of Pathology, The University of Hong Kong, Hong Kong, Guangdong, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Manbo Cai
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
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15
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Zhang J, Chen F, Tang M, Xu W, Tian Y, Liu Z, Shu Y, Yang H, Zhu Q, Lu X, Peng B, Liu X, Xu X, Gullerova M, Zhu WG. The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. Cell Rep 2024; 43:113779. [PMID: 38358891 DOI: 10.1016/j.celrep.2024.113779] [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: 07/12/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
R-loops are three-stranded structures that can pose threats to genome stability. RNase H1 precisely recognizes R-loops to drive their resolution within the genome, but the underlying mechanism is unclear. Here, we report that ARID1A recognizes R-loops with high affinity in an ATM-dependent manner. ARID1A recruits METTL3 and METTL14 to the R-loop, leading to the m6A methylation of R-loop RNA. This m6A modification facilitates the recruitment of RNase H1 to the R-loop, driving its resolution and promoting DNA end resection at DSBs, thereby ensuring genome stability. Depletion of ARID1A, METTL3, or METTL14 leads to R-loop accumulation and reduced cell survival upon exposure to cytotoxic agents. Therefore, ARID1A, METTL3, and METTL14 function in a coordinated, temporal order at DSB sites to recruit RNase H1 and to ensure efficient R-loop resolution. Given the association of high ARID1A levels with resistance to genotoxic therapies in patients, these findings open avenues for exploring potential therapeutic strategies for cancers with ARID1A abnormalities.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hui Yang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Bin Peng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China; Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China; Department of Biochemistry and Molecular Biology, Peking University Health Science Centre, Beijing 100191, China.
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16
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Sengodan SK, Hu X, Peddibhotla V, Balamurugan K, Mitrophanov AY, McKennett L, Kharat SS, Sanawar R, Singh VK, Albaugh ME, Burkett SS, Zhao Y, Tran B, Malys T, Sterneck E, De S, Sharan SK. Mismatch repair protein MLH1 suppresses replicative stress in BRCA2-deficient breast tumors. J Clin Invest 2024; 134:e173718. [PMID: 38271119 PMCID: PMC10977984 DOI: 10.1172/jci173718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
Loss of BRCA2 (breast cancer 2) is lethal for normal cells. Yet it remains poorly understood how, in BRCA2 mutation carriers, cells undergoing loss of heterozygosity overcome the lethality and undergo tissue-specific neoplastic transformation. Here, we identified mismatch repair gene mutL homolog 1 (MLH1) as a genetic interactor of BRCA2 whose overexpression supports the viability of Brca2-null cells. Mechanistically, we showed that MLH1 interacts with Flap endonuclease 1 (FEN1) and competes to process the RNA flaps of Okazaki fragments. Together, they restrained the DNA2 nuclease activity on the reversed forks of lagging strands, leading to replication fork (RF) stability in BRCA2-deficient cells. In these cells, MLH1 also attenuated R-loops, allowing the progression of stable RFs, which suppressed genomic instability and supported cell viability. We demonstrated the significance of their genetic interaction by the lethality of Brca2-mutant mice and inhibition of Brca2-deficient tumor growth in mice by Mlh1 loss. Furthermore, we described estrogen as inducing MLH1 expression through estrogen receptor α (ERα), which might explain why the majority of BRCA2 mutation carriers develop ER-positive breast cancer. Taken together, our findings reveal a role of MLH1 in relieving replicative stress and show how it may contribute to the establishment of BRCA2-deficient breast tumors.
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Affiliation(s)
- Satheesh K. Sengodan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Xiaoju Hu
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Vaishnavi Peddibhotla
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Kuppusamy Balamurugan
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Lois McKennett
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Suhas S. Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Rahul Sanawar
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Vinod Kumar Singh
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Mary E. Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sandra S. Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Yongmei Zhao
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bao Tran
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Esta Sterneck
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
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17
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Mueller F, Witteveldt J, Macias S. Antiviral Defence Mechanisms during Early Mammalian Development. Viruses 2024; 16:173. [PMID: 38399949 PMCID: PMC10891733 DOI: 10.3390/v16020173] [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: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The type-I interferon (IFN) response constitutes the major innate immune pathway against viruses in mammals. Despite its critical importance for antiviral defence, this pathway is inactive during early embryonic development. There seems to be an incompatibility between the IFN response and pluripotency, the ability of embryonic cells to develop into any cell type of an adult organism. Instead, pluripotent cells employ alternative ways to defend against viruses that are typically associated with safeguard mechanisms against transposable elements. The absence of an inducible IFN response in pluripotent cells and the constitutive activation of the alternative antiviral pathways have led to the hypothesis that embryonic cells are highly resistant to viruses. However, some findings challenge this interpretation. We have performed a meta-analysis that suggests that the susceptibility of pluripotent cells to viruses is directly correlated with the presence of receptors or co-receptors for viral adhesion and entry. These results challenge the current view of pluripotent cells as intrinsically resistant to infections and raise the fundamental question of why these cells have sacrificed the major antiviral defence pathway if this renders them susceptible to viruses.
