351
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Zhou J, Zhou XA, Zhang N, Wang J. Evolving insights: how DNA repair pathways impact cancer evolution. Cancer Biol Med 2020; 17:805-827. [PMID: 33299637 PMCID: PMC7721097 DOI: 10.20892/j.issn.2095-3941.2020.0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Viewing cancer as a large, evolving population of heterogeneous cells is a common perspective. Because genomic instability is one of the fundamental features of cancer, this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation, development, metastasis, and relapse. With the increased mutation rate and abundant diversity of the gene pool, this heterogeneity leads to cancer evolution, which is the major obstacle in the clinical treatment of cancer. Cells rely on the integrity of DNA repair machineries to maintain genomic stability, but these machineries often do not function properly in cancer cells. The deficiency of DNA repair could contribute to the generation of cancer genomic instability, and ultimately promote cancer evolution. With the rapid advance of new technologies, such as single-cell sequencing in recent years, we have the opportunity to better understand the specific processes and mechanisms of cancer evolution, and its relationship with DNA repair. Here, we review recent findings on how DNA repair affects cancer evolution, and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
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Affiliation(s)
- Jiadong Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ning Zhang
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Biomedical Pioneering Innovation Center (BIOPIC) and Translational Cancer Research Center, School of Life Sciences, First Hospital, Peking University, Beijing 100871, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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352
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Lee SY, Kim JJ, Miller KM. Emerging roles of RNA modifications in genome integrity. Brief Funct Genomics 2020; 20:106-112. [PMID: 33279952 DOI: 10.1093/bfgp/elaa022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Post-translational modifications of proteins are well-established participants in DNA damage response (DDR) pathways, which function in the maintenance of genome integrity. Emerging evidence is starting to reveal the involvement of modifications on RNA in the DDR. RNA modifications are known regulators of gene expression but how and if they participate in DNA repair and genome maintenance has been poorly understood. Here, we review several studies that have now established RNA modifications as key components of DNA damage responses. RNA modifying enzymes and the binding proteins that recognize these modifications localize to and participate in the repair of UV-induced and DNA double-strand break lesions. RNA modifications have a profound effect on DNA-RNA hybrids (R-loops) at DNA damage sites, a structure known to be involved in DNA repair and genome stability. Given the importance of the DDR in suppressing mutations and human diseases such as neurodegeneration, immunodeficiencies, cancer and aging, RNA modification pathways may be involved in human diseases not solely through their roles in gene expression but also by their ability to impact DNA repair and genome stability.
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Affiliation(s)
- Seo Yun Lee
- Miller laboratory at the University of Texas at Austin
| | - Jae Jin Kim
- Miller laboratory at the University of Texas at Austin
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353
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Ono D, Asada K, Yui D, Sakaue F, Yoshioka K, Nagata T, Yokota T. Separation-related rapid nuclear transport of DNA/RNA heteroduplex oligonucleotide: unveiling distinctive intracellular trafficking. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 23:1360-1370. [PMID: 33738132 PMCID: PMC7933600 DOI: 10.1016/j.omtn.2020.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/28/2020] [Indexed: 12/13/2022]
Abstract
DNA/RNA heteroduplex oligonucleotide (HDO), composed of DNA/locked nucleic acid (LNA) antisense oligonucleotide (ASO) and complementary RNA, is a next-generation antisense therapeutic agent. HDO is superior to the parental ASO in delivering to target tissues, and it exerts a more potent gene-silencing effect. In this study, we aimed to elucidate the intracellular trafficking mechanism of HDO-dependent gene silencing. HDO was more preferably transferred to the nucleus after transfection compared to the parental ASO. To determine when and where HDO is separated into the antisense strand (AS) and complementary strand (CS), we performed live-cell time-lapse imaging and fluorescence resonance energy transfer (FRET) assays. These assays demonstrated that HDO had a different intracellular trafficking mechanism than ASO. After endocytosis, HDO was separated in the early endosomes, and both AS and CS were released into the cytosol. AS was more efficiently transported to the nucleus than CS. Separation, endosomal release, and initiation of nuclear transport were a series of time-locked events occurring at a median of 30 s. CS cleavage was associated with efficient nuclear distribution and gene silencing in the nucleus. Understanding the unique intracellular silencing mechanisms of HDO will help us design more efficient drugs and might also provide insight into innate DNA/RNA cellular biology.
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Affiliation(s)
- Daisuke Ono
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Ken Asada
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Daishi Yui
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Fumika Sakaue
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
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354
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Panagopoulos A, Altmeyer M. The Hammer and the Dance of Cell Cycle Control. Trends Biochem Sci 2020; 46:301-314. [PMID: 33279370 DOI: 10.1016/j.tibs.2020.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Cell cycle checkpoints secure ordered progression from one cell cycle phase to the next. They are important to signal cell stress and DNA lesions and to stop cell cycle progression when severe problems occur. Recent work suggests, however, that the cell cycle control machinery responds in more subtle and sophisticated ways when cells are faced with naturally occurring challenges, such as replication impediments associated with endogenous replication stress. Instead of following a stop and go approach, cells use fine-tuned deceleration and brake release mechanisms under the control of ataxia telangiectasia and Rad3-related protein kinase (ATR) and checkpoint kinase 1 (CHK1) to more flexibly adapt their cell cycle program to changing conditions. We highlight emerging examples of such intrinsic cell cycle checkpoint regulation and discuss their physiological and clinical relevance.
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Affiliation(s)
- Andreas Panagopoulos
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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355
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Abstract
This Outlook discusses the findings by Pérez-Calero et al. reporting that, in addition to its RNA processing role, UAP56/DDX39B is a key helicase required to eliminate harmful cotranscriptional RNA structures that otherwise would block transcription and replication. R loops arise from hybridization of RNA transcripts with template DNA during transcription. Unrepaired R loops lead to transcription–replication collisions, causing DNA damage and genomic instability. In this issue of Genes & Development, Pérez-Calero and colleagues (pp. 898–912) identify UAP56 as a cotranscriptional RNA–DNA helicase that unwinds R loops. They found that UAP56 helicase activity is required to remove R loops formed from different sources and prevent R-loop accumulation genome-wide at actively transcribed genes.
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Affiliation(s)
- Jacob P Matson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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356
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Ferrand J, Rondinelli B, Polo SE. Histone Variants: Guardians of Genome Integrity. Cells 2020; 9:E2424. [PMID: 33167489 PMCID: PMC7694513 DOI: 10.3390/cells9112424] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin integrity is key for cell homeostasis and for preventing pathological development. Alterations in core chromatin components, histone proteins, recently came into the spotlight through the discovery of their driving role in cancer. Building on these findings, in this review, we discuss how histone variants and their associated chaperones safeguard genome stability and protect against tumorigenesis. Accumulating evidence supports the contribution of histone variants and their chaperones to the maintenance of chromosomal integrity and to various steps of the DNA damage response, including damaged chromatin dynamics, DNA damage repair, and damage-dependent transcription regulation. We present our current knowledge on these topics and review recent advances in deciphering how alterations in histone variant sequence, expression, and deposition into chromatin fuel oncogenic transformation by impacting cell proliferation and cell fate transitions. We also highlight open questions and upcoming challenges in this rapidly growing field.
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Affiliation(s)
| | | | - Sophie E. Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, 75013 Paris, France; (J.F.); (B.R.)
