101
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Pérez-Calero C, Bayona-Feliu A, Xue X, Barroso SI, Muñoz S, González-Basallote VM, Sung P, Aguilera A. UAP56/DDX39B is a major cotranscriptional RNA-DNA helicase that unwinds harmful R loops genome-wide. Genes Dev 2020; 34:898-912. [PMID: 32439635 PMCID: PMC7328515 DOI: 10.1101/gad.336024.119] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 01/10/2023]
Abstract
In this study, Pérez-Calero et al. set out to investigate the role of UAP56/DDX39B in R-loop removal. Using in vitro and in vivo approaches, the authors demonstrate that UAP56 functions as a DNA–RNA helicase required to eliminate harmful cotranscriptional RNA structures that otherwise would block transcription and replication. Nonscheduled R loops represent a major source of DNA damage and replication stress. Cells have different ways to prevent R-loop accumulation. One mechanism relies on the conserved THO complex in association with cotranscriptional RNA processing factors including the RNA-dependent ATPase UAP56/DDX39B and histone modifiers such as the SIN3 deacetylase in humans. We investigated the function of UAP56/DDX39B in R-loop removal. We show that UAP56 depletion causes R-loop accumulation, R-loop-mediated genome instability, and replication fork stalling. We demonstrate an RNA–DNA helicase activity in UAP56 and show that its overexpression suppresses R loops and genome instability induced by depleting five different unrelated factors. UAP56/DDX39B localizes to active chromatin and prevents the accumulation of RNA–DNA hybrids over the entire genome. We propose 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.
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Affiliation(s)
- Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Xiaoyu Xue
- Molecular Biophysics and Biochemistry, School of Medicine, University of Yale, New Haven, Connecticut 06510, USA.,Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, USA
| | - Sonia I Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Sergio Muñoz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Víctor M González-Basallote
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Patrick Sung
- Molecular Biophysics and Biochemistry, School of Medicine, University of Yale, New Haven, Connecticut 06510, USA.,Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
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102
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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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103
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Turi Z, Lacey M, Mistrik M, Moudry P. Impaired ribosome biogenesis: mechanisms and relevance to cancer and aging. Aging (Albany NY) 2020; 11:2512-2540. [PMID: 31026227 PMCID: PMC6520011 DOI: 10.18632/aging.101922] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
The biosynthesis of ribosomes is a complex process that requires the coordinated action of many factors and a huge energy investment from the cell. Ribosomes are essential for protein production, and thus for cellular survival, growth and proliferation. Ribosome biogenesis is initiated in the nucleolus and includes: the synthesis and processing of ribosomal RNAs, assembly of ribosomal proteins, transport to the cytoplasm and association of ribosomal subunits. The disruption of ribosome biogenesis at various steps, with either increased or decreased expression of different ribosomal components, can promote cell cycle arrest, senescence or apoptosis. Additionally, interference with ribosomal biogenesis is often associated with cancer, aging and age-related degenerative diseases. Here, we review current knowledge on impaired ribosome biogenesis, discuss the main factors involved in stress responses under such circumstances and focus on examples with clinical relevance.
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Affiliation(s)
- Zsofia Turi
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Matthew Lacey
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Pavel Moudry
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
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104
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DNA polymerase ε relies on a unique domain for efficient replisome assembly and strand synthesis. Nat Commun 2020; 11:2437. [PMID: 32415104 PMCID: PMC7228970 DOI: 10.1038/s41467-020-16095-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
DNA polymerase epsilon (Pol ε) is required for genome duplication and tumor suppression. It supports both replisome assembly and leading strand synthesis; however, the underlying mechanisms remain to be elucidated. Here we report that a conserved domain within the Pol ε catalytic core influences both of these replication steps in budding yeast. Modeling cancer-associated mutations in this domain reveals its unexpected effect on incorporating Pol ε into the four-member pre-loading complex during replisome assembly. In addition, genetic and biochemical data suggest that the examined domain supports Pol ε catalytic activity and symmetric movement of replication forks. Contrary to previously characterized Pol ε cancer variants, the examined mutants cause genome hyper-rearrangement rather than hyper-mutation. Our work thus suggests a role of the Pol ε catalytic core in replisome formation, a reliance of Pol ε strand synthesis on a unique domain, and a potential tumor-suppressive effect of Pol ε in curbing genome re-arrangements.
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105
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Xu W, Li K, Li S, Hou Q, Zhang Y, Liu K, Sun Q. The R-Loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli. THE PLANT CELL 2020; 32:888-903. [PMID: 32075864 PMCID: PMC7145480 DOI: 10.1105/tpc.19.00802] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/31/2020] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
R-loops are a common chromatin feature with essential functions in multiple cellular processes and diseases. However, little is known about the dynamic patterns of R-loops in a given organism. Here, using our recently developed genome-wide R-loop profiling method, we generated a comprehensive atlas quantifying the R-loop patterns of Arabidopsis (Arabidopsis thaliana) in 53 samples during development and during responses to environmental stimuli. The R-loop patterns were fairly stable in plants at the vegetative stage and in response to different light spectra and other environmental stimuli. Notably, the R-loops showed turnover during the plant life cycle, with patterns switching between generations. Importantly, R-loop dynamics was not strongly associated with RNA abundance, indicating that the mechanisms regulating R-loop formation and RNA accumulation are independent. We also observed enrichment of R-loops in transcription factor binding regions, suggesting that R-loops could function as potential cis-transcriptional regulators. This study provides an overview of R-loop dynamics in Arabidopsis during development and stress responses, highlights the unique dynamics of R-loops in the flowering plant Arabidopsis, and lays the groundwork for elucidating the functions of R-loops.
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Affiliation(s)
- Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Quancan Hou
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yushun Zhang
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kunpeng Liu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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106
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Nava GM, Grasso L, Sertic S, Pellicioli A, Muzi Falconi M, Lazzaro F. One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA. Int J Mol Sci 2020; 21:E1706. [PMID: 32131532 PMCID: PMC7084774 DOI: 10.3390/ijms21051706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo.
