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Barroso S, Herrera‐Moyano E, Muñoz S, García‐Rubio M, Gómez‐González B, Aguilera A. The DNA damage response acts as a safeguard against harmful DNA-RNA hybrids of different origins. EMBO Rep 2019; 20:e47250. [PMID: 31338941 PMCID: PMC6726908 DOI: 10.15252/embr.201847250] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/14/2022] Open
Abstract
Despite playing physiological roles in specific situations, DNA-RNA hybrids threat genome integrity. To investigate how cells do counteract spontaneous DNA-RNA hybrids, here we screen an siRNA library covering 240 human DNA damage response (DDR) genes and select siRNAs causing DNA-RNA hybrid accumulation and a significant increase in hybrid-dependent DNA breakage. We identify post-replicative repair and DNA damage checkpoint factors, including those of the ATM/CHK2 and ATR/CHK1 pathways. Thus, spontaneous DNA-RNA hybrids are likely a major source of replication stress, but they can also accumulate and menace genome integrity as a consequence of unrepaired DSBs and post-replicative ssDNA gaps in normal cells. We show that DNA-RNA hybrid accumulation correlates with increased DNA damage and chromatin compaction marks. Our results suggest that different mechanisms can lead to DNA-RNA hybrids with distinct consequences for replication and DNA dynamics at each cell cycle stage and support the conclusion that DNA-RNA hybrids are a common source of spontaneous DNA damage that remains unsolved under a deficient DDR.
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Affiliation(s)
- Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - Emilia Herrera‐Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - Sergio Muñoz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - María García‐Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - Belén Gómez‐González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
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52
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Landsverk HB, Sandquist LE, Sridhara SC, Rødland GE, Sabino JC, de Almeida SF, Grallert B, Trinkle-Mulcahy L, Syljuåsen RG. Regulation of ATR activity via the RNA polymerase II associated factors CDC73 and PNUTS-PP1. Nucleic Acids Res 2019; 47:1797-1813. [PMID: 30541148 PMCID: PMC6393312 DOI: 10.1093/nar/gky1233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/23/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Ataxia telangiectasia mutated and Rad3-related (ATR) kinase is a key factor activated by DNA damage and replication stress. An alternative pathway for ATR activation has been proposed to occur via stalled RNA polymerase II (RNAPII). However, how RNAPII might signal to activate ATR remains unknown. Here, we show that ATR signaling is increased after depletion of the RNAPII phosphatase PNUTS-PP1, which dephosphorylates RNAPII in its carboxy-terminal domain (CTD). High ATR signaling was observed in the absence and presence of ionizing radiation, replication stress and even in G1, but did not correlate with DNA damage or RPA chromatin loading. R-loops were enhanced, but overexpression of EGFP-RNaseH1 only slightly reduced ATR signaling after PNUTS depletion. However, CDC73, which interacted with RNAPII in a phospho-CTD dependent manner, was required for the high ATR signaling, R-loop formation and for activation of the endogenous G2 checkpoint after depletion of PNUTS. In addition, ATR, RNAPII and CDC73 co-immunoprecipitated. Our results suggest a novel pathway involving RNAPII, CDC73 and PNUTS-PP1 in ATR signaling and give new insight into the diverse functions of ATR.
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Affiliation(s)
- Helga B Landsverk
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Lise E Sandquist
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sreerama C Sridhara
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Gro Elise Rødland
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - João C Sabino
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Beata Grallert
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Randi G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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53
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Mersaoui SY, Yu Z, Coulombe Y, Karam M, Busatto FF, Masson J, Richard S. Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids. EMBO J 2019; 38:e100986. [PMID: 31267554 PMCID: PMC6669924 DOI: 10.15252/embj.2018100986] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 05/15/2019] [Accepted: 05/28/2019] [Indexed: 01/09/2023] Open
Abstract
Aberrant transcription-associated RNA:DNA hybrid (R-loop) formation often causes catastrophic conflicts during replication, resulting in DNA double-strand breaks and genomic instability. Preventing such conflicts requires hybrid dissolution by helicases and/or RNase H. Little is known about how such helicases are regulated. Herein, we identify DDX5, an RGG/RG motif-containing DEAD-box family RNA helicase, as crucial player in R-loop resolution. In vitro, recombinant DDX5 resolves R-loops in an ATP-dependent manner, leading to R-loop degradation by the XRN2 exoribonuclease. DDX5-deficient cells accumulate R-loops at loci with propensity to form such structures based on RNA:DNA immunoprecipitation (DRIP)-qPCR, causing spontaneous DNA double-strand breaks and hypersensitivity to replication stress. DDX5 associates with XRN2 and resolves R-loops at transcriptional termination regions downstream of poly(A) sites, to facilitate RNA polymerase II release associated with transcriptional termination. Protein arginine methyltransferase 5 (PRMT5) binds and methylates DDX5 at its RGG/RG motif. This motif is required for DDX5 interaction with XRN2 and repression of cellular R-loops, but not essential for DDX5 helicase enzymatic activity. PRMT5-deficient cells accumulate R-loops, resulting in increased formation of γH2AX foci. Our findings exemplify a mechanism by which an RNA helicase is modulated by arginine methylation to resolve R-loops, and its potential role in regulating transcription.