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357
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Mishra PK, Chakraborty A, Yeh E, Feng W, Bloom KS, Basrai MA. R-loops at centromeric chromatin contribute to defects in kinetochore integrity and chromosomal instability in budding yeast. Mol Biol Cell 2020; 32:74-89. [PMID: 33147102 PMCID: PMC8098821 DOI: 10.1091/mbc.e20-06-0379] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
R-loops, the byproduct of DNA–RNA hybridization and the displaced single-stranded DNA (ssDNA), have been identified in bacteria, yeasts, and other eukaryotic organisms. The persistent presence of R-loops contributes to defects in DNA replication and repair, gene expression, and genomic integrity. R-loops have not been detected at centromeric (CEN) chromatin in wild-type budding yeast. Here we used an hpr1∆ strain that accumulates R-loops to investigate the consequences of R-loops at CEN chromatin and chromosome segregation. We show that Hpr1 interacts with the CEN-histone H3 variant, Cse4, and prevents the accumulation of R-loops at CEN chromatin for chromosomal stability. DNA–RNA immunoprecipitation (DRIP) analysis showed an accumulation of R-loops at CEN chromatin that was reduced by overexpression of RNH1 in hpr1∆ strains. Increased levels of ssDNA, reduced levels of Cse4 and its assembly factor Scm3, and mislocalization of histone H3 at CEN chromatin were observed in hpr1∆ strains. We determined that accumulation of R-loops at CEN chromatin contributes to defects in kinetochore biorientation and chromosomal instability (CIN) and these phenotypes are suppressed by RNH1 overexpression in hpr1∆ strains. In summary, our studies provide mechanistic insights into how accumulation of R-loops at CEN contributes to defects in kinetochore integrity and CIN.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Wenyi Feng
- SUNY Upstate Medical University, Syracuse, NY 13210
| | - Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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358
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Brüning JG, Marians KJ. Replisome bypass of transcription complexes and R-loops. Nucleic Acids Res 2020; 48:10353-10367. [PMID: 32926139 PMCID: PMC7544221 DOI: 10.1093/nar/gkaa741] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
The vast majority of the genome is transcribed by RNA polymerases. G+C-rich regions of the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA to form R-loops, which have been shown to block DNA replication and promote genome instability. However, it is unclear whether the R-loops themselves are sufficient to cause this instability or if additional factors are required. We have investigated replisome collisions with transcription complexes and R-loops using a reconstituted bacterial DNA replication system. RNA polymerase transcription complexes co-directionally oriented with the replication fork were transient blockages, whereas those oriented head-on were severe, stable blockages. On the other hand, replisomes easily bypassed R-loops on either template strand. Replication encounters with R-loops on the leading-strand template (co-directional) resulted in gaps in the nascent leading strand, whereas lagging-strand template R-loops (head-on) had little impact on replication fork progression. We conclude that whereas R-loops alone can act as transient replication blocks, most genome-destabilizing replication fork stalling likely occurs because of proteins bound to the R-loops.
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Affiliation(s)
- Jan-Gert Brüning
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Kenneth J Marians
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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359
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Gómez-González B, Aguilera A. Origin matters: spontaneous DNA-RNA hybrids do not form in trans as a source of genome instability. Curr Genet 2020; 67:93-97. [PMID: 33095299 DOI: 10.1007/s00294-020-01117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/30/2022]
Abstract
Multiple exogenous and endogenous genotoxic agents threaten the integrity of the genome, but one major source of spontaneous DNA damage is the formation of unscheduled DNA-RNA hybrids. These can be genetically detected by their ability to induce recombination. The origin of spontaneous hybrids has been mainly attributed to the nascent RNA formed co-transcriptionally in cis invading its own DNA template. However, it was unclear whether hybrids could also be spontaneously generated by RNA produced in a different locus (in trans). Using new genetic systems in the yeast Saccharomyces cerevisiae, we recently tested whether hybrids could be formed in trans and compromise genome integrity. Whereas we detected recombinogenic DNA-RNA hybrids in cis and in a Rad51-independent manner, we found no evidence for recombinogenic DNA-RNA hybrids to be formed with RNAs produced in trans. Here, we further discuss the implications in the field for the origin of genetic instability and the threats coming from RNAs.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain. .,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
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360
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Abstract
Physiological and pathological roles for R-loop structures continue to be discovered, and studies suggest that R-loops could contribute to human disease. R-loops are nucleic acid structures characterized by a DNA:RNA hybrid and displaced single-stranded DNA that occur in connection with transcription. R-loops form naturally and have been shown to be important for a number of physiological processes such as mitochondrial replication initiation, class switch recombination, DNA repair, modulating DNA topology, and regulation of gene expression. However, subsets of R-loops or persistent R-loops lead to DNA breaks, chromosome rearrangement, and genome instability. In addition, R-loops have been linked to human diseases, specifically neurological disorders and cancer. Of the large amount of research produced recently on R-loops, this review covers evidence for R-loop involvement in normal cellular physiology and pathophysiology, as well as describing factors that contribute to R-loop regulation.
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Affiliation(s)
- Ryan Patrick Mackay
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Qinqin Xu
- Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Paul M Weinberger
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA.,Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
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361
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Feretzaki M, Pospisilova M, Valador Fernandes R, Lunardi T, Krejci L, Lingner J. RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature 2020; 587:303-308. [PMID: 33057192 PMCID: PMC7116795 DOI: 10.1038/s41586-020-2815-6] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Telomeres which are present at the ends of eukaryotic chromosomes mediate genome stability and determine cellular lifespan1. Telomeric repeat containing RNAs (TERRA) are long noncoding RNAs transcribed from chromosome ends2,3, which regulate telomeric chromatin structure and telomere maintenance via telomerase and homology directed repair (HDR)4,5. The mechanisms by which TERRA is recruited to chromosome ends remain poorly defined. Here we develop a reporter system to dissect the underlying mechanisms and demonstrate that the UUAGGG-repeats of TERRA are both necessary and sufficient to target TERRA to chromosome ends. TERRA preferentially associates with short telomeres through the formation of telomeric DNA:RNA hybrid (R-loop) structures that can form in trans. Telomere association and R-loop formation triggers telomere fragility and is promoted by the RAD51 recombinase and its interacting partner BRCA2 but counteracted by RNA surveillance factors, RNaseH1 and TRF1. RAD51 physically interacts with TERRA and catalyzes R-loop formation with TERRA in vitro supporting a direct involvement of this DNA recombinase in TERRA recruitment by strand invasion. Together, our findings reveal a RAD51-dependent pathway that governs TERRA mediated R-loop formation post transcription providing a mechanism of how lncRNAs can be recruited to new loci in trans.