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Affiliation(s)
- Felix Mueller
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
- Centre for Virus Research, MRC-University of Glasgow, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
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18
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Milano L, Gautam A, Caldecott KW. DNA damage and transcription stress. Mol Cell 2024; 84:70-79. [PMID: 38103560 DOI: 10.1016/j.molcel.2023.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
Genome damage and transcription are intimately linked. Tens to hundreds of thousands of DNA lesions arise in each cell each day, many of which can directly or indirectly impede transcription. Conversely, the process of gene expression is itself a source of endogenous DNA lesions as a result of the susceptibility of single-stranded DNA to damage, conflicts with the DNA replication machinery, and engagement by cells of topoisomerases and base excision repair enzymes to regulate the initiation and progression of gene transcription. Although such processes are tightly regulated and normally accurate, on occasion, they can become abortive and leave behind DNA breaks that can drive genome rearrangements, instability, or cell death.
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Affiliation(s)
- Larissa Milano
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Amit Gautam
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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19
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Jaiswal AS, Dutta A, Srinivasan G, Yuan Y, Zhou D, Shaheen M, Sadideen D, Kirby A, Williamson E, Gupta Y, Olsen SK, Xu M, Loranc E, Mukhopadhyay P, Pertsemlidis A, Bishop AR, Sung P, Nickoloff J, Hromas R. TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells. Nucleic Acids Res 2023; 51:12224-12241. [PMID: 37953292 PMCID: PMC10711561 DOI: 10.1093/nar/gkad952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.
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Affiliation(s)
- Aruna S Jaiswal
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Montaser Shaheen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Doraid T Sadideen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Austin Kirby
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K Gupta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Mingjiang Xu
- Department of Molecular Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Eva Loranc
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Pramiti Mukhopadhyay
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander Pertsemlidis
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
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20
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Wu Y, Song T, Xu Q. R-LOOPs on Short Tandem Repeat Expansion Disorders in Neurodegenerative Diseases. Mol Neurobiol 2023; 60:7185-7195. [PMID: 37540313 DOI: 10.1007/s12035-023-03531-4] [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: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
Expansions of short tandem repeats (STRs) have been found to be present in more than 50 diseases and have a close connection with neurodegenerative diseases. Transcriptional silencing and R-LOOP formation, RNA-mediated sequestration of RNA-binding proteins (RBPs), gain-of-function (GOF) proteins containing expanded repeats, and repeat-associated non-AUG (RAN) translation of toxic repeat peptides are some potential molecular mechanisms underlying STR expansion disorders. R-LOOP, a byproduct of transcription, is a three-stranded nucleic acid structure with abnormal accumulation that participates in the pathogenesis of STR expansion disorders by inducing DNA damage and genome instability. R-LOOPs can engender a series of DNA damage, such as DNA double-strand breaks (DSBs), single-strand breaks (SSBs), DNA recombination, or mutations in the DNA replication, transcription, or repair processes. In this review, we provide an in-depth discussion of recent advancements in R-LOOP and systematically elaborate on its genetic destabilizing effects in several neurodegenerative diseases. These molecular mechanisms will provide novel targets for drug design and therapeutic upgrading of these devastating diseases.
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Affiliation(s)
- Yiting Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingwei Song
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.
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21
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Heuzé J, Kemiha S, Barthe A, Vilarrubias AT, Aouadi E, Aiello U, Libri D, Lin Y, Lengronne A, Poli J, Pasero P. RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. EMBO J 2023; 42:e113104. [PMID: 37855233 PMCID: PMC10690446 DOI: 10.15252/embj.2022113104] [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: 11/20/2022] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
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Affiliation(s)
- Jonathan Heuzé
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Samira Kemiha
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Antoine Barthe
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Alba Torán Vilarrubias
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Elyès Aouadi
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Present address:
Institut de Génétique Moléculaire de MontpellierUniversité de Montpellier, CNRSMontpellierFrance
| | - Yea‐Lih Lin
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Armelle Lengronne
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jérôme Poli
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
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22
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Zhang B, Li Y, Zhang J, Wang Y, Liang C, Lu T, Zhang C, Liu L, Qin Y, He J, Zhao X, Yu J, Hao J, Yang J, Li MJ, Yao Z, Ma S, Cheng H, Cheng T, Shi L. ADAR1 links R-loop homeostasis to ATR activation in replication stress response. Nucleic Acids Res 2023; 51:11668-11687. [PMID: 37831098 PMCID: PMC10681745 DOI: 10.1093/nar/gkad839] [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: 06/22/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to accumulate at R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.