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Affiliation(s)
| | | | | | | | - Marco Muzi Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
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107
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Storci G, Bacalini MG, Bonifazi F, Garagnani P, De Carolis S, Salvioli S, Olivieri F, Bonafè M. Ribosomal DNA instability: An evolutionary conserved fuel for inflammaging. Ageing Res Rev 2020; 58:101018. [PMID: 31926964 DOI: 10.1016/j.arr.2020.101018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/07/2019] [Accepted: 01/08/2020] [Indexed: 02/07/2023]
Abstract
Across eukaryotes, ribosomal DNA (rDNA) loci are characterized by intrinsic genomic instability due to their repetitive nature and their base composition that facilitate DNA double strand breaks and RNA:DNA hybrids formation. In the yeast, ribosomal DNA instability affects lifespan via the formation of extrachromosomal rDNA circles (ERC) that accrue into aged cells. In humans, rDNA instability has long been reported in a variety of progeric syndromes caused by the dysfunction of DNA helicases, but its role in physiological aging and longevity still needs to be clarified. Here we propose that rDNA instability leads to the activation of innate immunity and inflammation via the interaction with the cytoplasmic DNA sensing machinery. Owing to the recent clarified role of cytoplasmic DNA in the pro-inflammatory phenotype of senescent cells, we hypothesize that the accrual of rDNA derived molecules (i.e. ERC and RNA:DNA hybrids) may have a role in aging by contributing to inflammaging i.e. the systemic pro-inflammatory drift that associates with the onset of geriatric syndromes and age related dysfunctions in humans.
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Affiliation(s)
- Gianluca Storci
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy.
| | | | - Francesca Bonifazi
- Institute of Hematology "L. and A. Seràgnoli", University Hospital S. Orsola-Malpighi, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Sabrina De Carolis
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy; Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA National Institute, Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy; Center for Applied Biomedical Research, CRBA, S. Orsola-Malpighi, University Hospital, Bologna, Italy.
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108
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O'Neill RJ. Seq'ing identity and function in a repeat-derived noncoding RNA world. Chromosome Res 2020; 28:111-127. [PMID: 32146545 PMCID: PMC7393779 DOI: 10.1007/s10577-020-09628-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 01/06/2023]
Abstract
Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts and chromatin-associated and DNA-interacting RNAs. Coupled with emerging genome assembly and analytical approaches, the field is poised to achieve a comprehensive catalog of nuclear noncoding RNAs, including those derived from repetitive regions within eukaryotic genomes. Herein, particular attention is paid to the challenges and advances in the sequence analyses of repeat and transposable element-derived noncoding RNAs and in ascribing specific function(s) to such RNAs.
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Affiliation(s)
- Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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109
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Brambati A, Zardoni L, Nardini E, Pellicioli A, Liberi G. The dark side of RNA:DNA hybrids. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108300. [PMID: 32430097 DOI: 10.1016/j.mrrev.2020.108300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/07/2020] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. In this review, we summarize recent advances in the understanding of the mechanisms by which the impairment of hybrid turnover promotes DNA damage and genome instability via the interference with DNA replication and DNA double-strand break repair. We also discuss how hybrids could contribute to cancer, neurodegeneration and susceptibility to viral infections, focusing on dysfunctions associated with the anti-R-loop helicase Senataxin.
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Affiliation(s)
- Alessandra Brambati
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| | - Luca Zardoni
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; Scuola Universitaria Superiore, IUSS, 27100, Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Achille Pellicioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; IFOM Foundation, Via Adamello 16, 20139, Milan, Italy.
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110
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Chedin F, Benham CJ. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem 2020; 295:4684-4695. [PMID: 32107311 DOI: 10.1074/jbc.rev119.006364] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.
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Affiliation(s)
- Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616 .,Genome Center, University of California, Davis, California 95616
| | - Craig J Benham
- Genome Center, University of California, Davis, California 95616 .,Departments of Mathematics and Biomedical Engineering, University of California, Davis, California 95616
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111
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Intrinsically disordered protein RBM14 plays a role in generation of RNA:DNA hybrids at double-strand break sites. Proc Natl Acad Sci U S A 2020; 117:5329-5338. [PMID: 32094185 DOI: 10.1073/pnas.1913280117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence suggests participation of RNA-binding proteins with intrinsically disordered domains (IDPs) in the DNA damage response (DDR). These IDPs form liquid compartments at DNA damage sites in a poly(ADP ribose) (PAR)-dependent manner. However, it is greatly unknown how the IDPs are involved in DDR. We have shown previously that one of the IDPs RBM14 is required for the canonical nonhomologous end joining (cNHEJ). Here we show that RBM14 is recruited to DNA damage sites in a PARP- and RNA polymerase II (RNAPII)-dependent manner. Both KU and RBM14 are required for RNAPII-dependent generation of RNA:DNA hybrids at DNA damage sites. In fact, RBM14 binds to RNA:DNA hybrids. Furthermore, RNA:DNA hybrids and RNAPII are detected at gene-coding as well as at intergenic areas when double-strand breaks (DSBs) are induced. We propose that the cNHEJ pathway utilizes damage-induced transcription and intrinsically disordered protein RBM14 for efficient repair of DSBs.
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112
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Regulatory R-loops as facilitators of gene expression and genome stability. Nat Rev Mol Cell Biol 2020; 21:167-178. [PMID: 32005969 DOI: 10.1038/s41580-019-0206-3] [Citation(s) in RCA: 256] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 12/23/2022]
Abstract
R-loops are three-stranded structures that harbour an RNA-DNA hybrid and frequently form during transcription. R-loop misregulation is associated with DNA damage, transcription elongation defects, hyper-recombination and genome instability. In contrast to such 'unscheduled' R-loops, evidence is mounting that cells harness the presence of RNA-DNA hybrids in scheduled, 'regulatory' R-loops to promote DNA transactions, including transcription termination and other steps of gene regulation, telomere stability and DNA repair. R-loops formed by cellular RNAs can regulate histone post-translational modification and may be recognized by dedicated reader proteins. The two-faced nature of R-loops implies that their formation, location and timely removal must be tightly regulated. In this Perspective, we discuss the cellular processes that regulatory R-loops modulate, the regulation of R-loops and the potential differences that may exist between regulatory R-loops and unscheduled R-loops.