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Affiliation(s)
- Marianna Feretzaki
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michaela Pospisilova
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Rita Valador Fernandes
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Thomas Lunardi
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic. .,International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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362
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Komar D, Juszczynski P. Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 2020; 12:147. [PMID: 33054831 PMCID: PMC7556946 DOI: 10.1186/s13148-020-00941-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background With the discovery that more than half of human cancers harbor mutations in chromatin proteins, deregulation of epigenetic mechanisms has been recognized a hallmark of malignant transformation. Post-translational modifications (PTMs) of histone proteins, as main components of epigenetic regulatory machinery, are also broadly accepted as therapeutic target. Current “epigenetic” therapies target predominantly writers, erasers and readers of histone acetylation and (to a lesser extent) methylation, leaving other types of PTMs largely unexplored. One of them is the phosphorylation of serine 10 on histone H3 (H3S10ph). Main body H3S10ph is emerging as an important player in the initiation and propagation of cancer, as it facilitates cellular malignant transformation and participates in fundamental cellular functions. In normal cells this histone mark dictates the hierarchy of additional histone modifications involved in the formation of protein binding scaffolds, transcriptional regulation, blocking repressive epigenetic information and shielding gene regions from heterochromatin spreading. During cell division, this mark is essential for chromosome condensation and segregation. It is also involved in the function of specific DNA–RNA hybrids, called R-loops, which modulate transcription and facilitate chromosomal instability. Increase in H3S10ph is observed in numerous cancer types and its abundance has been associated with inferior prognosis. Many H3S10-kinases, including MSK1/2, PIM1, CDK8 and AURORA kinases, have been long considered targets in cancer therapy. However, since these proteins also participate in other critical processes, including signal transduction, apoptotic signaling, metabolic fitness and transcription, their chromatin functions are often neglected. Conclusions H3S10ph and enzymes responsible for deposition of this histone modification are important for chromatin activity and oncogenesis. Epigenetic-drugs targeting this axis of modifications, potentially in combination with conventional or targeted therapy, provide a promising angle in search for knowledge-driven therapeutic strategies in oncology.
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Affiliation(s)
- Dorota Komar
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland.
| | - Przemyslaw Juszczynski
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland
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363
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The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress. Nat Commun 2020; 11:5117. [PMID: 33037203 PMCID: PMC7547021 DOI: 10.1038/s41467-020-18857-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 09/16/2020] [Indexed: 02/07/2023] Open
Abstract
Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-κB signaling upon innate immune recognition of the lipopolysaccharide biosynthetic intermediate β-ADP-heptose by the ALPK1/TIFA signaling pathway. DNA damage depends on the bi-functional RfaE enzyme and the Cag pathogenicity island of H. pylori, is accompanied by replication fork stalling and can be observed also in primary cells derived from gastric organoids. Importantly, H. pylori-induced replication stress and DNA damage depend on the presence of co-transcriptional RNA/DNA hybrids (R-loops) that form in infected cells during S-phase as a consequence of β-ADP-heptose/ ALPK1/TIFA/NF-κB signaling. H. pylori resides in close proximity to S-phase cells in the gastric mucosa of gastritis patients. Taken together, our results link bacterial infection and NF-κB-driven innate immune responses to R-loop-dependent replication stress and DNA damage. The bacterial pathogen Helicobacter pylori is known for its ability to induce DNA double-strand breaks in the genome of its target cells. Here, we show that H. pylori-induced DNA damage and replication stress occurs in S-phase cells as a result of R-loop-mediated transcription/replication conflicts that are triggered by activation of the ALPK1/TIFA/NF-κB signaling axis.
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364
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Martin JC, Hoegel TJ, Lynch ML, Woloszynska A, Melendy T, Ohm JE. Exploiting Replication Stress as a Novel Therapeutic Intervention. Mol Cancer Res 2020; 19:192-206. [PMID: 33020173 DOI: 10.1158/1541-7786.mcr-20-0651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/01/2020] [Accepted: 09/29/2020] [Indexed: 11/16/2022]
Abstract
Ewing sarcoma is an aggressive pediatric tumor of the bone and soft tissue. The current standard of care is radiation and chemotherapy, and patients generally lack targeted therapies. One of the defining molecular features of this tumor type is the presence of significantly elevated levels of replication stress as compared with both normal cells and many other types of cancers, but the source of this stress is poorly understood. Tumors that harbor elevated levels of replication stress rely on the replication stress and DNA damage response pathways to retain viability. Understanding the source of the replication stress in Ewing sarcoma may reveal novel therapeutic targets. Ewing sarcomagenesis is complex, and in this review, we discuss the current state of our knowledge regarding elevated replication stress and the DNA damage response in Ewing sarcoma, one contributor to the disease process. We will also describe how these pathways are being successfully targeted therapeutically in other tumor types, and discuss possible novel, evidence-based therapeutic interventions in Ewing sarcoma. We hope that this consolidation will spark investigations that uncover new therapeutic targets and lead to the development of better treatment options for patients with Ewing sarcoma. IMPLICATIONS: This review uncovers new therapeutic targets in Ewing sarcoma and highlights replication stress as an exploitable vulnerability across multiple cancers.
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Affiliation(s)
- Jeffrey C Martin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Tamara J Hoegel
- Department of Pediatric Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Miranda L Lynch
- Hauptman-Woodward Medical Research Institute, Buffalo, New York
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Thomas Melendy
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, New York
| | - Joyce E Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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365
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RNA-cDNA hybrids mediate transposition via different mechanisms. Sci Rep 2020; 10:16034. [PMID: 32994470 PMCID: PMC7524711 DOI: 10.1038/s41598-020-73018-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 11/21/2022] Open
Abstract
Retrotransposons can represent half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to various human diseases. Emerging regulators of retromobility include RNA–DNA hybrid-containing structures known as R-loops. Accumulation of these structures at the transposons of yeast 1 (Ty1) elements has been shown to increase Ty1 retromobility through an unknown mechanism. Here, via a targeted genetic screen, we identified the rnh1Δ rad27Δ yeast mutant, which lacked both the Ty1 inhibitor Rad27 and the RNA–DNA hybrid suppressor Rnh1. The mutant exhibited elevated levels of Ty1 cDNA-associated RNA–DNA hybrids that promoted Ty1 mobility. Moreover, in this rnh1Δ rad27Δ mutant, but not in the double RNase H mutant rnh1Δ rnh201Δ, RNA–DNA hybrids preferentially existed as duplex nucleic acid structures and increased Ty1 mobility in a Rad52-dependent manner. The data indicate that in cells lacking RNA–DNA hybrid and Ty1 repressors, elevated levels of RNA-cDNA hybrids, which are associated with duplex nucleic acid structures, boost Ty1 mobility via a Rad52-dependent mechanism. In contrast, in cells lacking RNA–DNA hybrid repressors alone, elevated levels of RNA-cDNA hybrids, which are associated with triplex nucleic acid structures, boost Ty1 mobility via a Rad52-independent process. We propose that duplex and triplex RNA–DNA hybrids promote transposon mobility via Rad52-dependent or -independent mechanisms.