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Affiliation(s)
- Biao Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yi Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jieyou Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yuejiao Wang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Can Liang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Chunyong Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yan Qin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jiahuan He
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100006, Beijing, China
| | - Xiangnan Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jia Yu
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100006, Beijing, China
| | - Jihui Hao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Yao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shuai Ma
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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23
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Tsao N, Ashour ME, Mosammaparast N. How RNA impacts DNA repair. DNA Repair (Amst) 2023; 131:103564. [PMID: 37776841 PMCID: PMC11232704 DOI: 10.1016/j.dnarep.2023.103564] [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: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
The central dogma of molecular biology posits that genetic information flows unidirectionally, from DNA, to RNA, and finally to protein. However, this directionality is broken in some cases, such as reverse transcription where RNA is converted to DNA by retroviruses and certain transposable elements. Our genomes have evolved and adapted to the presence of reverse transcription. Similarly, our genome is continuously maintained by several repair pathways to reverse damage due to various endogenous and exogenous sources. More recently, evidence has revealed that RNA, while in certain contexts may be detrimental for genome stability, is involved in promoting certain types of DNA repair. Depending on the pathway in question, the size of these DNA repair-associated RNAs range from one or a few ribonucleotides to long fragments of RNA. Moreover, RNA is highly modified, and RNA modifications have been revealed to be functionally associated with specific DNA repair pathways. In this review, we highlight aspects of this unexpected layer of genomic maintenance, demonstrating how RNA may influence DNA integrity.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohamed E Ashour
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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24
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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25
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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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26
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Krishnan R, Lapierre M, Gautreau B, Nixon KCJ, El Ghamrasni S, Patel P, Hao J, Yerlici V, Guturi K, St-Germain J, Mateo F, Saad A, Algouneh A, Earnshaw R, Shili D, Seitova A, Miller J, Khosraviani N, Penn A, Ho B, Sanchez O, Hande MP, Masson JY, Brown G, Alaoui-Jamali M, Reynolds J, Arrowsmith C, Raught B, Pujana M, Mekhail K, Stewart G, Hakem A, Hakem R. RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells. Nucleic Acids Res 2023; 51:10484-10505. [PMID: 37697435 PMCID: PMC10602868 DOI: 10.1093/nar/gkad733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
Breast cancer linked with BRCA1/2 mutations commonly recur and resist current therapies, including PARP inhibitors. Given the lack of effective targeted therapies for BRCA1-mutant cancers, we sought to identify novel targets to selectively kill these cancers. Here, we report that loss of RNF8 significantly protects Brca1-mutant mice against mammary tumorigenesis. RNF8 deficiency in human BRCA1-mutant breast cancer cells was found to promote R-loop accumulation and replication fork instability, leading to increased DNA damage, senescence, and synthetic lethality. Mechanistically, RNF8 interacts with XRN2, which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1-mutant breast cancer cells decreases XRN2 occupancy at R-loop-prone sites, thereby promoting R-loop accumulation, transcription-replication collisions, excessive genomic instability, and cancer cell death. Collectively, our work identifies a synthetic lethal interaction between RNF8 and BRCA1, which is mediated by a pathological accumulation of R-loops.
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Affiliation(s)
- Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Mariah Lapierre
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brandon Gautreau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Kevin C J Nixon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada
| | - Jun Hao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - V Talya Yerlici
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | - Amine Saad
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Arash Algouneh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Rebecca Earnshaw
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Duan Shili
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Joshua Miller
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Adam Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Otto Sanchez
- Ontario Tech University, 2000 Simcoe Street North Oshawa, Ontario L1G 0C5, Canada
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 2J6, Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Moulay Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Cheryl Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada
| | - Miguel A Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Anne Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada
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27
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Quttina M, Waiters KD, Khan AF, Karami S, Peidl AS, Babajide MF, Pennington J, Merchant FA, Bawa-Khalfe T. Exosc9 Initiates SUMO-Dependent lncRNA TERRA Degradation to Impact Telomeric Integrity in Endocrine Therapy Insensitive Hormone Receptor-Positive Breast Cancer. Cells 2023; 12:2495. [PMID: 37887339 PMCID: PMC10605189 DOI: 10.3390/cells12202495] [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: 08/16/2023] [Revised: 10/11/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Long, noncoding RNAs (lncRNAs) are indispensable for normal cell physiology and, consequently, are tightly regulated in human cells. Yet, unlike mRNA, substantially less is known about the mechanisms for lncRNA degradation. It is important to delineate the regulatory control of lncRNA degradation, particularly for lncRNA telomeric repeat-containing RNA (TERRA), as the TERRA-telomere R-loops dictate cell cycle progression and genomic stability. We now report that the exosome complex component Exosc9 degrades lncRNA TERRA in human mammary epithelial cells. Heterochromatin protein 1 alpha (HP1α) recruits Exosc9 to the telomeres; specifically, the SUMO-modified form of HP1α supports interaction with Exosc9 and, as previously reported, lncRNA TERRA. The telomeric enrichment of Exosc9 is cell cycle-dependent and consistent with the loss of telomeric TERRA in the S/G2 phase. Elevated Exosc9 is frequently observed and drives the growth of endocrine therapy-resistant (ET-R) HR+ breast cancer (BCa) cells. Specifically, the knockdown of Exosc9 inversely impacts telomeric R-loops and the integrity of the chromosome ends of ET-R cells. Consistently, Exosc9 levels dictate DNA damage and the sensitivity of ET-R BCa cells to PARP inhibitors. In this regard, Exosc9 may serve as a promising biomarker for predicting the response to PARP inhibitors as a targeted monotherapy for ET-R HR+ BCa.