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113
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Hegazy YA, Fernando CM, Tran EJ. The balancing act of R-loop biology: The good, the bad, and the ugly. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49903-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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114
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Hegazy YA, Fernando CM, Tran EJ. The balancing act of R-loop biology: The good, the bad, and the ugly. J Biol Chem 2019; 295:905-913. [PMID: 31843970 DOI: 10.1074/jbc.rev119.011353] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An R-loop is a three-stranded nucleic acid structure that consists of a DNA:RNA hybrid and a displaced strand of DNA. R-loops occur frequently in genomes and have significant physiological importance. They play vital roles in regulating gene expression, DNA replication, and DNA and histone modifications. Several studies have uncovered that R-loops contribute to fundamental biological processes in various organisms. Paradoxically, although they do play essential positive functions required for important biological processes, they can also contribute to DNA damage and genome instability. Recent evidence suggests that R-loops are involved in a number of human diseases, including neurological disorders, cancer, and autoimmune diseases. This review focuses on the molecular basis for R-loop-mediated gene regulation and genomic instability and briefly discusses methods for identifying R-loops in vivo It also highlights recent studies indicating the role of R-loops in DNA double-strand break repair with an updated view of much-needed future goals in R-loop biology.
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Affiliation(s)
- Youssef A Hegazy
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | | | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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115
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Wreczycka K, Franke V, Uyar B, Wurmus R, Bulut S, Tursun B, Akalin A. HOT or not: examining the basis of high-occupancy target regions. Nucleic Acids Res 2019; 47:5735-5745. [PMID: 31114922 PMCID: PMC6582337 DOI: 10.1093/nar/gkz460] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/02/2019] [Accepted: 05/13/2019] [Indexed: 01/16/2023] Open
Abstract
High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solely defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed ‘hyper-ChIPable’ regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA–DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies.
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Affiliation(s)
- Katarzyna Wreczycka
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ricardo Wurmus
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Selman Bulut
- Gene Regulation and Cell Fate Decision in C. elegans, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Baris Tursun
- Gene Regulation and Cell Fate Decision in C. elegans, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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116
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Drolet M, Brochu J. R-loop-dependent replication and genomic instability in bacteria. DNA Repair (Amst) 2019; 84:102693. [DOI: 10.1016/j.dnarep.2019.102693] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022]
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117
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Meng X, Wei L, Peng XP, Zhao X. Sumoylation of the DNA polymerase ε by the Smc5/6 complex contributes to DNA replication. PLoS Genet 2019; 15:e1008426. [PMID: 31765372 PMCID: PMC6876774 DOI: 10.1371/journal.pgen.1008426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022] Open
Abstract
DNA polymerase epsilon (Pol ε) is critical for genome duplication, but little is known about how post-translational modification regulates its function. Here we report that the Pol ε catalytic subunit Pol2 in yeast is sumoylated at a single lysine within a catalytic domain insertion uniquely possessed by Pol2 family members. We found that Pol2 sumoylation occurs specifically in S phase and is increased under conditions of replication fork blockade. Analyses of the genetic requirements of this modification indicate that Pol2 sumoylation is associated with replication fork progression and dependent on the Smc5/6 SUMO ligase known to promote DNA synthesis. Consistently, the pol2 sumoylation mutant phenotype suggests impaired replication progression and increased levels of gross chromosomal rearrangements. Our findings thus indicate a direct role for SUMO in Pol2-mediated DNA synthesis and a molecular basis for Smc5/6-mediated regulation of genome stability. DNA replication factors are tightly regulated to ensure genome duplication accuracy and efficiency. Among these factors, the Pol ε replicative polymerase plays a vital role by copying half of the genome every cell cycle. However, little is known about how this critical enzyme is regulated. Here we describe SUMO-based regulation of the catalytic subunit of Pol ε, Pol2. Our data suggest that Pol2 sumoylation occurs during replication elongation, particularly when replication forks encounter template obstacles. This modification is mediated by the conserved Smc5/6 SUMO ligase complex and occurs at a single site within the Pol2 catalytic domain. Several observations suggest that Pol2 sumoylation makes positive contributions to the synthesis of DNA regions enriched with template barriers and helps to prevent large-scale genomic alterations. Our work thus provides new insights into DNA polymerase regulation, specifically the role played by contributions from SUMO and the Smc5/6 complex.
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Affiliation(s)
- Xiangzhou Meng
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Lei Wei
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Xiao P. Peng
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Tri-Institutional MD-PhD Program of Weill Cornell Medical School, Rockefeller University, and Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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118
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R Loops: From Physiological to Pathological Roles. Cell 2019; 179:604-618. [PMID: 31607512 DOI: 10.1016/j.cell.2019.08.055] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/19/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
Abstract
DNA-RNA hybrids play a physiological role in cellular processes, but often, they represent non-scheduled co-transcriptional structures with a negative impact on transcription, replication and DNA repair. Accumulating evidence suggests that they constitute a source of replication stress, DNA breaks and genome instability. Reciprocally, DNA breaks facilitate DNA-RNA hybrid formation by releasing the double helix torsional conformation. Cells avoid DNA-RNA accumulation by either preventing or removing hybrids directly or by DNA repair-coupled mechanisms. Given the R-loop impact on chromatin and genome organization and its potential relation with genetic diseases, we review R-loop homeostasis as well as their physiological and pathological roles.
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119
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Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
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Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
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120
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Chen CF, Pohl TJ, Chan A, Slocum JS, Zakian VA. Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics 2019; 213:465-479. [PMID: 31391265 PMCID: PMC6781895 DOI: 10.1534/genetics.119.302528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Two common features of centromeres are their transcription into noncoding centromere RNAs (cen-RNAs) and their assembly into nucleosomes that contain a centromere-specific histone H3 (cenH3). Here, we show that Saccharomyces cerevisiae cen-RNA was present in low amounts in wild-type (WT) cells, and that its appearance was tightly cell cycle-regulated, appearing and disappearing in a narrow window in S phase after centromere replication. In cells lacking Cbf1, a centromere-binding protein, cen-RNA was 5-12 times more abundant throughout the cell cycle. In WT cells, cen-RNA appearance occurred at the same time as loss of Cbf1's centromere binding, arguing that the physical presence of Cbf1 inhibits cen-RNA production. Binding of the Pif1 DNA helicase, which happens in mid-late S phase, occurred at about the same time as Cbf1 loss from the centromere, suggesting that Pif1 may facilitate this loss by its known ability to displace proteins from DNA. Cen-RNAs were more abundant in rnh1Δ cells but only in mid-late S phase. However, fork pausing at centromeres was not elevated in rnh1Δ cells but rather was due to centromere-binding proteins, including Cbf1 Strains with increased cen-RNA lost centromere plasmids at elevated rates. In cbf1Δ cells, where both the levels and the cell cycle-regulated appearance of cen-RNA were disrupted, the timing and levels of cenH3 centromere binding were perturbed. Thus, cen-RNAs are highly regulated, and disruption of this regulation correlates with changes in centromere structure and function.