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366
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Crossley MP, Bocek MJ, Hamperl S, Swigut T, Cimprich KA. qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide. Nucleic Acids Res 2020; 48:e84. [PMID: 32544226 PMCID: PMC7641308 DOI: 10.1093/nar/gkaa500] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA–DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA–RNA immunoprecipitation (qDRIP), a method combining synthetic RNA–DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. We also use these quantitative comparisons to make the first estimates of the absolute count of RNA–DNA hybrids per cell and their half-lives genome-wide. Finally, we identify a subset of RNA–DNA hybrids with high GC skew which are partially resistant to RNase H. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephan Hamperl
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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367
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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368
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Yu Z, Mersaoui SY, Guitton-Sert L, Coulombe Y, Song J, Masson JY, Richard S. DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions. NAR Cancer 2020; 2:zcaa028. [PMID: 33015627 PMCID: PMC7520851 DOI: 10.1093/narcan/zcaa028] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
R-loops are three-stranded structures consisting of a DNA/RNA hybrid and a displaced DNA strand. The regulatory factors required to process this fundamental genetic structure near double-strand DNA breaks (DSBs) are not well understood. We previously reported that cellular depletion of the ATP-dependent DEAD box RNA helicase DDX5 increases R-loops genome-wide causing genomic instability. In this study, we define a pivotal role for DDX5 in clearing R-loops at or near DSBs enabling proper DNA repair to avoid aberrations such as chromosomal deletions. Remarkably, using the non-homologous end joining reporter gene (EJ5-GFP), we show that DDX5-deficient U2OS cells exhibited asymmetric end deletions on the side of the DSBs where there is overlap with a transcribed gene. Cross-linking and immunoprecipitation showed that DDX5 bound RNA transcripts near DSBs and required its helicase domain and the presence of DDX5 near DSBs was also shown by chromatin immunoprecipitation. DDX5 was excluded from DSBs in a transcription- and ATM activation-dependent manner. Using DNA/RNA immunoprecipitation, we show DDX5-deficient cells had increased R-loops near DSBs. Finally, DDX5 deficiency led to delayed exonuclease 1 and replication protein A recruitment to laser irradiation-induced DNA damage sites, resulting in homologous recombination repair defects. Our findings define a role for DDX5 in facilitating the clearance of RNA transcripts overlapping DSBs to ensure proper DNA repair.
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Affiliation(s)
- Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Sofiane Y Mersaoui
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Laure Guitton-Sert
- 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 3S3, Canada
| | - Yan Coulombe
- 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 3S3, Canada
| | - Jingwen Song
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - 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 3S3, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
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369
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Yan Q, Shields EJ, Bonasio R, Sarma K. Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach. Cell Rep 2020; 29:1369-1380.e5. [PMID: 31665646 PMCID: PMC6870988 DOI: 10.1016/j.celrep.2019.09.052] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
R-loops are three-stranded DNA:RNA hybrids that are implicated in many nuclear processes. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in neurological disorders and cancers. Current methods to assess their genome-wide distribution rely on affinity purification, which is plagued by large input requirements, high noise, and poor sensitivity for dynamic R-loops. Here, we present MapR, a method that utilizes RNase H to guide micrococcal nuclease to R-loops, which are subsequently cleaved, released, and identified by sequencing. MapR detects R-loops formed at promoters and active enhancers that are likely to form transient R-loops due to the low transcriptional output of these regulatory elements and the short-lived nature of enhancer RNAs. MapR is as specific as existing techniques and more sensitive, allowing for genomewide coverage with low input material in a fraction of the time. Yan et al. report a fast, easy, antibodyindependent strategy, MapR, to identify native R-loops in vivo without the need for generating stable cell lines. MapR uses the natural affinity and specificity of RNase H to detect R-loops. MapR identifies dynamic R-loops formed at enhancers with high sensitivity.
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Affiliation(s)
- Qingqing Yan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Shields
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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370
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Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res 2020; 48:7218-7238. [PMID: 32542338 PMCID: PMC7367208 DOI: 10.1093/nar/gkaa501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflict (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or ATAD5-interacting RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
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Affiliation(s)
- Sangin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - James Wells
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada
| | - Taejoo Hwang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Peter Stirling
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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371
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Li M, Klungland A. Modifications and interactions at the R-loop. DNA Repair (Amst) 2020; 96:102958. [PMID: 32961406 DOI: 10.1016/j.dnarep.2020.102958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
R-loops are tripartite structures consisting of an RNA:DNA hybrid and a displaced single-stranded DNA [1]. They are widespread and occupy up to 5 % of the mammalian genomes [2]. R-loops have a key role in genome stability, and known functions associated with gene regulation, DNA replication, chromatin patterning, immunoglobuline gene recombination and DNA Double-strand break repair [3-7]. Novel methodology, including the application of the S9.6 antibody, have more recently led to detailed knowledge on the genome-wide distribution of the R-loops as well as the identification of the R-loop interactome [8-10]. The regulation of R-loops was recently shown to also depend on dynamic RNA-methylation, including METTL3/14 dependent 6-methylAdenines (m6As) and METTL8 dependent 3-methylCytosines (m3Cs) [11-13].
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Affiliation(s)
- Miaomiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway.
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372
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Francis NJ, Sihou D. Inheritance of Histone (H3/H4): A Binary Choice? Trends Biochem Sci 2020; 46:5-14. [PMID: 32917507 DOI: 10.1016/j.tibs.2020.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/09/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
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Affiliation(s)
- Nicole J Francis
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada.
| | - Djamouna Sihou
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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373
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Eaton JD, West S. Termination of Transcription by RNA Polymerase II: BOOM! Trends Genet 2020; 36:664-675. [DOI: 10.1016/j.tig.2020.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/22/2022]
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374
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Carbone M, Arron ST, Beutler B, Bononi A, Cavenee W, Cleaver JE, Croce CM, D'Andrea A, Foulkes WD, Gaudino G, Groden JL, Henske EP, Hickson ID, Hwang PM, Kolodner RD, Mak TW, Malkin D, Monnat RJ, Novelli F, Pass HI, Petrini JH, Schmidt LS, Yang H. Tumour predisposition and cancer syndromes as models to study gene-environment interactions. Nat Rev Cancer 2020; 20:533-549. [PMID: 32472073 PMCID: PMC8104546 DOI: 10.1038/s41568-020-0265-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/18/2022]
Abstract
Cell division and organismal development are exquisitely orchestrated and regulated processes. The dysregulation of the molecular mechanisms underlying these processes may cause cancer, a consequence of cell-intrinsic and/or cell-extrinsic events. Cellular DNA can be damaged by spontaneous hydrolysis, reactive oxygen species, aberrant cellular metabolism or other perturbations that cause DNA damage. Moreover, several environmental factors may damage the DNA, alter cellular metabolism or affect the ability of cells to interact with their microenvironment. While some environmental factors are well established as carcinogens, there remains a large knowledge gap of others owing to the difficulty in identifying them because of the typically long interval between carcinogen exposure and cancer diagnosis. DNA damage increases in cells harbouring mutations that impair their ability to correctly repair the DNA. Tumour predisposition syndromes in which cancers arise at an accelerated rate and in different organs - the equivalent of a sensitized background - provide a unique opportunity to examine how gene-environment interactions influence cancer risk when the initiating genetic defect responsible for malignancy is known. Understanding the molecular processes that are altered by specific germline mutations, environmental exposures and related mechanisms that promote cancer will allow the design of novel and effective preventive and therapeutic strategies.
