PARP1 associates with R-loops to promote their resolution and genome stability

Nucleic Acids Research, Год журнала: 2023, Номер 51(5), С. 2215 - 2237

Опубликована: Фев. 16, 2023

Abstract PARP1 is a DNA-dependent ADP-Ribose transferase with ADP-ribosylation activity that triggered by DNA breaks and non-B structures to mediate their resolution. was also recently identified as component of the R-loop-associated protein-protein interaction network, suggesting potential role for in resolving this structure. R-loops are three-stranded nucleic acid consist RNA–DNA hybrid displaced non-template strand. involved crucial physiological processes but can be source genome instability if persistently unresolved. In study, we demonstrate binds vitro associates R-loop formation sites cells which activates its activity. Conversely, inhibition or genetic depletion causes an accumulation unresolved promotes genomic instability. Our study reveals novel sensor highlights suppressor

Язык: Английский

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Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor

Nucleic Acids Research, Год журнала: 2023, Номер 51(6), С. 2818 - 2837

Опубликована: Март 2, 2023

Abstract Prolonged pausing of the transcription machinery may lead to formation three-stranded nucleic acid structures, called R-loops, typically resulting from annealing nascent RNA with template DNA. Unscheduled persistence R-loops and polymerases interfere itself other essential processes such as DNA replication repair. Senataxin (SETX) is a putative helicase, mutated in two neurodegenerative disorders, which has been implicated control R-loop accumulation termination. However, understanding precise role SETX these precluded by absence direct characterisation biochemical activities. Here, we purify characterise helicase domain parallel its yeast orthologue, Sen1. Importantly, show that bona fide ability resolve R-loops. Furthermore, retained termination activity Sen1 but functions species-specific manner. Finally, subsequent variants harbouring disease-associated mutations shed light into effect on folding properties. Altogether, results broaden our function gene expression maintenance genome integrity provide clues elucidate molecular basis SETX-associated diseases.

Язык: Английский

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Helicases in R-loop Formation and Resolution

Journal of Biological Chemistry, Год журнала: 2023, Номер 299(11), С. 105307 - 105307