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Affiliation(s)
- Maram Quttina
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
- Engineering Technology College of Technology, University of Houston at Sugarland, 13850 University Blvd, SAB1 Bldg, Rm 348, Sugarland, TX 77479, USA
| | - Kacie D. Waiters
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Ashfia Fatima Khan
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Samaneh Karami
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Anthony S. Peidl
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Mariam Funmi Babajide
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Justus Pennington
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
| | - Fatima A. Merchant
- Engineering Technology College of Technology, University of Houston at Sugarland, 13850 University Blvd, SAB1 Bldg, Rm 348, Sugarland, TX 77479, USA
| | - Tasneem Bawa-Khalfe
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg, Rm 3010, Houston, TX 77204-5056, USA (A.F.K.)
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28
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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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29
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560505. [PMID: 37873120 PMCID: PMC10592897 DOI: 10.1101/2023.10.02.560505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations in Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome of rnh201-G42S than in wild-type and rnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.
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Affiliation(s)
- Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Zeel H Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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30
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Heuzé J, Lin YL, Lengronne A, Poli J, Pasero P. Impact of R-loops on oncogene-induced replication stress in cancer cells. C R Biol 2023; 346:95-105. [PMID: 37779381 DOI: 10.5802/crbiol.123] [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: 01/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 10/03/2023]
Abstract
Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.
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31
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [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
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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32
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Zhang X, Duan J, Li Y, Jin X, Wu C, Yang X, Lu W, Ge W. NKAP acts with HDAC3 to prevent R-loop associated genome instability. Cell Death Differ 2023; 30:1811-1828. [PMID: 37322264 PMCID: PMC10307950 DOI: 10.1038/s41418-023-01182-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/09/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Persistent R-loop accumulation can cause DNA damage and lead to genome instability, which contributes to various human diseases. Identification of molecules and signaling pathways in controlling R-loop homeostasis provide important clues about their physiological and pathological roles in cells. Here, we show that NKAP (NF-κB activating protein) is essential for preventing R-loop accumulation and maintaining genome integrity through forming a protein complex with HDAC3. NKAP depletion causes DNA damage and genome instability. Aberrant accumulation of R-loops is present in NKAP-deficient cells and leads to DNA damage and DNA replication fork progression defects. Moreover, NKAP depletion induced R-loops and DNA damage are dependent on transcription. Consistently, the NKAP interacting protein HDAC3 exhibits a similar role in suppressing R-loop associated DNA damage and replication stress. Further analysis uncovers that HDAC3 functions to stabilize NKAP protein, independent of its deacetylase activity. In addition, NKAP prevents R-loop formation by maintaining RNA polymerase II pausing. Importantly, R-loops induced by NKAP or HDAC3 depletion are processed into DNA double-strand breaks by XPF and XPG endonucleases. These findings indicate that both NKAP and HDAC3 are novel key regulators of R-loop homeostasis, and their dysregulation might drive tumorigenesis by causing R-loop associated genome instability.
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Affiliation(s)
- Xing Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Jingwei Duan
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Xiaoye Jin
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Cheng Wu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Weiguo Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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33
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Elsakrmy N, Cui H. R-Loops and R-Loop-Binding Proteins in Cancer Progression and Drug Resistance. Int J Mol Sci 2023; 24:ijms24087064. [PMID: 37108225 PMCID: PMC10138518 DOI: 10.3390/ijms24087064] [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: 02/26/2023] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
R-loops are three-stranded DNA/RNA hybrids that form by the annealing of the mRNA transcript to its coding template while displacing the non-coding strand. While R-loop formation regulates physiological genomic and mitochondrial transcription and DNA damage response, imbalanced R-loop formation can be a threat to the genomic integrity of the cell. As such, R-loop formation is a double-edged sword in cancer progression, and perturbed R-loop homeostasis is observed across various malignancies. Here, we discuss the interplay between R-loops and tumor suppressors and oncogenes, with a focus on BRCA1/2 and ATR. R-loop imbalances contribute to cancer propagation and the development of chemotherapy drug resistance. We explore how R-loop formation can cause cancer cell death in response to chemotherapeutics and be used to circumvent drug resistance. As R-loop formation is tightly linked to mRNA transcription, their formation is unavoidable in cancer cells and can thus be explored in novel cancer therapeutics.