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Affiliation(s)
- Chi-Fu Chen
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Thomas J Pohl
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Joshua S Slocum
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
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121
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Kuznetsov VA, Bondarenko V, Wongsurawat T, Yenamandra SP, Jenjaroenpun P. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. Nucleic Acids Res 2019; 46:7566-7585. [PMID: 29945198 PMCID: PMC6125637 DOI: 10.1093/nar/gky554] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales. The preferential co-localization of RLFS with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidence for the mechanical linkage between DNA tertiary structures, transcription initiation and R-loops in critical regulatory genome regions. We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. The RLFS co-localization with promoters and transcriptionally active enhancers suggested new models for in cis and in trans regulation by RNA:DNA hybrids of transcription initiation and formation of 3D-chromatin loops. Overall, this study provides a rationale for the discovery and characterization of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome as the basis for an emerging quantitative R-loop biology and pathobiology.
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Affiliation(s)
- Vladimir A Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vladyslav Bondarenko
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Thidathip Wongsurawat
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Surya P Yenamandra
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Piroon Jenjaroenpun
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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122
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Sakhtemani R, Senevirathne V, Stewart J, Perera MLW, Pique-Regi R, Lawrence MS, Bhagwat AS. Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing. J Biol Chem 2019; 294:15037-15051. [PMID: 31431505 DOI: 10.1074/jbc.ra119.008053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 08/13/2019] [Indexed: 12/16/2022] Open
Abstract
Activation-induced deaminase (AID) and apolipoprotein B mRNA-editing enzyme catalytic subunit (APOBEC) enzymes convert cytosines to uracils, creating signature mutations that have been used to predict sites targeted by these enzymes. Mutation-based targeting maps are distorted by the error-prone or error-free repair of these uracils and by selection pressures. To directly map uracils created by AID/APOBEC enzymes, here we used uracil-DNA glycosylase and an alkoxyamine to covalently tag and sequence uracil-containing DNA fragments (UPD-Seq). We applied this technique to the genome of repair-defective, APOBEC3A-expressing bacterial cells and created a uracilation genome map, i.e. uracilome. The peak uracilated regions were in the 5'-ends of genes and operons mainly containing tRNA genes and a few protein-coding genes. We validated these findings through deep sequencing of pulldown regions and whole-genome sequencing of independent clones. The peaks were not correlated with high transcription rates or stable RNA:DNA hybrid formation. We defined the uracilation index (UI) as the frequency of occurrence of TT in UPD-Seq reads at different original TC dinucleotides. Genome-wide UI calculation confirmed that APOBEC3A modifies cytosines in the lagging-strand template during replication and in short hairpin loops. APOBEC3A's preference for tRNA genes was observed previously in yeast, and an analysis of human tumor sequences revealed that in tumors with a high percentage of APOBEC3 signature mutations, the frequency of tRNA gene mutations was much higher than in the rest of the genome. These results identify multiple causes underlying selection of cytosines by APOBEC3A for deamination, and demonstrate the utility of UPD-Seq.
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Affiliation(s)
- Ramin Sakhtemani
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | | | - Jessica Stewart
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Madusha L W Perera
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Michael S Lawrence
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202 .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan 48201
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123
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Prister LL, Ozer EA, Cahoon LA, Seifert HS. Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae. Mol Microbiol 2019; 112:1219-1234. [PMID: 31338863 DOI: 10.1111/mmi.14356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2019] [Indexed: 02/06/2023]
Abstract
Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis-acting sRNA (G4-sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal Av frequencies. Using chromatin immunoprecipitation (ChIP) assays, we show that cellular G4s are less abundant when sRNA transcription is lower. In addition, using ChIP, we demonstrate that the G4-sRNA forms a stable RNA:DNA hybrid (R-loop) with its template strand. However, modulating R-loop levels by controlling RNase HI expression does not alter G4 abundance quantified through ChIP. Since pilin Av frequencies were not altered when modulating R-loop levels by controlling RNase HI expression, we conclude that transcription of the sRNA is necessary, but stable R-loops are not required to promote pilin Av.
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Affiliation(s)
- Lauren L Prister
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Laty A Cahoon
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hank S Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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124
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Morris KJ, Corbett AH. The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts. Nucleic Acids Res 2019; 46:6561-6575. [PMID: 29912477 PMCID: PMC6061872 DOI: 10.1093/nar/gky446] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
The polyadenosine RNA-binding protein ZC3H14 is important in RNA processing. Although ZC3H14 is ubiquitously expressed, mutation of the ZC3H14 gene causes a non-syndromic form of intellectual disability. Here, we examine the function of ZC3H14 in the brain by identifying ZC3H14-interacting proteins using unbiased mass spectrometry. Through this analysis, we identified physical interactions between ZC3H14 and multiple RNA processing factors. Notably, proteins that comprise the THO complex were amongst the most enriched proteins. We demonstrate that ZC3H14 physically interacts with THO components and that these proteins are required for proper RNA processing, as loss of ZC3H14 or THO components leads to extended bulk poly(A) tail length. Furthermore, we identified the transcripts Atp5g1 and Psd95 as shared RNA targets of ZC3H14 and the THO complex. Our data suggest that ZC3H14 and the THO complex are important for proper processing of Atp5g1 and Psd95 RNA, as depletion of ZC3H14 or THO components leads to decreased steady-state levels of each mature transcript accompanied by accumulation of Atp5g1 and Psd95 pre-mRNA in the cytoplasm. Taken together, this work provides the first unbiased identification of nuclear ZC3H14-interacting proteins from the brain and links the functions of ZC3H14 and the THO complex in the processing of RNA.
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Affiliation(s)
- Kevin J Morris
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, James T. Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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125
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Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates? DNA Repair (Amst) 2019; 81:102661. [PMID: 31331819 DOI: 10.1016/j.dnarep.2019.102661] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Although long overlooked, it is now well understood that DNA does not systematically assemble into a canonical double helix, known as B-DNA, throughout the entire genome but can also accommodate other structures including DNA hairpins, G-quadruplexes and RNA:DNA hybrids. Notably, these non-canonical DNA structures form preferentially at transcriptionally active loci. Acting as replication roadblocks and being targeted by multiple machineries, these structures weaken the genome and render it prone to damage, including DNA double-strand breaks (DSB). In addition, secondary structures also further accumulate upon DSB formation. Here we discuss the potential functions of pre-existing or de novo formed nucleic acid structures, as bona fide repair intermediates or repair roadblocks, especially during Transcription-Coupled DNA Double-Strand Break repair (TC-DSBR), and provide an update on the specialized protein complexes displaying the ability to remove these structures to safeguard genome integrity.