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Affiliation(s)
- Michele Carbone
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA.
| | - Sarah T Arron
- STA, JEC, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Beutler
- Center for Genetic Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Angela Bononi
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Webster Cavenee
- Ludwig Institute, University of California, San Diego, San Diego, CA, USA
| | - James E Cleaver
- STA, JEC, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH, USA
| | - Alan D'Andrea
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Giovanni Gaudino
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Elizabeth P Henske
- Center for LAM Research, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Paul M Hwang
- Cardiovascular Branch, National Institutes of Health, Bethesda, MD, USA
| | - Richard D Kolodner
- Ludwig Institute, University of California, San Diego, San Diego, CA, USA
| | - Tak W Mak
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - David Malkin
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Raymond J Monnat
- Department Pathology, Washington University, Seattle, WA, USA
- Department of Genome Science, Washington University, Seattle, WA, USA
| | - Flavia Novelli
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Harvey I Pass
- Department of Cardiovascular Surgery, New York University, New York, NY, USA
| | - John H Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Haining Yang
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
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375
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Khosravi S, Schindele P, Gladilin E, Dunemann F, Rutten T, Puchta H, Houben A. Application of Aptamers Improves CRISPR-Based Live Imaging of Plant Telomeres. FRONTIERS IN PLANT SCIENCE 2020; 11:1254. [PMID: 32973827 PMCID: PMC7468473 DOI: 10.3389/fpls.2020.01254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/30/2020] [Indexed: 06/01/2023]
Abstract
Development of live imaging techniques for providing information how chromatin is organized in living cells is pivotal to decipher the regulation of biological processes. Here, we demonstrate the improvement of a live imaging technique based on CRISPR/Cas9. In this approach, the sgRNA scaffold is fused to RNA aptamers including MS2 and PP7. When the dead Cas9 (dCas9) is co-expressed with chimeric sgRNA, the fluorescent coat protein-tagged for MS2 and PP7 aptamers (tdMCP-FP and tdPCP-FP) are recruited to the targeted sequence. Compared to previous work with dCas9:GFP, we show that the quality of telomere labeling was improved in transiently transformed Nicotiana benthamiana using aptamer-based CRISPR-imaging constructs. Labeling is influenced by the copy number of aptamers and less by the promoter types. The same constructs were not applicable for labeling of repeats in stably transformed plants and roots. The constant interaction of the RNP complex with its target DNA might interfere with cellular processes.
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Affiliation(s)
- Solmaz Khosravi
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Evgeny Gladilin
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Frank Dunemann
- Institute for Breeding Research on Horticultural Crops, Julius Kühn-Institut (JKI), Quedlinburg, Germany
| | - Twan Rutten
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andreas Houben
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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376
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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377
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Promonet A, Padioleau I, Liu Y, Sanz L, Biernacka A, Schmitz AL, Skrzypczak M, Sarrazin A, Mettling C, Rowicka M, Ginalski K, Chedin F, Chen CL, Lin YL, Pasero P. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat Commun 2020; 11:3940. [PMID: 32769985 PMCID: PMC7414224 DOI: 10.1038/s41467-020-17858-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, here, we map RNA:DNA hybrids, replication stress markers and DNA double-strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR is only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also accumulate at TTS, leading to persistent checkpoint activation, spreading of γ-H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.
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Affiliation(s)
- Alexy Promonet
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
- Institut Gustave Roussy, Villejuif, France
| | - Yaqun Liu
- Institut Curie, PSL Research University, CNRS, UMR3244, Sorbonne Université, Paris, France
| | - Lionel Sanz
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Anne-Lyne Schmitz
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Amélie Sarrazin
- BioCampus Montpellier, CNRS et Université de Montpellier, Montpellier, France
| | - Clément Mettling
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Montpellier, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Frédéric Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS, UMR3244, Sorbonne Université, Paris, France.
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
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378
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379
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Dou P, Li Y, Sun H, Xie W, Zhang X, Zhang X, Zhang D, Qiao S, Ci Y, Nie H, Han F, Li Y. C1orf109L binding DHX9 promotes DNA damage depended on the R-loop accumulation and enhances camptothecin chemosensitivity. Cell Prolif 2020; 53:e12875. [PMID: 32761833 PMCID: PMC7507383 DOI: 10.1111/cpr.12875] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Objectives R‐loop is a three‐stranded nucleic acid structure of RNA/DNA hybrid, which occurs naturally during transcription, and more R‐loop accumulation can trigger serious DNA damage. There has been increasing attention to the issue of R‐loop accumulation acted as a target for cancer therapy. However, the regulation of R‐loop‐associated proteins is poorly explored. Material and method Quantitative real‐time PCR and Western blot were used to measure the expression of C1orf109 in cell lines. In addition, C1orf109L (C1orf109 longest isoform) protein binding partner was identified and validated using immunoprecipitation‐mass spectrometric (IP‐MS) and immunoprecipitation assays. DNA‐RNA immunoprecipitation (DR‐IP) and immunofluorescence determined the C1orf109L location on R‐loop. R‐loop accumulation was determined by immunofluorescence. Cell cycle was determined by flow cytometry. Finally, time‐lapse assay and cell counting were conducted to determined cell survival in response to camptothecin (CPT). Results We found that C1orf109L could mediate cell cycle arrest in the G2/M phase and DNA damage depended on R‐loop accumulation. Meanwhile, C1orf109L could bind with DHX9 to trigger R‐loop accumulation. And C1orf109L was competitive with PARP1 binding to DHX9, which would block the function of DHX9‐PARP1 to prevent the R‐loop accumulation. Furthermore, C1orf109L could enhance the chemosensitivity of CPT, a chemotherapeutic drug capable of promoting R‐loop formation. Conclusions Our data demonstrate that C1orf109L triggers R‐loop accumulation and DNA damage to arrest cell cycle.
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Affiliation(s)
- Peng Dou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Haoxiu Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Wanqiu Xie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Xiaoqing Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Xiaohan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Dandan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Shupei Qiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yanpeng Ci
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin City, China
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380
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Sharma M, Wente SR. Nucleocytoplasmic shuttling of Gle1 impacts DDX1 at transcription termination sites. Mol Biol Cell 2020; 31:2398-2408. [PMID: 32755435 PMCID: PMC7851961 DOI: 10.1091/mbc.e20-03-0215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gle1 is a nucleocytoplasmic shuttling protein with well-documented cytoplasmic roles as a modulator of ATP-dependent DEAD-box RNA helicases involved in messenger (m)RNA export, translation initiation and termination, and stress granule dynamics. Here, we identify a novel nuclear role for Gle1 during transcription termination. In HeLa cells treated with a peptide that disrupts Gle1 nucleocytoplasmic shuttling, we detected nuclear accumulation of specific mRNAs with elongated 3′-UTR (untranslated region). Enriched mRNAs were nascently transcribed and accumulated in the nucleus due to a change in transcription state and not due to altered nuclear export. Whereas Gle1 shuttling inhibition did not appear to perturb nuclear DDX19 functions, it did result in increased DDX1 nucleoplasmic localization and decreased DDX1 interactions with Gle1 and the pre-mRNA cleavage stimulation factor CstF-64. An increase in nuclear R-loop signal intensity was also observed with diminished Gle1 shuttling, as well as colocalization of Gle1 at R-loops. Taken together, these studies reveal a nuclear role for Gle1 in coordinating DDX1 function in transcription termination complexes.
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Affiliation(s)
- Manisha Sharma
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
| | - Susan R Wente
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
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381
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Villarreal OD, Mersaoui SY, Yu Z, Masson JY, Richard S. Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution. Life Sci Alliance 2020; 3:3/10/e202000762. [PMID: 32747416 PMCID: PMC7409538 DOI: 10.26508/lsa.202000762] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 01/22/2023] Open
Abstract
Genome-wide analysis of R-loop alterations in U2OS cells deficient of DDX5, XRN2, and PRMT5 identify >50,650 DRIP-seq peaks spanning ∼4.5% of the genomic sequence. R-loops near TSS generated intergenic antisense transcription. DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.