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Affiliation(s)
- Noha Elsakrmy
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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34
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Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [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: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
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Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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35
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Stoy H, Zwicky K, Kuster D, Lang KS, Krietsch J, Crossley MP, Schmid JA, Cimprich KA, Merrikh H, Lopes M. Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids. Nat Struct Mol Biol 2023; 30:348-359. [PMID: 36864174 PMCID: PMC10023573 DOI: 10.1038/s41594-023-00928-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/23/2023] [Indexed: 03/04/2023]
Abstract
Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.
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Affiliation(s)
- Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Katharina Zwicky
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Kevin S Lang
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonas A Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Houra Merrikh
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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36
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Saha S, Pommier Y. R-loops, type I topoisomerases and cancer. NAR Cancer 2023; 5:zcad013. [PMID: 37600974 PMCID: PMC9984992 DOI: 10.1093/narcan/zcad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
R-loops are abundant and dynamic structures ubiquitously present in human cells both in the nuclear and mitochondrial genomes. They form in cis in the wake of transcription complexes and in trans apart from transcription complexes. In this review, we focus on the relationship between R-loops and topoisomerases, and cancer genomics and therapies. We summarize the topological parameters associated with the formation and resolution of R-loops, which absorb and release high levels of genomic negative supercoiling (Sc-). We review the deleterious consequences of excessive R-loops and rationalize how human type IA (TOP3B) and type IB (TOP1) topoisomerases regulate and resolve R-loops in coordination with helicase and RNase H enzymes. We also review the drugs (topoisomerase inhibitors, splicing inhibitors, G4 stabilizing ligands) and cancer predisposing genes (BRCA1/2, transcription, and splicing genes) known to induce R-loops, and whether stabilizing R-loops and thereby inducing genomic damage can be viewed as a strategy for cancer treatment.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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37
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Zeinoun B, Teixeira MT, Barascu A. TERRA and Telomere Maintenance in the Yeast Saccharomyces cerevisiae. Genes (Basel) 2023; 14:genes14030618. [PMID: 36980890 PMCID: PMC10048448 DOI: 10.3390/genes14030618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Telomeres are structures made of DNA, proteins and RNA found at the ends of eukaryotic linear chromosomes. These dynamic nucleoprotein structures protect chromosomal tips from end-to-end fusions, degradation, activation of damage checkpoints and erroneous DNA repair events. Telomeres were thought to be transcriptionally silent regions because of their constitutive heterochromatin signature until telomeric long non-coding RNAs (LncRNAs) were discovered. One of them, TERRA (TElomeric Repeat-containing RNA), starts in the subtelomeric regions towards the chromosome ends from different telomeres and has been extensively studied in many evolutionarily distant eukaryotes. Changes in TERRA’s expression can lead to telomeric dysfunction, interfere with the replicative machinery and impact telomere length. TERRA also co-localizes in vivo with telomerase, and can form RNA:DNA hybrid structures called R-loops, which have been implicated in the onset of senescence and the alternative lengthening of telomere (ALT) pathway. Yet, the molecular mechanisms involving TERRA, as well as its function, remain elusive. Here, we review the current knowledge of TERRA transcription, structure, expression, regulation and its multiple telomeric and extra-telomeric functions in the budding yeast Saccharomyces cerevisiae.
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38
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Eghbalsaied S, Kues WA. CRISPR/Cas9-mediated targeted knock-in of large constructs using nocodazole and RNase HII. Sci Rep 2023; 13:2690. [PMID: 36792645 PMCID: PMC9931768 DOI: 10.1038/s41598-023-29789-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
On-target integration of large cassettes via homology-directed repair (HDR) has several applications. However, the HDR-mediated targeted knock-in suffered from low efficiency. In this study, we made several large plasmids (12.1-13.4 kb) which included the CRISPR/Cas9 system along with a puromycin transgene as part of the large DNA donor (5.3-7.1 kb insertion cassettes) and used them to evaluate their targeted integration efficiency into a transgenic murine embryonic fibroblast (MEF) cell line carrying a single copy of a Venus transgene. We established a detection assay by which HDR events could be discriminated from the error-prone non-homologous end-joining (NHEJ) events. Improving the plasmid quality could considerably leverage the cell toxicity impediment of large plasmids. The use of the TILD (targeted integration with linearized dsDNA) cassettes did not improve the HDR rate compared to the circular plasmids. However, the direct inclusion of nocodazole into the electroporation solution significantly improved the HDR rate. Also, simultaneous delivery of RNase HII and the donor plasmids into the electroporated cells considerably improved the HDR events. In conclusion, the results of this study showed that using cell synchronization reagents in the electroporation medium can efficiently induce HDR rate in the mammalian genome.