Опубликована: Сен. 29, 2023

With the development and wide usage of CRISPR technology, presence R-loop structures, which consist an RNA–DNA hybrid a displaced single-strand (ss) DNA, has become well accepted. structures have been implicated in variety circumstances play critical roles metabolism nucleic acid relevant biological processes, including transcription, DNA repair, telomere maintenance. Helicases are enzymes that use ATP-driven motor force to unwind double-strand (ds) dsRNA, or hybrids. Additionally, certain helicases strand-annealing activity. Thus, possess unique positions for biogenesis: they utilize their activity promote hybridization RNA leading formation R-loops; conversely, unwinding separate hybrids resolve R-loops. Indeed, numerous such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, several DEAD/H-box proteins reported while other helicases, Cas3 UPF1, stimulate formation. Moreover, like DDX1, DDX17, DHX9 identified both resolution. In this review, we will summarize latest understandings regarding metabolism. highlight challenges associated with drug discovery context targeting these helicases. R-loops three-stranded consisting single-stranded DNA. They various transcriptional regulation replication, genomic instability, class switch recombination B cells, damage maintenance (1Brickner J.R. Garzon J.L. Cimprich K.A. Walking tightrope: complex balancing act genome stability.Mol. Cell. 2022; 82: 2267-2297Google Scholar, 2Petermann E. Lan L. Zou Sources, resolution physiological relevance RNA-DNA hybrids.Nat. Rev. Mol. Cell Biol. 23: 521-540Google 3Hegazy Y.A. Fernando C.M. Tran E.J. The biology: good, bad, ugly.J. Chem. 2020; 295: 905-913Google 4Niehrs C. Luke B. Regulatory facilitators gene expression stability.Nat. 21: 167-178Google 5Garcia-Muse T. Aguilera A. R loops: from pathological roles.Cell. 2019; 179: 604-618Google Scholar). group molecular motors energy nucleoside triphosphate hydrolysis remodel molecules, protein–nucleic interactions (6Brosh Jr., R.M. Bohr V.A. Human premature aging, repair RecQ helicases.Nucleic Acids Res. 2007; 35: 7527-7544Google 7Dillingham M.S. Superfamily I modular components DNA-processing machines.Biochem. Soc. Trans. 2011; 39: 413-423Google 8Bernstein Gangloff S. Rothstein R. repair.Annu. Genet. 2010; 44: 393-417Google 9Jankowsky at work: binding rearranging.Trends Biochem. Sci. 36: 19-29Google Notably, some also strand annealing (10Wu Y. Unwinding rewinding: double faces helicase?.J. Nucleic Acids. 2012; 2012140601Google This property allows them crucial biogenesis. can double-stranded facilitate invasion, hybridize ssDNA, enabling Conversely, assembly disassembly. For example, SETX (Senataxin), AQR (Aquarius), WRN (Werner syndrome), BLM (Bloom RTEL1 (Regulator elongation helicase 1), PIF1 (Petite integration factor FANCM (Fanconi anemia complementation M), CasDinG (CRISPR-associated DinG protein), contrast, UPF1 (Up-frameshift protein 1) involved Several excellent reviews available functions Specific metabolism, nuclease RNase H (11Cerritelli S.M. Sakhuja K. Crouch R.J. H1, gold standard detection.Methods 2528: 91-114Google 12Silva Guillen-Mendoza H1 hybrid-binding domain-based tools cellular biology studies DNA-RNA mammalian cells.Methods 115-125Google 13Wulfridge P. Yan Q. Sarma Targeted approaches mapping native R-loops.Methods 373-380Google Scholar) topoisomerase (14Patel P.S. Krishnan Hakem Emerging topoisomerases R-loops.Mutat. Toxicol. Environ. Mutagen. 876-877503450Google 15Saha Pommier R-loops, type cancer.NAR Cancer. 