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Affiliation(s)
- Oscar D Villarreal
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Canada
| | - Sofiane Y Mersaoui
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Canada.,Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Canada
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382
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Lat PK, Liu K, Kumar DN, Wong KKL, Verheyen EM, Sen D. High specificity and tight spatial restriction of self-biotinylation by DNA and RNA G-Quadruplexes complexed in vitro and in vivo with Heme. Nucleic Acids Res 2020; 48:5254-5267. [PMID: 32329781 PMCID: PMC7261162 DOI: 10.1093/nar/gkaa281] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/24/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Guanine-rich, single-stranded DNAs and RNAs that fold to G-quadruplexes (GQs) are able to complex tightly with heme and display strongly enhanced peroxidase activity. Phenolic compounds are particularly good substrates for these oxidative DNAzymes and ribozymes; we recently showed that the use of biotin-tyramide as substrate can lead to efficient GQ self-biotinylation. Such biotinylated GQs are amenable to polymerase chain reaction amplification and should be useful for a relatively non-perturbative investigation of GQs as well as GQ-heme complexes within living cells. Here, we report that in mixed solutions of GQ and duplex DNA in vitro, GQ biotinylation is specifically >104-fold that of the duplex, even in highly concentrated DNA gels; that a three-quartet GQ is tagged by up to four biotins, whose attachment occurs more or less uniformly along the GQ but doesn't extend significantly into a duplex appended to the GQ. This self-biotinylation can be modulated or even abolished in the presence of strong GQ ligands that compete with heme. Finally, we report strong evidence for the successful use of this methodology for labeling DNA and RNA within live, freshly dissected Drosophila larval salivary glands.
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Affiliation(s)
- Prince Kumar Lat
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kun Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dev N Kumar
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kenneth K L Wong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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383
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Cerritelli SM, Iranzo J, Sharma S, Chabes A, Crouch RJ, Tollervey D, El Hage A. High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase. Nucleic Acids Res 2020; 48:4274-4297. [PMID: 32187369 PMCID: PMC7192613 DOI: 10.1093/nar/gkaa103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion.
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Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - David Tollervey
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aziz El Hage
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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384
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Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing. Methods Mol Biol 2020. [PMID: 32681515 DOI: 10.1007/978-1-0716-0680-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
R-loops are three-stranded structures that form during transcription when the nascent RNA hybridizes with the template DNA resulting in a DNA:RNA hybrid and a looped-out single-stranded DNA (ssDNA) strand. These structures are important for normal cellular processes and aberrant R-loop formation has been implicated in a number of pathological outcomes, including certain cancers and neurodegenerative diseases. Mapping R-loops has primarily been performed using DRIP (DNA:RNA immunoprecipitation) based methods that are dependent on the anti-DNA:RNA hybrid S9.6 antibody and short-read sequencing. While DRIP-based methods are robust and report R-loop formation genome-wide, they only do so at the population average level; interrogating R-loop formation at the single molecule level is not feasible with such approaches. Here we present single molecule R-loop footprinting (SMRF-seq), a method that relies on the chemical reactivity of the displaced ssDNA strand to non-denaturing sodium bisulfite and single molecule long-read sequencing as a readout, to characterize R-loops. SMRF-seq can be used independently of S9.6 to generate high resolution, strand-specific, maps of individual R-loops at ultra-deep coverage on kilobases-length DNA fragments.
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385
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Herbert A. Simple Repeats as Building Blocks for Genetic Computers. Trends Genet 2020; 36:739-750. [PMID: 32690316 DOI: 10.1016/j.tig.2020.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 11/15/2022]
Abstract
Processing of RNA involves heterogeneous nuclear ribonucleoproteins. The simple sequence repeats (SSRs) they bind can also adopt alternative DNA structures, like Z DNA, triplexes, G quadruplexes, and I motifs. Those SSRs capable of switching conformation under physiological conditions (called flipons) are genetic elements that can encode alternative RNA processing by their effects on RNA processivity, most likely as DNA:RNA hybrids. Flipons are elements of a binary, instructive genetic code directing how genomic sequences are compiled into transcripts. The combinatorial nature of this code provides a rich set of options for creating genetic computers able to reproduce themselves and use a heritable and evolvable code to optimize survival. The underlying computational logic potentiates a diverse set of genetic programs that modify cis-mediated heritability and disease risk.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA.
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386
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Zhang C, Chen L, Peng D, Jiang A, He Y, Zeng Y, Xie C, Zhou H, Luo X, Liu H, Chen L, Ren J, Wang W, Zhao Y. METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation. Mol Cell 2020; 79:425-442.e7. [PMID: 32615088 DOI: 10.1016/j.molcel.2020.06.017] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/15/2020] [Accepted: 06/09/2020] [Indexed: 12/20/2022]
Abstract
Double-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may lead to genome instability or cell death. Here, we report that, in response to DSBs, the RNA methyltransferase METTL3 is activated by ATM-mediated phosphorylation at S43. Phosphorylated METTL3 is then localized to DNA damage sites, where it methylates the N6 position of adenosine (m6A) in DNA damage-associated RNAs, which recruits the m6A reader protein YTHDC1 for protection. In this way, the METTL3-m6A-YTHDC1 axis modulates accumulation of DNA-RNA hybrids at DSBs sites, which then recruit RAD51 and BRCA1 for homologous recombination (HR)-mediated repair. METTL3-deficient cells display defective HR, accumulation of unrepaired DSBs, and genome instability. Accordingly, depletion of METTL3 significantly enhances the sensitivity of cancer cells and murine xenografts to DNA damage-based therapy. These findings uncover the function of METTL3 and YTHDC1 in HR-mediated DSB repair, which may have implications for cancer therapy.
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Affiliation(s)
- Canfeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Liping Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Di Peng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510006, China
| | - Ao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yunru He
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yanru Zeng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510006, China
| | - Chen Xie
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaotong Luo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jian Ren
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510006, China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510006, China.
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387
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Forrer Charlier C, Martins RAP. Protective Mechanisms Against DNA Replication Stress in the Nervous System. Genes (Basel) 2020; 11:E730. [PMID: 32630049 PMCID: PMC7397197 DOI: 10.3390/genes11070730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
The precise replication of DNA and the successful segregation of chromosomes are essential for the faithful transmission of genetic information during the cell cycle. Alterations in the dynamics of genome replication, also referred to as DNA replication stress, may lead to DNA damage and, consequently, mutations and chromosomal rearrangements. Extensive research has revealed that DNA replication stress drives genome instability during tumorigenesis. Over decades, genetic studies of inherited syndromes have established a connection between the mutations in genes required for proper DNA repair/DNA damage responses and neurological diseases. It is becoming clear that both the prevention and the responses to replication stress are particularly important for nervous system development and function. The accurate regulation of cell proliferation is key for the expansion of progenitor pools during central nervous system (CNS) development, adult neurogenesis, and regeneration. Moreover, DNA replication stress in glial cells regulates CNS tumorigenesis and plays a role in neurodegenerative diseases such as ataxia telangiectasia (A-T). Here, we review how replication stress generation and replication stress response (RSR) contribute to the CNS development, homeostasis, and disease. Both cell-autonomous mechanisms, as well as the evidence of RSR-mediated alterations of the cellular microenvironment in the nervous system, were discussed.