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Affiliation(s)
- Sofiane Y Mersaoui
- Departments of Oncology and MedicineSegal Cancer CenterLady Davis Institute for Medical ResearchMcGill UniversityMontréalQCCanada
| | - Zhenbao Yu
- Departments of Oncology and MedicineSegal Cancer CenterLady Davis Institute for Medical ResearchMcGill UniversityMontréalQCCanada
| | - Yan Coulombe
- Genome Stability LaboratoryOncology DivisionCHU de Québec‐Université LavalQuébecQCCanada
- Department of Molecular Biology, Medical Biochemistry and PathologyLaval University Cancer Research CenterQuébecQCCanada
| | - Martin Karam
- Departments of Oncology and MedicineSegal Cancer CenterLady Davis Institute for Medical ResearchMcGill UniversityMontréalQCCanada
| | - Franciele F Busatto
- Genome Stability LaboratoryOncology DivisionCHU de Québec‐Université LavalQuébecQCCanada
- Department of Molecular Biology, Medical Biochemistry and PathologyLaval University Cancer Research CenterQuébecQCCanada
| | - Jean‐Yves Masson
- Genome Stability LaboratoryOncology DivisionCHU de Québec‐Université LavalQuébecQCCanada
- Department of Molecular Biology, Medical Biochemistry and PathologyLaval University Cancer Research CenterQuébecQCCanada
| | - Stéphane Richard
- Departments of Oncology and MedicineSegal Cancer CenterLady Davis Institute for Medical ResearchMcGill UniversityMontréalQCCanada
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54
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Abstract
Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription-replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.
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55
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Chuang TW, Lu CC, Su CH, Wu PY, Easwvaran S, Lee CC, Kuo HC, Hung KY, Lee KM, Tsai CY, Tarn WY. The RNA Processing Factor Y14 Participates in DNA Damage Response and Repair. iScience 2019; 13:402-415. [PMID: 30901577 PMCID: PMC6428943 DOI: 10.1016/j.isci.2019.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 02/01/2023] Open
Abstract
DNA repair deficiency leads to genome instability and hence human disease. Depletion of the RNA processing factor Y14/RBM8A in cultured cells or Rbm8a haplodeficiency in the developing mouse cortex results in the accumulation of DNA damage. Y14 depletion differentially affected the expression of DNA damage response (DDR) factors and induced R-loops, both of which threaten genomic stability. Immunoprecipitation coupled with mass spectrometry revealed DDR factors as potential Y14-interacting partners. Further results confirmed that Y14 interacts with Ku and several DDR factors in an ATM-dependent manner. Y14 co-fractionated with Ku in chromatin-enriched fractions and further accumulated on chromatin upon DNA damage. Y14 knockdown delayed recruitment of DDR factors to DNA damage sites and formation of γH2AX foci and also led to Ku retention on chromatin. Accordingly, Y14 depletion compromised the efficiency of DNA end joining. Therefore Y14 likely plays a direct role in DNA damage repair via its interaction with DDR factors. Y14 deficiency leads to DNA damage accumulation Y14 depletion disturbs DNA damage response and induces R-loops Y14 promotes Ku70/80 recruitment to DNA damage sites Y14 participates in DNA damage repair
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Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Chun-Hao Su
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Pei-Yu Wu
- Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
| | - Sarasvathi Easwvaran
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chi-Chieh Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Hung-Che Kuo
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuan-Yang Hung
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Ching-Yen Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan.