2023; 5: zcad013Google Scholar), discussed extensively. However, comprehensive understanding biogenesis is missing. knowledge addition, review address related efforts While were first observed vitro 1976 (16Thomas M. White R.L. Davis R.W. Hybridization DNA: R-loops.Proc. Natl. Acad. U. 1976; 73: 2294-2298Google existence vivo was not until 1995 bacteria (17Drolet Phoenix Menzel Masse Liu L.F. Overexpression partially complements growth defect Escherichia coli delta topA mutant: major problem absence I.Proc. 1995; 92: 3526-3530Google initially considered by-product transcription where nascent transcribed by polymerase remains base paired its template leaving non-template ssDNA. Now, it known occur genome-wide present all organisms, humans (18Jiang Huang F. Chen Gu J.H. Wu Y.W. Jia M.Y. et al.Genome-wide map reveals interplay integrity during germ cell meiosis.J Adv 51: 45-57Google 19Jauregui-Lozano J. Cottingham Hall H. Tissue-specific, Drosophila using MapR.Bio Protoc. 12e4516Google 20Ginno P.A. Lott P.L. Christensen H.C. Korf I. Chedin distinctive characteristic unmethylated human CpG island promoters.Mol. 45: 814-825Google 21Scheuren Mohner Zischler landscape mature sperm: regulatory evolutionary implications.Front. 141069871Google techniques demonstrate exist naturally cells. system, ssRNA (guide RNA) targeted displaces forms structure; endonuclease Cas then cleaves (5Garcia-Muse 22Crossley M.P. Bocek regulators threats.Mol. 398-411Google form breaks (DSBs) telomeres (Fig. 1). Generally, categorized either programmed, whereas nonprogrammed. Pathological threaten stability ways, generating transcription-replication collisions, (SSBs), DSBs (23Li X. Manley Inactivation SR splicing ASF/SF2 results instability.Cell. 2005; 122: 365-378Google 24Paulsen R.D. Soni D.V. Wollman Hahn A.T. Yee M.C. Guan al.A siRNA screen diverse processes pathways mediate 2009; 228-239Google On hand, comprise immunoglobulin switching cells vertebrates (25Yu Hsieh C.L. Wilson T.E. Lieber M.R. regions chromosomes stimulated cells.Nat. Immunol. 2003; 4: 442-451Google editing CRISPR-Cas9 (26Jiang Taylor D.W. J.S. Kornfeld J.E. Zhou Thompson A.J. al.Structures primed cleavage.Science. 2016; 351: 867-871Google mitochondrial replication (27Holt I.J. metabolism.Methods 173-202Google specific steps (28Huertas Cotranscriptionally formed DNA:RNA impairment transcription-associated recombination.Mol. 12: 711-721Google DSB (29Ouyang Yadav Zhang J.M. Yang Rheinbay Guo al.RNA transcripts homologous forming DR-loops.Nature. 2021; 594: 283-288Google CGG repeat contraction (30Lee H.G. Imaichi Kraeutler Aguilar Lee Sheridan S.D. al.Site-specific induce fragile X reactivation.Cell. 186: 2593-2609.e18Google maintaining homeostasis (31Ngo G.H.P. Grimstead J.W. Baird D.M. promotes loops break repair.Nat. Commun. 3849Google Furthermore, III catalyze DSBs, transient protect 3ʹ overhang degradation before A (RPA) binding, demonstrating essential intermediate process (HR)-mediated (32Liu Hua Wang Li Yuan required recombination.Cell. 184: 1314-1329.e1310Google These findings indicate cause negative positive outcomes depending on environment R-loop. must be tightly regulated balance properly. neurodegenerative disorders cancers dysregulated more than half patients neuroinflammatory Aicardi-Goutières syndrome (AGS) biallelic mutations H2 (33Crow Y.J. Chase D.S. Lowenstein Schmidt Szynkiewicz Forte G.M. Gornall H.L. al.Characterization disease phenotypes TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, IFIH1.Am. Med. 2015; 167A: 296-312Google 34Lim Sanz L.A. Xu Hartono S.R. Genome-wide hypomethylation RNA:DNA accumulation Aicardi-Goutieres syndrome.Elife. 