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Affiliation(s)
- Shahin Eghbalsaied
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany ,grid.411463.50000 0001 0706 2472Department of Animal Science, Isfahan (Khorasgan) Branch, Islamic Azad University, Tehran, Iran ,grid.1008.90000 0001 2179 088XSchool of Biosciences, Royal Parade, The University of Melbourne, Melbourne, VIC Australia
| | - Wilfried A. Kues
- grid.417834.dBiotechnology/Stem Cell Physiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany
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39
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Zhou J, Zhang W, Sun Q. R-loop: The new genome regulatory element in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2275-2289. [PMID: 36223078 DOI: 10.1111/jipb.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
An R-loop is a three-stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by-product of transcription. However, recent genome-wide data have shown that R-loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R-loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R-loop levels. Here, we summarize our current understanding of the biogenesis and effects of R-loops, the mechanisms that regulate them, and methods of R-loop profiling, reviewing recent research advances on R-loops in plants. Furthermore, we provide perspectives on future research directions for R-loop biology in plants, which might lead to a more comprehensive understanding of R-loop functions in plant genome regulation and contribute to future agricultural improvements.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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40
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Zhao W, Pei Q, Zhu Y, Zhan D, Mao G, Wang M, Qiu Y, Zuo K, Pei H, Sun LQ, Wen M, Tan R. The Association of R-Loop Binding Proteins Subtypes with CIN Implicates Therapeutic Strategies in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14225607. [PMID: 36428700 PMCID: PMC9688457 DOI: 10.3390/cancers14225607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Chromosomal instability (CIN) covers approximately 65 to 70% of colorectal cancer patients and plays an essential role in cancer progression. However, the molecular features and therapeutic strategies related to those patients are still controversial. R-loop binding proteins (RLBPs) exert significant roles in transcription and replication. Here, integrative colorectal cancer proteogenomic analysis identified two RLBPs subtypes correlated with distinct prognoses. Cluster I (CI), represented by high expression of RLBPs, was associated with the CIN phenotype. While Cluster II (CII) with the worst prognosis and low expression of RLBPs was composed of a high percentage of patients with mucinous adenocarcinoma or right-sided colon cancer. The molecular feature analysis revealed that the active RNA processing, ribosome synthesis, and aberrant DNA damage repair were shown in CI, a high inflammatory signaling pathway, and lymphocyte infiltration was enriched in CII. In addition, we revealed 42 tumor-associated RLBPs proteins. The CI with high expression of tumor-associated proteins was sensitive to drugs targeting genome integrity and EGFR in both cell and organoid models. Thus, our study unveils a significant molecular association of the CIN phenotype with RLBPs, and also provides a powerful resource for further functional exploration of RLBPs in cancer progression and therapeutic application.
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Affiliation(s)
- Wenchao Zhao
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qian Pei
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yongwei Zhu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Guo Mao
- Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Meng Wang
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
| | - Yanfang Qiu
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
| | - Ke Zuo
- Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Haiping Pei
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lun-Quan Sun
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ming Wen
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (M.W.); (R.T.); Tel.: +86-731-84327212 (M.W.); +86-731-84327212 (R.T.)
| | - Rong Tan
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (M.W.); (R.T.); Tel.: +86-731-84327212 (M.W.); +86-731-84327212 (R.T.)
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41
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Raducanu VS, Tehseen M, Al-Amodi A, Joudeh LI, De Biasio A, Hamdan SM. Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Nat Commun 2022; 13:6973. [PMID: 36379932 PMCID: PMC9666535 DOI: 10.1038/s41467-022-34751-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The final steps of lagging strand synthesis induce maturation of Okazaki fragments via removal of the RNA primers and ligation. Iterative cycles between Polymerase δ (Polδ) and Flap endonuclease-1 (FEN1) remove the primer, with an intermediary nick structure generated for each cycle. Here, we show that human Polδ is inefficient in releasing the nick product from FEN1, resulting in non-processive and remarkably slow RNA removal. Ligase 1 (Lig1) can release the nick from FEN1 and actively drive the reaction toward ligation. These mechanisms are coordinated by PCNA, which encircles DNA, and dynamically recruits Polδ, FEN1, and Lig1 to compete for their substrates. Our findings call for investigating additional pathways that may accelerate RNA removal in human cells, such as RNA pre-removal by RNase Hs, which, as demonstrated herein, enhances the maturation rate ~10-fold. They also suggest that FEN1 may attenuate the various activities of Polδ during DNA repair and recombination.
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Affiliation(s)
- Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Amani Al-Amodi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Luay I Joudeh
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. EPIGENOMES 2022; 6:epigenomes6030026. [PMID: 36135313 PMCID: PMC9498298 DOI: 10.3390/epigenomes6030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/24/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis.