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56
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Vítor AC, Sridhara SC, Sabino JC, Afonso AI, Grosso AR, Martin RM, de Almeida SF. Single-molecule imaging of transcription at damaged chromatin. SCIENCE ADVANCES 2019; 5:eaau1249. [PMID: 30662944 PMCID: PMC6326756 DOI: 10.1126/sciadv.aau1249] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/29/2018] [Indexed: 05/11/2023]
Abstract
How DNA double-strand breaks (DSBs) affect ongoing transcription remains elusive due to the lack of single-molecule resolution tools directly measuring transcription dynamics upon DNA damage. Here, we established new reporter systems that allow the visualization of individual nascent RNAs with high temporal and spatial resolution upon the controlled induction of a single DSB at two distinct chromatin locations: a promoter-proximal (PROP) region downstream the transcription start site and a region within an internal exon (EX2). Induction of a DSB resulted in a rapid suppression of preexisting transcription initiation regardless of the genomic location. However, while transcription was irreversibly suppressed upon a PROP DSB, damage at the EX2 region drove the formation of promoter-like nucleosome-depleted regions and transcription recovery. Two-color labeling of transcripts at sequences flanking the EX2 lesion revealed bidirectional break-induced transcription initiation. Transcriptome analysis further showed pervasive bidirectional transcription at endogenous intragenic DSBs. Our data provide a novel framework for interpreting the reciprocal interactions between transcription and DNA damage at distinct chromatin regions.
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57
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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58
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Okamoto Y, Abe M, Itaya A, Tomida J, Ishiai M, Takaori-Kondo A, Taoka M, Isobe T, Takata M. FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress. FEBS J 2018; 286:139-150. [PMID: 30431240 DOI: 10.1111/febs.14700] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/02/2018] [Accepted: 11/12/2018] [Indexed: 01/19/2023]
Abstract
R-loops, which consist of DNA : RNA hybrids and displaced single-strand DNA, are a major threat to genome stability. We have previously reported that a key Fanconi anemia protein, FANCD2, accumulates on large fragile genes during mild replication stress in a manner depending on R-loops. In this study, we found that FANCD2 suppresses R-loop levels. Furthermore, we identified FANCD2 interactions with RNA processing factors, including hnRNP U and DDX47. Our data suggest that FANCD2, which accumulates with R-loops in chromatin, recruits these factors and thereby promotes efficient processing of long RNA transcripts. This may lead to a reduction in transcription-replication collisions, as detected by PLA between PCNA and RNA Polymerase II, and hence, lowered R-loop levels. We propose that this mechanism might contribute to maintenance of genome stability during mild replication stress.
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Affiliation(s)
- Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masako Abe
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Akiko Itaya
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Junya Tomida
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
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59
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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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60
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Kotsantis P, Petermann E, Boulton SJ. Mechanisms of Oncogene-Induced Replication Stress: Jigsaw Falling into Place. Cancer Discov 2018; 8:537-555. [PMID: 29653955 DOI: 10.1158/2159-8290.cd-17-1461] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022]
Abstract
Oncogene activation disturbs cellular processes and accommodates a complex landscape of changes in the genome that contribute to genomic instability, which accelerates mutation rates and promotes tumorigenesis. Part of this cellular turmoil involves deregulation of physiologic DNA replication, widely described as replication stress. Oncogene-induced replication stress is an early driver of genomic instability and is attributed to a plethora of factors, most notably aberrant origin firing, replication-transcription collisions, reactive oxygen species, and defective nucleotide metabolism.Significance: Replication stress is a fundamental step and an early driver of tumorigenesis and has been associated with many activated oncogenes. Deciphering the mechanisms that contribute to the replication stress response may provide new avenues for targeted cancer treatment. In this review, we discuss the latest findings on the DNA replication stress response and examine the various mechanisms through which activated oncogenes induce replication stress. Cancer Discov; 8(5); 537-55. ©2018 AACR.