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126
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Pohl TJ, Zakian VA. Pif1 family DNA helicases: A helpmate to RNase H? DNA Repair (Amst) 2019; 84:102633. [PMID: 31231063 DOI: 10.1016/j.dnarep.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 01/21/2023]
Abstract
An R-loop is a structure that forms when an RNA transcript stays bound to the DNA strand that encodes it and leaves the complementary strand exposed as a loop of single stranded DNA. R-loops accumulate when the processing of RNA transcripts is impaired. The failure to remove these RNA-DNA hybrids can lead to replication fork stalling and genome instability. Resolution of R-loops is thought to be mediated mainly by RNase H enzymes through the removal and degradation of the RNA in the hybrid. However, DNA helicases can also dismantle R-loops by displacing the bound RNA. In particular, the Pif1 family DNA helicases have been shown to regulate R-loop formation at specific genomic loci, such as tRNA genes and centromeres. Here we review the roles of Pif1 family helicases in vivo and in vitro and discuss evidence that Pif1 family helicases act on RNA-DNA hybrids and highlight their potential roles in complementing RNase H for R-loop resolution.
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Affiliation(s)
- Thomas J Pohl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States.
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127
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Feldman JL, Peterson CL. Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability. Cell Rep 2019; 27:2978-2989.e5. [PMID: 31167142 PMCID: PMC6640630 DOI: 10.1016/j.celrep.2019.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of Hst3 and Hst4, increased transcription is associated with excessive DNA-RNA hybrids (R-loops) that appear to lead to new DNA double-strand breaks. Importantly, dissolution of R-loops suppresses the genome instability phenotypes of hst3 hst4 mutants, suggesting that the sirtuins maintain genome stability by acting as a rheostat to prevent promiscuous transcription.
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Affiliation(s)
- Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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128
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Liu JH, Xi K, Zhang X, Bao L, Zhang X, Tan ZJ. Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling. Biophys J 2019; 117:74-86. [PMID: 31164196 DOI: 10.1016/j.bpj.2019.05.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022] Open
Abstract
DNA-RNA hybrid (DRH) duplexes play essential roles during the replication of DNA and the reverse transcription of RNA viruses, and their flexibility is important for their biological functions. Recent experiments indicated that A-form RNA and B-form DNA have a strikingly different flexibility in stretching and twist-stretch coupling, and the structural flexibility of DRH duplex is of great interest, especially in stretching and twist-stretch coupling. In this work, we performed microsecond all-atom molecular dynamics simulations with new AMBER force fields to characterize the structural flexibility of DRH duplex in stretching and twist-stretch coupling. We have calculated all the helical parameters, stretch modulus, and twist-stretch coupling parameters for the DRH duplex. First, our analyses on structure suggest that the DRH duplex exhibits an intermediate conformation between A- and B-forms and closer to A-form, which can be attributed to the stronger rigidity of the RNA strand than the DNA strand. Second, our calculations show that the DRH duplex has the stretch modulus of 834 ± 34 pN and a very weak twist-stretch coupling. Our quantitative analyses indicate that, compared with DNA and RNA duplexes, the different flexibility of the DRH duplex in stretching and twist-stretch coupling is mainly attributed to its apparently different basepair inclination in the helical structure.
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Affiliation(s)
- Ju-Hui Liu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xinghua Zhang
- College of Life Science, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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129
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High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing. Nat Protoc 2019; 14:1734-1755. [PMID: 31053798 DOI: 10.1038/s41596-019-0159-1] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/28/2019] [Indexed: 11/08/2022]
Abstract
R-loops are prevalent three-stranded non-B DNA structures composed of an RNA-DNA hybrid and a single strand of DNA. R-loops are implicated in various basic nuclear processes, such as class-switch recombination, transcription termination and chromatin patterning. Perturbations in R-loop metabolism have been linked to genomic instability and have been implicated in human disorders, including cancer. As a consequence, the accurate mapping of these structures has been of increasing interest in recent years. Here, we describe two related immunoprecipitation-based methods for mapping R-loop structures: basic DRIP-seq (DNA-RNA immunoprecipitation followed by high-throughput DNA sequencing), an easy, robust, but resolution-limited technique; and DRIPc-seq (DNA-RNA immunoprecipitation followed by cDNA conversion coupled to high-throughput sequencing), a high-resolution and strand-specific iteration of the method that permits accurate R-loop mapping genome wide. Briefly, after gentle DNA extraction and restriction digestion with a cocktail of enzymes, R-loop structures are immunoprecipitated with the anti-RNA-DNA hybrid S9.6 antibody. Compared with DRIP-seq, in which the immunoprecipitated DNA is directly sequenced, DRIPc-seq permits the recovery of the RNA moiety of R-loops, and these RNA strands are subjected to strand-specific RNA sequencing (RNA-seq) analysis. DRIPc-seq can be performed in 5 d and can be applied to any cell type, provided sufficient starting material can be collected. Accurately mapping R-loop distribution in various cell lines and under varied conditions is essential to understanding the formation, roles and dynamic resolution of these important structures.
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130
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Chen JY, Zhang X, Fu XD, Chen L. R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1. Nat Protoc 2019; 14:1661-1685. [PMID: 30996261 DOI: 10.1038/s41596-019-0154-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/21/2019] [Indexed: 11/09/2022]
Abstract
Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA-DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA-DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS).
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Affiliation(s)
- Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Liang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.