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Saha S, Yang X, Huang SYN, Agama K, Baechler SA, Sun Y, Zhang H, Saha LK, Su S, Jenkins LM, Wang W, Pommier Y. Resolution of R-loops by topoisomerase III-β (TOP3B) in coordination with the DEAD-box helicase DDX5. Cell Rep 2022; 40:111067. [PMID: 35830799 PMCID: PMC10575568 DOI: 10.1016/j.celrep.2022.111067] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/20/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
The present study demonstrates how TOP3B is involved in resolving R-loops. We observed elevated R-loops in TOP3B knockout cells (TOP3BKO), which are suppressed by TOP3B transfection. R-loop-inducing agents, the topoisomerase I inhibitor camptothecin, and the splicing inhibitor pladienolide-B also induce higher R-loops in TOP3BKO cells. Camptothecin- and pladienolide-B-induced R-loops are concurrent with the induction of TOP3B cleavage complexes (TOP3Bccs). RNA/DNA hybrid IP-western blotting show that TOP3B is physically associated with R-loops. Biochemical assays using recombinant TOP3B and oligonucleotides mimicking R-loops show that TOP3B cleaves the single-stranded DNA displaced by the R-loop RNA-DNA duplex. IP-mass spectrometry and IP-western experiments reveal that TOP3B interacts with the R-loop helicase DDX5 independently of TDRD3. Finally, we demonstrate that DDX5 and TOP3B are epistatic in resolving R-loops in a pathway parallel with senataxin. We propose a decatenation model for R-loop resolution by TOP3B-DDX5 protecting cells from R-loop-induced damage.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Keli Agama
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simone Andrea Baechler
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lisa M Jenkins
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency. PLoS Genet 2022; 18:e1010267. [PMID: 35714159 PMCID: PMC9246224 DOI: 10.1371/journal.pgen.1010267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/30/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated in a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target. Human genetic diseases, including cancers, are frequently driven by substantial changes to chromosomes, including translocations, where one arm of a chromosome is exchanged for another. The human nucleic acid binding protein Translin was first identified by its ability to bind to the chromosomal sites at which some of these translocations occur. This resulted in Translin being implicated in the mechanism that generated the translocation and thus the associated disease state. However, since its discovery there has been little evidence to directly indicate Translin does contribute to this process. It is, however, known to contribute to a number of biological functions including, amongst others, neurological regulation, sleep control, vascular stiffening, cancer immunomodulation and it has been recently identified as a potential therapeutic target in some cancers. Here we demonstrate that Translin has conserved function in genome stability maintenance when other primary pathways are defective, a function independent of a key binding partner protein, Trax. Specifically, we demonstrate that Translin contributes to minimizing the deleterious genome destabilizing effects of retaining gene expression machineries on chromosomes. This offers the first evidence for how Translin might contribute to genetic disease-causing chromosomal changes and offers insight to inform therapeutic design.
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46
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Detection of RNA-DNA hybrids by immunostaining in meiotic nuclei of Saccharomyces cerevisiae. STAR Protoc 2022; 3:101325. [PMID: 35479113 PMCID: PMC9035804 DOI: 10.1016/j.xpro.2022.101325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
RNA transcripts can anneal with template DNA strands to form RNA-DNA hybrids (or R-loops if the non-template DNA strands exist), which play a variety of roles in many physiological processes. Here, we provide an accessible and reproducible approach for immunofluorescent staining of RNA-DNA hybrids with the S9.6 antibody in spread meiotic nuclei of Saccharomyces cerevisiae. This protocol allows the examination of RNA-DNA hybrids as clearly distinguishable foci and the colocalizations of RNA-DNA hybrids with other proteins. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021). Protocol for sensitive detection of RNA-DNA hybrids in yeast meiotic nuclei Detailed description of optimized meiotic synchronization and chromosome spread General protocol for detection of RNA-DNA hybrids and interested proteins
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Cristini A, Tellier M, Constantinescu F, Accalai C, Albulescu LO, Heiringhoff R, Bery N, Sordet O, Murphy S, Gromak N. RNase H2, mutated in Aicardi-Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation. Nat Commun 2022; 13:2961. [PMID: 35618715 PMCID: PMC9135716 DOI: 10.1038/s41467-022-30604-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
RNase H2 is a specialized enzyme that degrades RNA in RNA/DNA hybrids and deficiency of this enzyme causes a severe neuroinflammatory disease, Aicardi Goutières syndrome (AGS). However, the molecular mechanism underlying AGS is still unclear. Here, we show that RNase H2 is associated with a subset of genes, in a transcription-dependent manner where it interacts with RNA Polymerase II. RNase H2 depletion impairs transcription leading to accumulation of R-loops, structures that comprise RNA/DNA hybrids and a displaced DNA strand, mainly associated with short and intronless genes. Importantly, accumulated R-loops are processed by XPG and XPF endonucleases which leads to DNA damage and activation of the immune response, features associated with AGS. Consequently, we uncover a key role for RNase H2 in the transcription of human genes by maintaining R-loop homeostasis. Our results provide insight into the mechanistic contribution of R-loops to AGS pathogenesis.