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Affiliation(s)
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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61
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Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops. Noncoding RNA 2018; 4:ncrna4020009. [PMID: 29657305 PMCID: PMC6027298 DOI: 10.3390/ncrna4020009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/26/2022] Open
Abstract
R-loops are evolutionarily conserved three-stranded structures that result from the formation of stable DNA:RNA hybrids in the genome. R-loops have attracted increasing interest in recent years as potent regulators of gene expression and genome stability. In particular, their strong association with severe replication stress makes them potential oncogenic structures. Despite their importance, the rules that govern their formation and their dynamics are still controversial and an in-depth description of their direct impact on chromatin organization and DNA transactions is still lacking. To better understand the diversity of R-loop functions, reliable, accurate, and quantitative mapping techniques, as well as functional assays are required. Here, I review the different approaches that are currently used to do so and to highlight their individual strengths and weaknesses. In particular, I review the advantages and disadvantages of using the S9.6 antibody to map R-loops in vivo in an attempt to propose guidelines for best practices.
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62
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Sloan KE, Bohnsack MT. Unravelling the Mechanisms of RNA Helicase Regulation. Trends Biochem Sci 2018; 43:237-250. [PMID: 29486979 DOI: 10.1016/j.tibs.2018.02.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/28/2018] [Accepted: 02/01/2018] [Indexed: 12/22/2022]
Abstract
RNA helicases are critical regulators at the nexus of multiple pathways of RNA metabolism, and in the complex cellular environment, tight spatial and temporal regulation of their activity is essential. Dedicated protein cofactors play key roles in recruiting helicases to specific substrates and modulating their catalytic activity. Alongside individual RNA helicase cofactors, networks of cofactors containing evolutionarily conserved domains such as the G-patch and MIF4G domains highlight the potential for cross-regulation of different aspects of gene expression. Structural analyses of RNA helicase-cofactor complexes now provide insight into the diverse mechanisms by which cofactors can elicit specific and coordinated regulation of RNA helicase action. Furthermore, post-translational modifications (PTMs) and long non-coding RNA (lncRNA) regulators have recently emerged as novel modes of RNA helicase regulation.
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Affiliation(s)
- Katherine E Sloan
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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63
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Lafuente-Barquero J, Luke-Glaser S, Graf M, Silva S, Gómez-González B, Lockhart A, Lisby M, Aguilera A, Luke B. The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage. PLoS Genet 2017; 13:e1007136. [PMID: 29281624 PMCID: PMC5760084 DOI: 10.1371/journal.pgen.1007136] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 01/09/2018] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery. In the absence of RNase H enzymes, RNA-DNA hybrids accumulate, resulting in replication stress, DNA damage and compromised genomic integrity. We demonstrate that Mph1, the yeast homolog of Fanconi anemia protein M (FANCM), is required for cell viability in the absence of RNase H enzymes. The integrity of the Mph1 helicase domain is crucial to prevent the accumulation of RNA-DNA hybrids and RNA-DNA hybrid-dependent DNA damage, as determined by Rad52 foci. Mph1 forms foci when RNA-DNA hybrids accumulate, e.g. in RNase H or THO-complex mutants and at short telomeres. Mph1, however is a double-edged sword, whose action at hybrids must be regulated by the Smc5/6 complex. This is underlined by the observation that simultaneous inactivation of RNase H2 and Smc5/6 results in Mph1-dependent synthetic lethality, which is likely due to an accumulation of toxic recombination intermediates. The data presented here support a model, where Mph1’s helicase activity plays a crucial role in responding to persistent RNA-DNA hybrids. DNA damage can either occur exogenously through DNA damaging agents such as UV light and exposure to chemotherapeutics, or endogenously via metabolic, cellular processes. The RNA product of transcription, for example, can engage in the formation of RNA-DNA hybrids. Such RNA-DNA hybrids can impede replication fork progression and cause genomic instability, a hallmark of cancer. The misregulation of RNA-DNA hybrids has also been implicated in several neurological disorders. Recently, it has become evident that RNA-DNA hybrids may also have beneficial roles and therefore, these structures have to be tightly controlled. We found that Mph1 (mutator phenotype 1), the budding yeast homolog of Fanconi Anemia protein M, counteracts the accumulation of RNA-DNA hybrids. The inactivation of MPH1 results in a severe growth defect when combined with mutations in the well-characterized RNase H enzymes, that degrade the RNA moiety of an RNA-DNA hybrid. Based on the data presented here, we propose a model, where Mph1 itself has to be kept in check by the SMC (structural maintenance of chromosome) 5/6 complex at replication forks stalled by RNA-DNA hybrids. Mph1 acts as a double-edged sword, as both its deletion and the inability to control its helicase activity cause DNA damage and growth arrest when RNA-DNA hybrids accumulate.