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131
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Fitzgerald DM, Rosenberg SM. What is mutation? A chapter in the series: How microbes "jeopardize" the modern synthesis. PLoS Genet 2019; 15:e1007995. [PMID: 30933985 PMCID: PMC6443146 DOI: 10.1371/journal.pgen.1007995] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mutations drive evolution and were assumed to occur by chance: constantly, gradually, roughly uniformly in genomes, and without regard to environmental inputs, but this view is being revised by discoveries of molecular mechanisms of mutation in bacteria, now translated across the tree of life. These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments-when stressed-potentially accelerating adaptation. Mutation is also nonrandom in genomic space, with multiple simultaneous mutations falling in local clusters, which may allow concerted evolution-the multiple changes needed to adapt protein functions and protein machines encoded by linked genes. Molecular mechanisms of stress-inducible mutation change ideas about evolution and suggest different ways to model and address cancer development, infectious disease, and evolution generally.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- The Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- The Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
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132
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Abstract
Three-stranded R-loop structures form during transcription when the nascent RNA transcript rehybridizes to the template DNA strand. This creates an RNA:DNA hybrid and forces the nontemplate DNA strand into a single-stranded, looped-out state. R-loops form universally over conserved hotspot regions. To date, the physicochemical bases underlying R-loop formation remain unclear. Using a “first-principle” mathematical approach backed by experimental validation, we elucidated the relative contributions of DNA sequence and DNA topology to R-loop formation. Our work provides a quantitative assessment of the energies underlying R-loop formation and of their interplay. It further reveals these structures as important regulators of the DNA topological state. R-loops are abundant three-stranded nucleic-acid structures that form in cis during transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms—junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription.
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133
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Crossley MP, Bocek M, Cimprich KA. R-Loops as Cellular Regulators and Genomic Threats. Mol Cell 2019; 73:398-411. [PMID: 30735654 PMCID: PMC6402819 DOI: 10.1016/j.molcel.2019.01.024] [Citation(s) in RCA: 413] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/03/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022]
Abstract
During transcription, the nascent RNA strand can base pair with its template DNA, displacing the non-template strand as ssDNA and forming a structure called an R-loop. R-loops are common across many domains of life and cause DNA damage in certain contexts. In this review, we summarize recent results implicating R-loops as important regulators of cellular processes such as transcription termination, gene regulation, and DNA repair. We also highlight recent work suggesting that R-loops can be problematic to cells as blocks to efficient transcription and replication that trigger the DNA damage response. Finally, we discuss how R-loops may contribute to cancer, neurodegeneration, and inflammatory diseases and compare the available next-generation sequencing-based approaches to map R-loops genome wide.
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Affiliation(s)
- Madzia P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Michael Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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134
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Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM. Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. Cell 2019; 176:127-143.e24. [PMID: 30633903 PMCID: PMC6344048 DOI: 10.1016/j.cell.2018.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 09/05/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.
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Affiliation(s)
- Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li-Ya Chiu
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - María Angélica Bravo Núñez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA
| | - Mercedes Perez
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Yin Zhai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Devon M Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - John P Pribis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumeng Wang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Reid T Powell
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Sandra A LaBonte
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA
| | - Ali Jalali
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meztli L Matadamas Guzmán
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alfred M Lentzsch
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Adam T Szafran
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohan C Joshi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan Richters
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Janet L Gibson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susan G Hilsenbeck
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA
| | - Deborah A Siegele
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Mancini
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kyle M Miller
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA.
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135
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Transcription-dependent regulation of replication dynamics modulates genome stability. Nat Struct Mol Biol 2018; 26:58-66. [PMID: 30598553 DOI: 10.1038/s41594-018-0170-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
Common fragile sites (CFSs) are loci that are hypersensitive to replication stress and hotspots for chromosomal rearrangements in cancers. CFSs replicate late in S phase, are cell-type specific and nest in large genes. The relative impact of transcription-replication conflicts versus a low density in initiation events on fragility is currently debated. Here we addressed the relationships between transcription, replication, and instability by manipulating the transcription of endogenous large genes in chicken and human cells. We found that inducing low transcription with a weak promoter destabilized large genes, whereas stimulating their transcription with strong promoters alleviated instability. Notably, strong promoters triggered a switch to an earlier replication timing, supporting a model in which high transcription levels give cells more time to complete replication before mitosis. Transcription could therefore contribute to maintaining genome integrity, challenging the dominant view that it is exclusively a threat.
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136
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Briggs E, Hamilton G, Crouch K, Lapsley C, McCulloch R. Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Res 2018; 46:11789-11805. [PMID: 30304482 PMCID: PMC6294496 DOI: 10.1093/nar/gky928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 01/09/2023] Open
Abstract
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, UK
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
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137
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Zhang C, Fu H, Yang Y, Zhou E, Tan Z, You H, Zhang X. The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers. Biophys J 2018; 116:196-204. [PMID: 30635125 DOI: 10.1016/j.bpj.2018.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022] Open
Abstract
RNA can anneal to its DNA template to generate an RNA-DNA hybrid (RDH) duplex and a displaced DNA strand, termed R-loop. RDH duplex occupies up to 5% of the mammalian genome and plays important roles in many biological processes. The functions of RDH duplex are affected by its mechanical properties, including the elasticity and the conformation transitions. The mechanical properties of RDH duplex, however, are still unclear. In this work, we studied the mechanical properties of RDH duplex using magnetic tweezers in comparison with those of DNA and RNA duplexes with the same sequences. We report that the contour length of RDH duplex is ∼0.30 nm/bp, and the stretching modulus of RDH duplex is ∼660 pN, neither of which is sensitive to NaCl concentration. The persistence length of RDH duplex depends on NaCl concentration, decreasing from ∼63 nm at 1 mM NaCl to ∼49 nm at 500 mM NaCl. Under high tension of ∼60 pN, the end-opened RDH duplex undergoes two distinct overstretching transitions; at high salt in which the basepairs are stable, it undergoes the nonhysteretic transition, leading to a basepaired elongated structure, whereas at low salt, it undergoes a hysteretic peeling transition, leading to the single-stranded DNA strand under force and the single-stranded RNA strand coils. The peeled RDH is difficult to reanneal back to the duplex conformation, which may be due to the secondary structures formed in the coiled single-stranded RNA strand. These results help us understand the full picture of the structures and mechanical properties of nucleic acid duplexes in solution and provide a baseline for studying the interaction of RDH with proteins at the single-molecule level.
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Affiliation(s)
- Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Yajun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Erchi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Zhijie Tan
- School of Physics and Technology, Wuhan University, Wuhan, China
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinghua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
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138
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Makharashvili N, Arora S, Yin Y, Fu Q, Wen X, Lee JH, Kao CH, Leung JWC, Miller KM, Paull TT. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. eLife 2018; 7:e42733. [PMID: 30523780 PMCID: PMC6296784 DOI: 10.7554/elife.42733] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023] Open
Abstract
The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5' flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.