4e08007Google ataxia oculomotor apraxia 2 (AOA2) (35Moreira Klur Watanabe Nemeth A.H. Le Ber Moniz J.C. al.Senataxin, ortholog yeast helicase, mutant ataxia-ocular 2.Nat. 2004; 225-227Google juvenile amyotrophic lateral sclerosis (ALS4) (36Chen Y.Z. Bennett Huynh H.M. Blair I.P. Puls Irobi al.DNA/RNA (ALS4).Am. Hum. 74: 1128-1135Google AOA2 autosomal recessive loss function, ALS4 dominant provoked toxic gain-of-function (37Mersaoui S.Y. Yu Z. Coulombe Karam Busatto F.F. Masson J.Y. al.Arginine methylation DDX5 RGG/RG motif PRMT5 regulates hybrids.EMBO 38e100986Google syndrome, expansion trinucleotide repeats FMR1 leads R–loop contributes chromosomal instability (38Chakraborty Jenjaroenpun McCulley Hilali S.E. Haarer al.Fragile mental retardation prevents global chromosome fragility.bioRxiv. ([preprint])https://doi.org/10.1101/601906Google TDP-43 aberrant formation, damaging contributing ALS (39Wood Quinet Lin Y.L. A.A. Pasero Ayala Y.M. al.TDP-43 dysfunction defects.J. 133jcs244129Google 40Giannini Bayona-Feliu Sproviero D. Barroso S.I. Cereda link loop-mediated damage.PLoS 16e1009260Google tumorigenesis, DDX41 myeloid neoplasms myelodysplastic syndromes (MDS) acute leukemia (AML) (41Truong Pimanda DDX41: poster child familial MDS/AML grows up.Blood. 141: 447-449Google excessive found mutated (42Weinreb J.T. Ghazale N. Pradhan Gupta V. Potts K.S. Tricomi al.Excessive trigger inflammatory cascade increased HSPC production.Dev. 56: 627-640.e625Google 43Shinriki Hirayama Nagamachi Yokoyama Kawamura Kanai al.DDX41 coordinates prevent stress hematopoietic cells.Leukemia. 2605-2620Google Similarly, EWS-FIL1 fusion Ewing sarcoma induces perturbs HR potentially mediating chemosensitivity (44Gorthi Romero Loranc Cao Lawrence Goodale al.EWS-FLI1 increases block BRCA1 sarcoma.Nature. 2018; 555: 387-391Google groups employed affinity pull-down BioID (proximity-dependent biotin identification) identify (45Cristini Groh Kristiansen Gromak RNA/DNA interactome identifies DXH9 player termination R-loop-associated damage.Cell Rep. 1891-1905Google 46Wu Nance Chu Fazzio T.G. Characterization R-loop-interacting embryonic stem rRNA processing expression.Mol. Proteomics. 20100142Google 47Wang I.X. Grunseich Fox Burdick Zhu Ravazian al.Human interact hybrids.Genome 28: 1405-1414Google 48Mosler Conte Longo G.M.C. Mikicic Kreim Mockel M.M. al.R-loop proximity proteomics role instability.Nat. 7314Google 49Yan Wulfridge Doherty Fernandez-Luna Real P.J. Tang H.Y. al.Proximity labeling repertoire site-specific modulators.Nat. 13: 53Google 50Shinriki 2605Google (Table S1). Kumar al. (51Kumar Fournier Stirling P.C. Integrative analysis prediction proteins.G3 (Bethesda). 12jkac142Google analyzed five datasets only 12 common proteins: DDX5, NAT10, NPM1, NOP2, DDX18, NOP58, ALYREF, U2AF1, ILF3, RBM14, PDCD11, MYBBP1A. More recently, Marchena-Cruz used screening coupled AID-induced readout 46 affect (52Marchena-Cruz Camino L.P. Bhandari Silva Marqueta-Gracia J.J. Amdeen S.A. al.DDX47, MeCP2, functionally heterogeneous factors harmful loops.Cell 42112148Google seven revealed varying results, no single datasets. Using similar approaches, S9.6 antibody Cristini (46Wu Myc-tagged (50Shinriki bait Mosler (48Mosler (49Yan largely different Collectively, suggest highly variable study conditions thus additional investigations fully elucidate identity proteins. diversity attributed factors. Firstly, methods may lead instance, capture stable complexes but weak interactions. partners, sensitivity detect potential indirect Secondly, flaws yield false positive—non-specific non-specific dsRNA (53Smolka J.A. Recognition creates pervasive artifacts when imaging hybrids.J. 220e202004079Google 54Crossley Brickner Song Zar S.M.T. Maw S.S. al.Catalytically inactive, purified H1: sensitive probe