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Affiliation(s)
| | - Rodrigo A. P. Martins
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil;
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388
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Matsui M, Sakasai R, Abe M, Kimura Y, Kajita S, Torii W, Katsuki Y, Ishiai M, Iwabuchi K, Takata M, Nishi R. USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA-RNA helicase DHX9. Oncogenesis 2020; 9:60. [PMID: 32541651 PMCID: PMC7296013 DOI: 10.1038/s41389-020-00244-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 01/05/2023] Open
Abstract
The nucleus of mammalian cells is compartmentalized by nuclear bodies such as nuclear speckles, however, involvement of nuclear bodies, especially nuclear speckles, in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, identified transcription-related nuclear speckle factors as potential HR regulators. Among the top hits, we provide evidence showing that USP42, which is a hitherto unidentified nuclear speckles protein, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localization to nuclear speckles is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. In conclusion, our data propose a model in which USP42 facilitates BRCA1 loading to DSB sites, resolution of DSB-induced R-loop and preferential DSB repair by HR, indicating the importance of nuclear speckle-mediated regulation of DSB repair.
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Affiliation(s)
- Misaki Matsui
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Masako Abe
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Yusuke Kimura
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yoko Katsuki
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Masamichi Ishiai
- Central Radioisotope Division, National Cancer Centre Research Institute, Chuoku, Tokyo, 104-0045, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Minoru Takata
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Ryotaro Nishi
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan. .,School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan.
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389
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Cofsky JC, Karandur D, Huang CJ, Witte IP, Kuriyan J, Doudna JA. CRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks. eLife 2020; 9:e55143. [PMID: 32519675 PMCID: PMC7286691 DOI: 10.7554/elife.55143] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Type V CRISPR-Cas interference proteins use a single RuvC active site to make RNA-guided breaks in double-stranded DNA substrates, an activity essential for both bacterial immunity and genome editing. The best-studied of these enzymes, Cas12a, initiates DNA cutting by forming a 20-nucleotide R-loop in which the guide RNA displaces one strand of a double-helical DNA substrate, positioning the DNase active site for first-strand cleavage. However, crystal structures and biochemical data have not explained how the second strand is cut to complete the double-strand break. Here, we detect intrinsic instability in DNA flanking the RNA-3' side of R-loops, which Cas12a can exploit to expose second-strand DNA for cutting. Interestingly, DNA flanking the RNA-5' side of R-loops is not intrinsically unstable. This asymmetry in R-loop structure may explain the uniformity of guide RNA architecture and the single-active-site cleavage mechanism that are fundamental features of all type V CRISPR-Cas systems.
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Affiliation(s)
- Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Carolyn J Huang
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Isaac P Witte
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- MBIB Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- MBIB Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Gladstone Institutes, University of California, San FranciscoSan FranciscoUnited States
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390
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Merrikh H, Kohli RM. Targeting evolution to inhibit antibiotic resistance. FEBS J 2020; 287:4341-4353. [PMID: 32434280 DOI: 10.1111/febs.15370] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022]
Abstract
Drug-resistant bacterial infections have led to a global health crisis. Although much effort is placed on the development of new antibiotics or variants that are less subject to existing resistance mechanisms, history shows that this strategy by itself is unlikely to solve the problem of drug resistance. Here, we discuss inhibiting evolution as a strategy that, in combination with antibiotics, may resolve the problem. Although mutagenesis is the main driver of drug resistance development, attacking the drivers of genetic diversification in pathogens has not been well explored. Bacteria possess active mechanisms that increase the rate of mutagenesis, especially at times of stress, such as during replication within eukaryotic host cells, or exposure to antibiotics. We highlight how the existence of these promutagenic proteins (evolvability factors) presents an opportunity that can be capitalized upon for the effective inhibition of drug resistance development. To help move this idea from concept to execution, we first describe a set of criteria that an 'optimal' evolvability factor would likely have to meet to be a viable therapeutic target. We then discuss the intricacies of some of the known mutagenic mechanisms and evaluate their potential as drug targets to inhibit evolution. In principle, and as suggested by recent studies, we argue that the inhibition of these and other evolvability factors should reduce resistance development. Finally, we discuss the challenges of transitioning anti-evolution drugs from the laboratory to the clinic.
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Affiliation(s)
- Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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391
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Chen H, Yang H, Zhu X, Yadav T, Ouyang J, Truesdell SS, Tan J, Wang Y, Duan M, Wei L, Zou L, Levine AS, Vasudevan S, Lan L. m 5C modification of mRNA serves a DNA damage code to promote homologous recombination. Nat Commun 2020; 11:2834. [PMID: 32503981 PMCID: PMC7275041 DOI: 10.1038/s41467-020-16722-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/19/2020] [Indexed: 12/02/2022] Open
Abstract
Recruitment of DNA repair proteins to DNA damage sites is a critical step for DNA repair. Post-translational modifications of proteins at DNA damage sites serve as DNA damage codes to recruit specific DNA repair factors. Here, we show that mRNA is locally modified by m5C at sites of DNA damage. The RNA methyltransferase TRDMT1 is recruited to DNA damage sites to promote m5C induction. Loss of TRDMT1 compromises homologous recombination (HR) and increases cellular sensitivity to DNA double-strand breaks (DSBs). In the absence of TRDMT1, RAD51 and RAD52 fail to localize to sites of reactive oxygen species (ROS)-induced DNA damage. In vitro, RAD52 displays an increased affinity for DNA:RNA hybrids containing m5C-modified RNA. Loss of TRDMT1 in cancer cells confers sensitivity to PARP inhibitors in vitro and in vivo. These results reveal an unexpected TRDMT1-m5C axis that promotes HR, suggesting that post-transcriptional modifications of RNA can also serve as DNA damage codes to regulate DNA repair. Post-translational modifications of proteins at DNA damage sites can facilitate the recruitment of DNA repair factors. Here, the authors show that mRNA is locally modified with m5C at sites of DNA damage by the RNA methyltransferase TRDMT1 to promote homologous recombination repair.
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Affiliation(s)
- Hao Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA
| | - Haibo Yang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Xiaolan Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Tribhuwan Yadav
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Samuel S Truesdell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Jun Tan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Yumin Wang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Meihan Duan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA
| | - Leizhen Wei
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Arthur S Levine
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, 5117 Centre Ave., Pittsburgh, PA, 15213, USA. .,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA. .,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA.
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392
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DNA methylation in satellite repeats disorders. Essays Biochem 2020; 63:757-771. [PMID: 31387943 DOI: 10.1042/ebc20190028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
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393
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Luna R, Rondón AG, Pérez-Calero C, Salas-Armenteros I, Aguilera A. The THO Complex as a Paradigm for the Prevention of Cotranscriptional R-Loops. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:105-114. [PMID: 32493765 DOI: 10.1101/sqb.2019.84.039594] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Different proteins associate with the nascent RNA and the RNA polymerase (RNAP) to catalyze the transcription cycle and RNA export. If these processes are not properly controlled, the nascent RNA can thread back and hybridize to the DNA template forming R-loops capable of stalling replication, leading to DNA breaks. Given the transcriptional promiscuity of the genome, which leads to large amounts of RNAs from mRNAs to different types of ncRNAs, these can become a major threat to genome integrity if they form R-loops. Consequently, cells have evolved nuclear factors to prevent this phenomenon that includes THO, a conserved eukaryotic complex acting in transcription elongation and RNA processing and export that upon inactivation causes genome instability linked to R-loop accumulation. We revise and discuss here the biological relevance of THO and a number of RNA helicases, including the THO partner UAP56/DDX39B, as a paradigm of the cellular mechanisms of cotranscriptional R-loop prevention.