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Affiliation(s)
- Juan Lafuente-Barquero
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | - Sarah Luke-Glaser
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marco Graf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sonia Silva
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Belén Gómez-González
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | | | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Andrés Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- * E-mail: (BL); (AA)
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Institute of Neurobiology and Developmental Biology, JGU Mainz, Mainz, Germany
- * E-mail: (BL); (AA)
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64
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Boulianne B, Feldhahn N. Transcribing malignancy: transcription-associated genomic instability in cancer. Oncogene 2017; 37:971-981. [DOI: 10.1038/onc.2017.402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
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Auboeuf D. Alternative mRNA processing sites decrease genetic variability while increasing functional diversity. Transcription 2017; 9:75-87. [PMID: 29099315 PMCID: PMC5834221 DOI: 10.1080/21541264.2017.1373891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions. However, this concept raises two main questions. First, do alternative mRNA processing pathways have a role other than generating mRNA and protein diversity? Second, is the cellular function of mRNA variants restricted to the biogenesis of functional protein isoforms? Here, I propose that the co-transcriptional use of alternative mRNA processing sites allows first, the resolution of co-transcriptional biophysical constraints that may otherwise result in DNA instability, and second, increases the diversity of cellular functions of mRNAs in a manner that is not restricted to protein synthesis.
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Affiliation(s)
- Didier Auboeuf
- a Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell , 46 Allée d'Italie Site Jacques Monod, Lyon , France
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66
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Salas-Armenteros I, Pérez-Calero C, Bayona-Feliu A, Tumini E, Luna R, Aguilera A. Human THO-Sin3A interaction reveals new mechanisms to prevent R-loops that cause genome instability. EMBO J 2017; 36:3532-3547. [PMID: 29074626 DOI: 10.15252/embj.201797208] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 09/22/2017] [Accepted: 09/28/2017] [Indexed: 11/09/2022] Open
Abstract
R-loops, formed by co-transcriptional DNA-RNA hybrids and a displaced DNA single strand (ssDNA), fulfill certain positive regulatory roles but are also a source of genomic instability. One key cellular mechanism to prevent R-loop accumulation centers on the conserved THO/TREX complex, an RNA-binding factor involved in transcription elongation and RNA export that contributes to messenger ribonucleoprotein (mRNP) assembly, but whose precise function is still unclear. To understand how THO restrains harmful R-loops, we searched for new THO-interacting factors. We found that human THO interacts with the Sin3A histone deacetylase complex to suppress co-transcriptional R-loops, DNA damage, and replication impairment. Functional analyses show that histone hypo-acetylation prevents accumulation of harmful R-loops and RNA-mediated genomic instability. Diminished histone deacetylase activity in THO- and Sin3A-depleted cell lines correlates with increased R-loop formation, genomic instability, and replication fork stalling. Our study thus uncovers physical and functional crosstalk between RNA-binding factors and chromatin modifiers with a major role in preventing R-loop formation and RNA-mediated genome instability.
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Affiliation(s)
- Irene Salas-Armenteros
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Emanuela Tumini
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
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67
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Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability. Proc Natl Acad Sci U S A 2017; 114:10942-10947. [PMID: 28973905 DOI: 10.1073/pnas.1707845114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During transcription, the mRNA may hybridize with DNA, forming an R loop, which can be physiological or pathological, constituting in this case a source of genomic instability. To understand the mechanism by which eukaryotic cells prevent harmful R loops, we used human activation-induced cytidine deaminase (AID) to identify genes preventing R loops. A screening of 400 Saccharomyces cerevisiae selected strains deleted in nuclear genes revealed that cells lacking the Mlp1/2 nuclear basket proteins show AID-dependent genomic instability and replication defects that were suppressed by RNase H1 overexpression. Importantly, DNA-RNA hybrids accumulated at transcribed genes in mlp1/2 mutants, indicating that Mlp1/2 prevents R loops. Consistent with the Mlp1/2 role in gene gating to nuclear pores, artificial tethering to the nuclear periphery of a transcribed locus suppressed R loops in mlp1∆ cells. The same occurred in THO-deficient hpr1∆ cells. We conclude that proximity of transcribed chromatin to the nuclear pore helps restrain pathological R loops.