imaging.J. 220e202101092Google consists two (H1 H2) specificities cycle subcellular location (55Holmes J.B. Akman G. Wood Cerritelli Moss al.Primer retention owing catastrophic replication.Proc. 112: 9334-9339Google 56Lockhart Pires V.B. Bento Kellner Luke-Glaser Yakoub al.RNase differentially hybrids.Cell 29: 2890-2900.e2895Google AID-based ssDNA Thirdly, types HeLa, HEK293, U2OS, mouse contribute results. Finally, there dynamic change undergo changes, resulting amongst Nevertheless, despite observations proteins, consistently S1, highlighted yellow). nucleases specifically target degrade molecule within (57Hyjek Figiel Nowotny RNases H: structure mechanism.DNA Repair (Amst). 84102672Google primarily localized mitochondria displays G2/M-phase (56Lockhart We believe large number released would robust eliminating Consistent initial observation threat stability, many accumulation, SETX, AQR, SMARCAL, ATRX, 1).Table 1Helicases metabolismHelicase familyNameRole R-loopDisease main phenotype/biological functionNoteReferencesForm R-loopResolve R-loopHumanYeastSF1SETXSen1√AOA2 ALS4(58Mischo H.E. Gomez-Gonzalez Grzechnik Rondon A.G. Wei W. Steinmetz al.Yeast Sen1 protects instability.Mol. 41: 21-32Google 149Alzu Bermejo Begnis Lucca Piccini Carotenuto al.Senataxin associates forks fork across RNA-polymerase-II-transcribed genes.Cell. 151: 835-846Google Scholar)AQR√Splicing factorAka IBP160(150Sollier Stork C.T. Garcia-Rubio M.L. Paulsen Transcription-coupled nucleotide excision R-loop-induced 2014; 777-785Google Scholar)UPF1Upf1√Nonsense mRNA surveillance(31Ngo Scholar)PIF1Rrm3, ScPif1, SpPfh1√Genomic nucleus mitochondriaS. cerevisiae members: Rrm3 ScPif1; pombe one: Pfh1(151Tran P.L.T. Pohl T.J. C.F. Chan Pott Zakian family suppress mediated tRNA genes.Nat. 2017; 815025Google Scholar)SF2WRN√Werner syndrome(63Marabitti Lillo Malacaria Palermo Sanchez Pichierri al.ATM pathway activation limits Werner cells.Nucleic 47: 3485-3502Google Scholar)BLMSgs1√Bloom syndrome(65Chang E.Y. Novoa C.A. Aristizabal M.J. Segovia Chaturvedi al.RECQ-like Sgs1 regulate instability.J. 216: 3991-4005Google Scholar)RTEL1√Telomere shorteningInteracts Poldip3(68Bjorkman Johansen S.L. Schertzer Kanellis D.C. Katsori A.M. Poldip3 responses resolution.Genes Dev. 34: 1065-1074Google Scholar)FANCMMph1√Congenital abnormalities, pancytopenia, infertility, cancer proneness(70Schwab R.A. Nieminuszczy Shah Langton Lopez Martinez Liang C.C. al.The fanconi maintains coordinating transcription.Mol. 60: 351-361Google 71Hodson van Twest Dylewska O'Rourke Tan Murphy V.J. al.Branchpoint translocation remodelers general mechanism removal.Cell 41111749Google 152Lafuente-Barquero Graf Lockhart Smc5/6 Mph1 hybrid-mediated 13e1007136Google Scholar)Polymerase θ (POLQ)√Xeroderma PigmentosumHelicase domain (1–894 aa) unwinds vitro(73Ozdemir A.Y. Rusanov Kent Siddique Pomerantz R.T. Polymerase theta-helicase efficiently 293: 5259-5269Google Scholar)CasDinG (Bacteria)√(74Domgaard Cahoon Armbrust Redman O. Jolley Thomas al.CasDinG 5'-3' dsDNA three accessory domains IV immunity.Nucleic 8115-8132Google 75Cui X.Y. al.Type IV-A CRISPR-Csf complex: assembly, targeting, recruitment.Mol. 83: 2493-2508.e2495Google Scholar)SNF2ATRXRad54√ATRX syndromeA recent report shows unable Scholar)(72Nguyen D.T. Voon H.P.J. Xella Scott Clynes Babbs chromatin remodelling suppresses telomeric repeats.EMBO 18: 914-928Google Scholar)SMARCAL1√Schimke Immunoosseous DysplasiaAka HARP, helicase(71Hodson 153Yusufzai Kadonaga HARP helicase.Science. 2008; 322: 748-750Google Scholar)ZRANB3√African-specific diabetesAka (AH2)(71Hodson Scholar)DEAD-boxDDX1√√Retinoblastoma neuroblastoma(100Li Germain D.R. Po