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Affiliation(s)
- Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Irene Salas-Armenteros
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
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394
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Jarad M, Antoniou-Kourounioti R, Hepworth J, Qüesta JI. Unique and contrasting effects of light and temperature cues on plant transcriptional programs. Transcription 2020; 11:134-159. [PMID: 33016207 PMCID: PMC7714439 DOI: 10.1080/21541264.2020.1820299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression in response to stress or to drive developmental transitions. Among the many signals that plants perceive, light and temperature are of particular interest due to their intensely fluctuating nature which is combined with a long-term seasonal trend. Whereas specific receptors are key in the light-sensing mechanism, the identity of plant thermosensors for high and low temperatures remains far from fully addressed. This review aims at discussing common as well as divergent characteristics of gene expression regulation in plants, controlled by light and temperature. Light and temperature signaling control the abundance of specific transcription factors, as well as the dynamics of co-transcriptional processes such as RNA polymerase elongation rate and alternative splicing patterns. Additionally, sensing both types of cues modulates gene expression by altering the chromatin landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light sensing is channeled through dedicated receptors, temperature can broadly affect chemical reactions inside plant cells. Thus, direct thermal modifications of the transcriptional machinery add another level of complexity to plant transcriptional regulation. Besides the rapid transcriptome changes that follow perception of environmental signals, plant developmental transitions and acquisition of stress tolerance depend on long-term maintenance of transcriptional states (active or silenced genes). Thus, the rapid transcriptional response to the signal (Phase I) can be distinguished from the long-term memory of the acquired transcriptional state (Phase II - remembering the signal). In this review we discuss recent advances in light and temperature signal perception, integration and memory in Arabidopsis thaliana, focusing on transcriptional regulation and highlighting the contrasting and unique features of each type of cue in the process.
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Affiliation(s)
- Mai Jarad
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | - Jo Hepworth
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julia I. Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
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395
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Tanaka H, Watanabe T. Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers. Trends Cancer 2020; 6:462-477. [PMID: 32383436 PMCID: PMC7285850 DOI: 10.1016/j.trecan.2020.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Focal copy-number increases (genomic amplification) pinpoint oncogenic driver genes and therapeutic targets in cancer genomes. With the advent of genomic technologies, recurrent genomic amplification has been mapped throughout the genome. Recurrent amplification could be solely due to positive selection for the tumor-promoting effects of amplified gene products. Alternatively, recurrence could result from the susceptibility of the loci to amplification. Distinguishing between these possibilities requires a full understanding of the amplification mechanisms. Two mechanisms, the formation of double minute (DM) chromosomes and breakage-fusion-bridge (BFB) cycles, have been repeatedly linked to genomic amplification, and the impact of both mechanisms has been confirmed in cancer genomics data. We review the details of these mechanisms and discuss the mechanisms underlying recurrence.
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Affiliation(s)
- Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA.
| | - Takaaki Watanabe
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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396
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Kafer GR, Cesare AJ. A Survey of Essential Genome Stability Genes Reveals That Replication Stress Mitigation Is Critical for Peri-Implantation Embryogenesis. Front Cell Dev Biol 2020; 8:416. [PMID: 32548123 PMCID: PMC7274024 DOI: 10.3389/fcell.2020.00416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Murine development demands that pluripotent epiblast stem cells in the peri-implantation embryo increase from approximately 120 to 14,000 cells between embryonic days (E) 4.5 and E7.5. This is possible because epiblast stem cells can complete cell cycles in under 3 h in vivo. To ensure conceptus fitness, epiblast cells must undertake this proliferative feat while maintaining genome integrity. How epiblast cells maintain genome health under such an immense proliferation demand remains unclear. To illuminate the contribution of genome stability pathways to early mammalian development we systematically reviewed knockout mouse data from 347 DDR and repair associated genes. Cumulatively, the data indicate that while many DNA repair functions are dispensable in embryogenesis, genes encoding replication stress response and homology directed repair factors are essential specifically during the peri-implantation stage of early development. We discuss the significance of these findings in the context of the unique proliferative demands placed on pluripotent epiblast stem cells.
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Affiliation(s)
| | - Anthony J. Cesare
- Genome Integrity Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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397
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Vydzhak O, Luke B, Schindler N. Non-coding RNAs at the Eukaryotic rDNA Locus: RNA-DNA Hybrids and Beyond. J Mol Biol 2020; 432:4287-4304. [PMID: 32446803 DOI: 10.1016/j.jmb.2020.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
The human ribosomal DNA (rDNA) locus encodes a variety of long non-coding RNAs (lncRNAs). Among them, the canonical ribosomal RNAs that are the catalytic components of the ribosomes, as well as regulatory lncRNAs including promoter-associated RNAs (pRNA), stress-induced promoter and pre-rRNA antisense RNAs (PAPAS), and different intergenic spacer derived lncRNA species (IGSRNA). In addition, externally encoded lncRNAs are imported into the nucleolus, which orchestrate the complex regulation of the nucleolar state in normal and stress conditions via a plethora of molecular mechanisms. This review focuses on the triplex and R-loop formation aspects of lncRNAs at the rDNA locus in yeast and human cells. We discuss the protein players that regulate R-loops at rDNA and how their misregulation contributes to DNA damage and disease. Furthermore, we speculate how DNA lesions such as rNMPs or 8-oxo-dG might affect RNA-DNA hybrid formation. The transcription of lncRNA from rDNA has been observed in yeast, plants, flies, worms, mouse and human cells. This evolutionary conservation highlights the importance of lncRNAs in rDNA function and maintenance.
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Affiliation(s)
- Olga Vydzhak
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Natalie Schindler
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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398
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Abstract
Until recently, our understanding of chromosome organization in higher eukaryotic cells has been based on analyses of large-scale, low-resolution changes in chromosomes structure. More recently, CRISPR-Cas9 technologies have allowed us to "zoom in" and visualize specific chromosome regions in live cells so that we can begin to examine in detail the dynamics of chromosome organization in individual cells. In this review, we discuss traditional methods of chromosome locus visualization and look at how CRISPR-Cas9 gene-targeting methodologies have helped improve their application. We also describe recent developments of the CRISPR-Cas9 technology that enable visualization of specific chromosome regions without the requirement for complex genetic manipulation.
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Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
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399
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SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations. Nat Struct Mol Biol 2020; 27:438-449. [PMID: 32398829 DOI: 10.1038/s41594-020-0419-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022]
Abstract
The SLX4 tumor suppressor is a scaffold that plays a pivotal role in several aspects of genome protection, including homologous recombination, interstrand DNA crosslink repair and the maintenance of common fragile sites and telomeres. Here, we unravel an unexpected direct interaction between SLX4 and the DNA helicase RTEL1, which, until now, were viewed as having independent and antagonistic functions. We identify cancer and Hoyeraal-Hreidarsson syndrome-associated mutations in SLX4 and RTEL1, respectively, that abolish SLX4-RTEL1 complex formation. We show that both proteins are recruited to nascent DNA, tightly co-localize with active RNA pol II, and that SLX4, in complex with RTEL1, promotes FANCD2/RNA pol II co-localization. Importantly, disrupting the SLX4-RTEL1 interaction leads to DNA replication defects in unstressed cells, which are rescued by inhibiting transcription. Our data demonstrate that SLX4 and RTEL1 interact to prevent replication-transcription conflicts and provide evidence that this is independent of the nuclease scaffold function of SLX4.
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400
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