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Affiliation(s)
- Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Flavia Constantinescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Clelia Accalai
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Robin Heiringhoff
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037, Toulouse, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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48
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Kermi C, Lau L, Asadi Shahmirzadi A, Classon M. Disrupting Mechanisms that Regulate Genomic Repeat Elements to Combat Cancer and Drug Resistance. Front Cell Dev Biol 2022; 10:826461. [PMID: 35602594 PMCID: PMC9114874 DOI: 10.3389/fcell.2022.826461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Despite advancements in understanding cancer pathogenesis and the development of many effective therapeutic agents, resistance to drug treatment remains a widespread challenge that substantially limits curative outcomes. The historical focus on genetic evolution under drug “pressure” as a key driver of resistance has uncovered numerous mechanisms of therapeutic value, especially with respect to acquired resistance. However, recent discoveries have also revealed a potential role for an ancient evolutionary balance between endogenous “viral” elements in the human genome and diverse factors involved in their restriction in tumor evolution and drug resistance. It has long been appreciated that the stability of genomic repeats such as telomeres and centromeres affect tumor fitness, but recent findings suggest that de-regulation of other repetitive genome elements, including retrotransposons, might also be exploited as cancer therapy. This review aims to present an overview of these recent findings.
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49
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Salvi JS, Kang J, Kim S, Colville AJ, de Morrée A, Billeskov TB, Larsen MC, Kanugovi A, van Velthoven CTJ, Cimprich KA, Rando TA. ATR activity controls stem cell quiescence via the cyclin F-SCF complex. Proc Natl Acad Sci U S A 2022; 119:e2115638119. [PMID: 35476521 PMCID: PMC9170012 DOI: 10.1073/pnas.2115638119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A key property of adult stem cells is their ability to persist in a quiescent state for prolonged periods of time. The quiescent state is thought to contribute to stem cell resilience by limiting accumulation of DNA replication–associated mutations. Moreover, cellular stress response factors are thought to play a role in maintaining quiescence and stem cell integrity. We utilized muscle stem cells (MuSCs) as a model of quiescent stem cells and find that the replication stress response protein, ATR (Ataxia Telangiectasia and Rad3-Related), is abundant and active in quiescent but not activated MuSCs. Concurrently, MuSCs display punctate RPA (replication protein A) and R-loop foci, both key triggers for ATR activation. To discern the role of ATR in MuSCs, we generated MuSC-specific ATR conditional knockout (ATRcKO) mice. Surprisingly, ATR ablation results in increased MuSC quiescence exit. Phosphoproteomic analysis of ATRcKO MuSCs reveals enrichment of phosphorylated cyclin F, a key component of the Skp1–Cul1–F-box protein (SCF) ubiquitin ligase complex and regulator of key cell-cycle transition factors, such as the E2F family of transcription factors. Knocking down cyclin F or inhibiting the SCF complex results in E2F1 accumulation and in MuSCs exiting quiescence, similar to ATR-deficient MuSCs. The loss of ATR could be counteracted by inhibiting casein kinase 2 (CK2), the kinase responsible for phosphorylating cyclin F. We propose a model in which MuSCs express cell-cycle progression factors but ATR, in coordination with the cyclin F–SCF complex, represses premature stem cell quiescence exit via ubiquitin–proteasome degradation of these factors.
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Affiliation(s)
- Jayesh S. Salvi
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Jengmin Kang
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Soochi Kim
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex J. Colville
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Antoine de Morrée
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Tine Borum Billeskov
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Mikkel Christian Larsen
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Abhijnya Kanugovi
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Cindy T. J. van Velthoven
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Karlene A. Cimprich
- cDepartment of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305–5441
| | - Thomas A. Rando
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
- dNeurology Service, VA Palo Alto Health Care System, Palo Alto, CA 94304
- 6To whom correspondence may be addressed.
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50
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Patel PS, Krishnan R, Hakem R. Emerging roles of DNA topoisomerases in the regulation of R-loops. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503450. [PMID: 35483781 DOI: 10.1016/j.mrgentox.2022.503450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/24/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
R-loops are comprised of a DNA:RNA hybrid and a displaced single-strand DNA (ssDNA) that reinvades the DNA duplex behind the moving RNA polymerase. Because they have several physiological functions within the cell, including gene expression, chromosomal segregation, and mitochondrial DNA replication, among others, R-loop homeostasis is tightly regulated to ensure normal functioning of cellular processes. Thus, several classes of enzymes including RNases, helicases, topoisomerases, as well as proteins involved in splicing and the biogenesis of messenger ribonucleoproteins, have been implicated in R-loop prevention, suppression, and resolution. There exist six topoisomerase enzymes encoded by the human genome that function to introduce transient DNA breaks to relax supercoiled DNA. In this mini-review, we discuss functions of DNA topoisomerases and their emerging role in transcription, replication, and regulation of R-loops, and we highlight how their role in maintaining genome stability can be exploited for cancer therapy.
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Affiliation(s)
- Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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