Язык: Английский

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R-loop and diseases: the cell cycle matters

Molecular Cancer, Год журнала: 2024, Номер 23(1)

Опубликована: Апрель 27, 2024

Abstract The cell cycle is a crucial biological process that involved in growth, development, and reproduction. It can be divided into G1, S, G2, M phases, each period closely regulated to ensure the production of two similar daughter cells with same genetic material. However, many obstacles influence cycle, including R-loop formed throughout this process. triple-stranded structure, composed an RNA: DNA hybrid single strand, which ubiquitous organisms from bacteria mammals. existence has important significance for regulation various physiological processes. aberrant accumulation due its limited resolving ability will detrimental cells. For example, damage genomic instability, caused by R-loop, activate checkpoints turn induce arrest death. At present, growing number factors have been proven prevent or eliminate thereby avoiding mutations. Therefore, we need gain detailed insight resolution at different stages cycle. In review, review current knowledge play role as well how mutations these lead onset progression diseases.

Язык: Английский

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PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 8, 2024

Abstract R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 is chromatin protein associated with transcriptional elongation complex, possesses histone chaperone activity, and implicated in recruiting RNA processing DNA repair factors sites. Here, we show interacts other proteins involved R-loop homeostasis, including PARP1. Genome-wide mapping of PSIP1, γ-H2AX PSIP1-depleted human mouse cell lines revealed an accumulation damage gene promoters the absence PSIP1. causes local arrest transcription-replication conflict, leading damage. depletion increases 53BP1 foci reduces RAD51 foci, suggesting altered choice. Furthermore, sensitivity cancer cells PARP1 inhibitors DNA-damaging agents induce R-loop-induced These findings provide insights into mechanism through which maintains integrity site transcription.

Язык: Английский

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Non-B DNA structures as a booster of genome instability

Biochimie, Год журнала: 2023, Номер 214, С. 176 - 192

Опубликована: Июль 8, 2023

Non-canonical secondary structures (NCSs) are alternative nucleic acid that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on sequence. The majority of these form context physiological processes, such as transcription-associated R-loops, G4s, well hairpins slipped-strand DNA, whose formation be dependent replication. It is therefore not surprising play important roles regulation key biological processes. In last years, increasing published data have supported their role thanks to genome-wide studies development bioinformatic prediction tools. Data also highlighted pathological structures. Indeed, alteration or stabilization cause impairment transcription replication, modification chromatin structure damage. These events lead a wide range recombination events, deletions, mutations chromosomal aberrations, well-known hallmarks genome instability which strongly associated with human diseases. this review, we summarize molecular processes through trigger instability, focus G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform multi-stranded known triplexes.

Язык: Английский

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Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures

Journal of Molecular Biology, Год журнала: 2023, Номер 436(1), С. 168207 - 168207

Опубликована: Июль 20, 2023

Alternative DNA structures that differ from the canonical B-form of can arise repetitive sequences and play beneficial roles in many cellular processes such as gene regulation chromatin organization. However, they also threaten genomic stability several ways including mutagenesis collisions with replication and/or transcription machinery, which lead to instability is associated human disease. Thus, careful non-B-DNA structure formation resolution crucial for maintenance genome integrity. Several protein factors have been demonstrated associate alternative facilitate their removal, one ADP-ribose transferase (ART) PARP1 (also called ADP-ribosyltransferase diphtheria toxin-like 1 or ARTD1), a multifaceted repair enzyme recognizes single- double-stranded breaks synthesizes chains poly (ADP-ribose) (PAR) recruit proteins. It now well appreciated nucleic acid beyond lesions, stalled forks, hairpins cruciforms, R-loops, G-quadruplexes (G4 DNA). In this review, we summarize current evidence direct association each these aforementioned structures, discuss role prevention structure-induced genetic instability. We will focus on mechanisms recognition binding by structure-based stimulation catalytic activity upon binding. Finally, some outstanding gaps literature offer speculative insight questions remain be experimentally addressed.

Язык: Английский

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Looping out of control: R-loops in transcription-replication conflict

Chromosoma, Год журнала: 2023, Номер 133(1), С. 37 - 56

Опубликована: Июль 7, 2023

Язык: Английский

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RNA biogenesis and RNA metabolism factors as R-loop suppressors: a hidden role in genome integrity

Genes & Development, Год журнала: 2024, Номер unknown

Опубликована: Июль 10, 2024

Genome integrity relies on the accuracy of DNA metabolism, but as appreciated for more than four decades, transcription enhances mutation and recombination frequencies. More recent research provided evidence a previously unforeseen link between RNA which is often related to accumulation DNA–RNA hybrids R-loops. In addition physiological roles, R-loops interfere with replication repair, providing molecular scenario origin genome instability. Here, we review current knowledge multiple factors that prevent or resolve consequent transcription–replication conflicts thus act modulators dynamics.

Язык: Английский

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Advancements and Challenges of R-loops in Cancers: Biological Insights and Future Directions

Cancer Letters, Год журнала: 2024, Номер 610, С. 217359 - 217359

Опубликована: Ноя. 27, 2024

Язык: Английский

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