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68
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García-Pichardo D, Cañas JC, García-Rubio ML, Gómez-González B, Rondón AG, Aguilera A. Histone Mutants Separate R Loop Formation from Genome Instability Induction. Mol Cell 2017; 66:597-609.e5. [PMID: 28575656 DOI: 10.1016/j.molcel.2017.05.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 04/03/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
R loops have positive physiological roles, but they can also be deleterious by causing genome instability, and the mechanisms for this are unknown. Here we identified yeast histone H3 and H4 mutations that facilitate R loops but do not cause instability. R loops containing single-stranded DNA (ssDNA), versus RNA-DNA hybrids alone, were demonstrated using ssDNA-specific human AID and bisulfite. Notably, they are similar size regardless of whether or not they induce genome instability. Contrary to mutants causing R loop-mediated instability, these histone mutants do not accumulate H3 serine-10 phosphate (H3S10-P). We propose a two-step mechanism in which, first, an altered chromatin facilitates R loops, and second, chromatin is modified, including H3S10-P, as a requisite for compromising genome integrity. Consistently, these histone mutations suppress the high H3S10 phosphorylation and genomic instability of hpr1 and sen1 mutants. Therefore, contrary to what was previously believed, R loops do not cause genome instability by themselves.
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Affiliation(s)
- Desiré García-Pichardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - Juan C Cañas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville 41092, Spain.
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69
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Song C, Hotz-Wagenblatt A, Voit R, Grummt I. SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability. Genes Dev 2017; 31:1370-1381. [PMID: 28790157 PMCID: PMC5580657 DOI: 10.1101/gad.300624.117] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/13/2017] [Indexed: 01/09/2023]
Abstract
Here, Song et al. show that the DEAD-box RNA helicase DDX21 efficiently unwinds RNA/DNA hybrids (R loops) in vivo and in vitro and prevents DNA damage. Their findings reveal a novel mechanism by which accumulation of R loops by DDX21 depletion leads to genomic instability. R loops are three-stranded nucleic acid structures consisting of an RNA:DNA heteroduplex and a “looped-out” nontemplate strand. As aberrant formation and persistence of R loops block transcription elongation and cause DNA damage, mechanisms that resolve R loops are essential for genome stability. Here we show that the DEAD (Asp–Glu–Ala–Asp)-box RNA helicase DDX21 efficiently unwinds R loops and that depletion of DDX21 leads to accumulation of cellular R loops and DNA damage. Significantly, the activity of DDX21 is regulated by acetylation. Acetylation by CBP inhibits DDX21 activity, while deacetylation by SIRT7 augments helicase activity and overcomes R-loop-mediated stalling of RNA polymerases. Knockdown of SIRT7 leads to the same phenotype as depletion of DDX21 (i.e., increased formation of R loops and DNA double-strand breaks), indicating that SIRT7 and DDX21 cooperate to prevent R-loop accumulation, thus safeguarding genome integrity. Moreover, DDX21 resolves estrogen-induced R loops on estrogen-responsive genes in breast cancer cells, which prevents the blocking of transcription elongation on these genes.
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Affiliation(s)
- Chenlin Song
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, D-69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Group, Core Facility Genomics and Proteomics, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, D-69120 Heidelberg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, D-69120 Heidelberg, Germany
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70
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Hodroj D, Serhal K, Maiorano D. Ddx19 links mRNA nuclear export with progression of transcription and replication and suppresses genomic instability upon DNA damage in proliferating cells. Nucleus 2017; 8:489-495. [PMID: 28696814 DOI: 10.1080/19491034.2017.1348448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The DEAD-box Helicase 19 (Ddx19) gene codes for an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. In unperturbed cells, Ddx19 localizes in the cytoplasm and at the cytoplasmic face of the nuclear pore. Here we review recent findings related to an additional Ddx19 function in the nucleus in resolving RNA:DNA hybrids (R-loops) generated during collision between transcription and replication, and upon DNA damage. Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of the Ddx19 protein from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops, and down regulation of Ddx19 expression induces DNA double strand breaks only in proliferating cells. Overall these observations put forward Ddx19 as an important novel mediator of the crosstalk between transcription and replication.