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Affiliation(s)
- Nodar Makharashvili
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Sucheta Arora
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Yizhi Yin
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Qiong Fu
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Xuemei Wen
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Ji-Hoon Lee
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Chung-Hsuan Kao
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Justin WC Leung
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockUnited States
| | - Kyle M Miller
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Tanya T Paull
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
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139
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Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks. Nature 2018; 564:287-290. [PMID: 30518856 PMCID: PMC6346745 DOI: 10.1038/s41586-018-0769-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/23/2018] [Indexed: 11/22/2022]
Abstract
Insertions of mobile elements1-4, mitochondrial
DNA5 and fragments of
nuclear chromosomes6 at DNA
double strand breaks (DSBs) threaten genome integrity and are common in
cancer7-9. Insertions of chromosome fragments at
V(D)J loci can stimulate antibody diversification10. The origin of insertions of chromosomal
fragments and the mechanisms that prevent such insertions remain unknown. Here
we found the first mutant, lacking evolutionarily conserved Dna2 nuclease, that
shows frequent insertions of ~0.1-1.5 kb long sequences into DSBs with
many events carrying multiple DNA fragments joined together. Sequencing of
~500 DNA inserts revealed that they originate from Ty retrotransposons
(~8%), rDNA (~15%) and from throughout the genome with preference
for fragile regions such as origins of replication, R-loops, centromeres,
telomeres or replication fork barriers. Inserted fragments are not lost from
their original loci and therefore represent duplications. These duplications
depend on nonhomologous end-joining (NHEJ) and Pol4. We propose a model in which
alternative processing of DNA structures arising in Dna2-deficient cells can
result in the release of DNA fragments and their capture at DSBs.Similar DNA
insertions at DSBs are expected in any cells with linear extrachromosomal DNA
fragments.
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140
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Tedeschi FA, Cloutier SC, Tran EJ, Jankowsky E. The DEAD-box protein Dbp2p is linked to noncoding RNAs, the helicase Sen1p, and R-loops. RNA (NEW YORK, N.Y.) 2018; 24:1693-1705. [PMID: 30262458 PMCID: PMC6239179 DOI: 10.1261/rna.067249.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and long noncoding RNA (lncRNA) function. It is not understood how Dbp2p performs these seemingly unrelated biological roles. An important step toward addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using UV-crosslinking, denaturing tandem affinity purification, and next generation sequencing. We find that Dbp2p crosslinks to mRNAs and ribosomal RNAs, and markedly to noncoding RNAs, including snoRNA, snRNAs, and tRNAs. In snoRNAs, Dbp2p preferentially crosslinks at sites near the 3' ends. These sites coincide with regions where RNA-DNA hybrids (R-loops) form and with binding sites of Sen1p, another RNA helicase that functions in transcription termination and 3' processing of noncoding RNAs. We show that Dbp2p interacts in an RNA-independent manner with Sen1p in vivo. Dbp2p crosslinks to tRNAs and other RNAs also at sites where R-loops form. Collectively, our data link Dbp2p to noncoding RNAs, Sen1p, and R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for diverse cellular roles of Dbp2p.
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Affiliation(s)
- Frank A Tedeschi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sara C Cloutier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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141
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Belotserkovskii BP, Tornaletti S, D'Souza AD, Hanawalt PC. R-loop generation during transcription: Formation, processing and cellular outcomes. DNA Repair (Amst) 2018; 71:69-81. [PMID: 30190235 PMCID: PMC6340742 DOI: 10.1016/j.dnarep.2018.08.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.
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Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Silvia Tornaletti
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Alicia D D'Souza
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Philip C Hanawalt
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States.
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142
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Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability. Proc Natl Acad Sci U S A 2018; 115:11024-11029. [PMID: 30301808 DOI: 10.1073/pnas.1807258115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
R loops are nucleic acid structures comprising an DNA-RNA hybrid and a displaced single-stranded DNA. These structures may occur transiently during transcription, playing essential biological functions. However, persistent R loops may become pathological as they are important drivers of genome instability and have been associated with human diseases. The mitochondrial degradosome is a functionally conserved complex from bacteria to human mitochondria. It is composed of the ATP-dependent RNA and DNA helicase SUV3 and the PNPase ribonuclease, playing a central role in mitochondrial RNA surveillance and degradation. Here we describe a new role for the mitochondrial degradosome in preventing the accumulation of pathological R loops in the mitochondrial DNA, in addition to preventing dsRNA accumulation. Our data indicate that, similar to the molecular mechanisms acting in the nucleus, RNA surveillance mechanisms in the mitochondria are crucial to maintain its genome integrity by counteracting pathological R-loop accumulation.
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143
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Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli. PLoS Genet 2018; 14:e1007668. [PMID: 30222737 PMCID: PMC6160223 DOI: 10.1371/journal.pgen.1007668] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/27/2018] [Accepted: 08/29/2018] [Indexed: 02/07/2023] Open
Abstract
Type 1A topoisomerases (topos) are the only ubiquitous topos. E. coli has two type 1A topos, topo I (topA) and topo III (topB). Topo I relaxes negative supercoiling in part to inhibit R-loop formation. To grow, topA mutants acquire compensatory mutations, base substitutions in gyrA or gyrB (gyrase) or amplifications of a DNA region including parC and parE (topo IV). topB mutants grow normally and topo III binds tightly to single-stranded DNA. What functions topo I and III share in vivo and how cells lacking these important enzymes can survive is unclear. Previously, a gyrB(Ts) compensatory mutation was used to construct topA topB null mutants. These mutants form very long filaments and accumulate diffuse DNA, phenotypes that appears to be related to replication from R-loops. Here, next generation sequencing and qPCR for marker frequency analysis were used to further define the functions of type 1A topos. The results reveal the presence of a RNase HI-sensitive origin of replication in the terminus (Ter) region of the chromosome that is more active in topA topB cells than in topA and rnhA (RNase HI) null cells. The S9.6 antibodies specific to DNA:RNA hybrids were used in dot-blot experiments to show the accumulation of R-loops in rnhA, topA and topA topB null cells. Moreover topA topB gyrB(Ts) strains, but not a topA gyrB(Ts) strain, were found to carry a parC parE amplification. When a topA gyrB(Ts) mutant carried a plasmid producing topo IV, topB null transductants did not have parC parE amplifications. Altogether, the data indicate that in E. coli type 1A topos are required to inhibit R-loop formation/accumulation mostly to prevent unregulated replication in Ter, and that they are essential to prevent excess negative supercoiling and its detrimental effects on cell growth and survival. DNA topoisomerases are nicking closing enzymes with strand passage activity that solves the topological problems inherent to the double-helical structure of DNA. Topos of the type 1A family are the only ubiquitous topos. They are classified in two subfamilies, topo I and topo III respectively found in bacteria only and in organisms from the three domains of life. The prototype enzymes of these two subfamilies are topo I and topo III from Escherichia coli. Recent data suggest that duplications leading to topo I and III subfamilies occurred in the Last Common Universal Ancestor of the three domains of life. In this context, our finding reported here that both E. coli topo I and III control R-loop formation/accumulation, mostly to inhibit unregulated replication, may suggest that R-loops have been a problem early in the evolution of life. Furthermore, our data show that E. coli cells can survive in the absence of type 1A topos, owing to the surproduction of topo IV that can relax excess negative supercoiling and prevent R-loop formation. Thus, our results strongly suggest that a major function of type 1A topos is to control R-loop formation to preserve the integrity of the genome.