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Affiliation(s)
- Dana Hodroj
- a Institute of Human Genetics, UMR9002 CNRS-UM, 141, Montpellier , France
| | - Kamar Serhal
- a Institute of Human Genetics, UMR9002 CNRS-UM, 141, Montpellier , France
| | - Domenico Maiorano
- a Institute of Human Genetics, UMR9002 CNRS-UM, 141, Montpellier , France
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71
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Aguilera A, Gómez-González B. DNA-RNA hybrids: the risks of DNA breakage during transcription. Nat Struct Mol Biol 2017; 24:439-443. [PMID: 28471430 DOI: 10.1038/nsmb.3395] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/05/2017] [Indexed: 12/28/2022]
Abstract
Although R loops can occur at different genomic locations, the factors that determine their formation and frequency remain unclear. Emerging evidence indicates that DNA breaks stimulate DNA-RNA hybrid formation. Here, we discuss the possibility that formation of hybrids may be an inevitable risk of DNA breaks that occur within actively transcribed regions. While such hybrids must be removed to permit repair, their potential role as repair intermediates remains to be established.
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Affiliation(s)
- Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
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72
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Bhatia V, Herrera-Moyano E, Aguilera A, Gómez-González B. The Role of Replication-Associated Repair Factors on R-Loops. Genes (Basel) 2017; 8:E171. [PMID: 28653981 PMCID: PMC5541304 DOI: 10.3390/genes8070171] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
The nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded DNA (ssDNA) is accompanied by a DNA-RNA hybrid. Unresolved R-loops can impede transcription and replication processes and lead to genomic instability by a mechanism still not fully understood. In this sense, a connection between R-loops and certain chromatin markers has been reported that might play a key role in R-loop homeostasis and genome instability. To counteract the potential harmful effect of R-loops, different conserved messenger ribonucleoprotein (mRNP) biogenesis and nuclear export factors prevent R-loop formation, while ubiquitously-expressed specific ribonucleases and DNA-RNA helicases resolve DNA-RNA hybrids. However, the molecular events associated with R-loop sensing and processing are not yet known. Given that R-loops hinder replication progression, it is plausible that some DNA replication-associated factors contribute to dissolve R-loops or prevent R-loop mediated genome instability. In support of this, R-loops accumulate in cells depleted of the BRCA1, BRCA2 or the Fanconi anemia (FA) DNA repair factors, indicating that they play an active role in R-loop dissolution. In light of these results, we review our current view of the role of replication-associated DNA repair pathways in preventing the harmful consequences of R-loops.
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Affiliation(s)
- Vaibhav Bhatia
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Emilia Herrera-Moyano
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Andrés Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| | - Belén Gómez-González
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
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73
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Czubaty A, Piekiełko-Witkowska A. Protein kinases that phosphorylate splicing factors: Roles in cancer development, progression and possible therapeutic options. Int J Biochem Cell Biol 2017; 91:102-115. [PMID: 28552434 DOI: 10.1016/j.biocel.2017.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/30/2022]
Abstract
Disturbed alternative splicing is a common feature of human tumors. Splicing factors that control alternative splicing are phosphorylated by multiple kinases, including these that specifically add phosphoryl groups to serine-arginine rich proteins (e.g. SR-protein kinases, cdc2-like kinases, topoisomerase 1), and protein kinases that govern key cellular signaling pathways (i.e. AKT). Phosphorylation of splicing factors regulates their subcellular localization and interactions with target transcripts and protein partners, and thus significantly contributes the final result of splicing reactions. In this review we aim to summarize the current knowledge on the role of splicing kinases in cancer. Published studies and recently released data of The Cancer Genome Atlas demonstrate that expressions and activities of splicing kinases are commonly disturbed in cancers. Aberrant functioning of splicing kinases results in changed alternative splicing of tumor suppressors (e.g. p53) and regulators of cell signaling (e.g. MAPKs), apoptosis (e.g. MCL), and angiogenesis (VEGF). Splicing kinases act in complicated regulatory networks in which they mutually affect each other's activity to provide tight control of cellular signaling. Dysregulation of these regulatory networks contributes to oncogenic transformation, uncontrolled proliferation, enhanced migration and invasion. Furthermore, the activities of splicing kinases significantly contribute to cellular responses to genotoxic stress. In conclusion, published data provide strong evidence that splicing kinases emerge as important regulators of key processes governing malignant transformation, progression, and response to therapeutic treatments, suggesting their potential as clinically relevant targets.
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Affiliation(s)
- Alicja Czubaty
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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