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144
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Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD. Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks. EMBO Rep 2018; 19:e46222. [PMID: 30104203 PMCID: PMC6123642 DOI: 10.15252/embr.201846222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/17/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022] Open
Abstract
Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome-wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild-type Rif1 and truncated Rif1 lacking the Rap1-interaction domain, we identify hundreds of Rap1-dependent and Rap1-independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1-independent manner, associating with both early and late-initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
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Affiliation(s)
| | | | - Yuki Katou
- Institute for Quantitative Biosciences, University of Tokyo, Tokyo, Japan
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Kate Rm Clark
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
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145
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Wang IX, Grunseich C, Fox J, Burdick J, Zhu Z, Ravazian N, Hafner M, Cheung VG. Human proteins that interact with RNA/DNA hybrids. Genome Res 2018; 28:1405-1414. [PMID: 30108179 PMCID: PMC6120628 DOI: 10.1101/gr.237362.118] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/27/2018] [Indexed: 12/16/2022]
Abstract
RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.
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Affiliation(s)
- Isabel X Wang
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland 20892, USA
| | - Jennifer Fox
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Joshua Burdick
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Niema Ravazian
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA
| | - Vivian G Cheung
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
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146
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Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse. Cell 2018; 174:1127-1142.e19. [PMID: 30078706 DOI: 10.1016/j.cell.2018.07.011] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/25/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
Abstract
Replication origins, fragile sites, and rDNA have been implicated as sources of chromosomal instability. However, the defining genomic features of replication origins and fragile sites are among the least understood elements of eukaryote genomes. Here, we map sites of replication initiation and breakage in primary cells at high resolution. We find that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(dA:dT) tracts flanking the initiation site. Paradoxically, long (>20 bp) (dA:dT) tracts are also preferential sites of polar replication fork stalling and collapse within early-replicating fragile sites (ERFSs) and late-replicating common fragile sites (CFSs) and at the rDNA replication fork barrier. Poly(dA:dT) sequences are fragile because long single-strand poly(dA) stretches at the replication fork are unprotected by the replication protein A (RPA). We propose that the evolutionary expansion of poly(dA:dT) tracts in eukaryotic genomes promotes replication initiation, but at the cost of chromosome fragility.
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147
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Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability. Mol Cell 2018; 71:487-497.e3. [PMID: 30078723 DOI: 10.1016/j.molcel.2018.06.037] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/23/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023]
Abstract
DNA-RNA hybrids associated with R-loops promote DNA damage and genomic instability. The capacity of hybrids at different genomic sites to cause DNA damage was not known, and the mechanisms leading from hybrid to damage were poorly understood. Here, we adopt a new strategy to map and characterize the sites of hybrid-induced damage genome-wide in budding yeast. We show that hybrid removal is essential for life because persistent hybrids cause irreparable DNA damage and cell death. We identify that a subset of hybrids is prone to cause damage, and the chromosomal context of hybrids dramatically impacts their ability to induce damage. Furthermore, persistent hybrids affect the repair pathway, generating large regions of single-stranded DNA (ssDNA) by two distinct mechanisms, likely resection and re-replication. These damaged regions may act as potential precursors to gross chromosomal rearrangements like deletions and duplications that are associated with R-loops and cancers.
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148
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Freudenreich CH. R-loops: targets for nuclease cleavage and repeat instability. Curr Genet 2018; 64:789-794. [PMID: 29327083 PMCID: PMC6039234 DOI: 10.1007/s00294-018-0806-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/09/2023]
Abstract
R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.
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Affiliation(s)
- Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Program in Genetics, Tufts University, Boston, MA, 02111, USA.
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149
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García-Rubio M, Aguilera P, Lafuente-Barquero J, Ruiz JF, Simon MN, Geli V, Rondón AG, Aguilera A. Yra1-bound RNA-DNA hybrids cause orientation-independent transcription-replication collisions and telomere instability. Genes Dev 2018; 32:965-977. [PMID: 29954833 PMCID: PMC6075034 DOI: 10.1101/gad.311274.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/16/2018] [Indexed: 12/25/2022]
Abstract
R loops are an important source of genome instability, largely due to their negative impact on replication progression. Yra1/ALY is an abundant RNA-binding factor conserved from yeast to humans and required for mRNA export, but its excess causes lethality and genome instability. Here, we show that, in addition to ssDNA and ssRNA, Yra1 binds RNA-DNA hybrids in vitro and, when artificially overexpressed, can be recruited to chromatin in an RNA-DNA hybrid-dependent manner, stabilizing R loops and converting them into replication obstacles in vivo. Importantly, an excess of Yra1 increases R-loop-mediated genome instability caused by transcription-replication collisions regardless of whether they are codirectional or head-on. It also induces telomere shortening in telomerase-negative cells and accelerates senescence, consistent with a defect in telomere replication. Our results indicate that RNA-DNA hybrids form transiently in cells regardless of replication and, after stabilization by excess Yra1, compromise genome integrity, in agreement with a two-step model of R-loop-mediated genome instability. This work opens new perspectives to understand transcription-associated genome instability in repair-deficient cells, including tumoral cells.
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Affiliation(s)
- María García-Rubio
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Paula Aguilera
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Juan Lafuente-Barquero
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José F Ruiz
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Vincent Geli
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Ana G Rondón
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Andrés Aguilera
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
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150
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Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res 2018; 46:3400-3411. [PMID: 29474582 PMCID: PMC5909445 DOI: 10.1093/nar/gky118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rajvardhan M Kapshikar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
| | - Jillella Mallikarjun
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
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