Walking a tightrope: The complex balancing act of R-loops in genome stability

Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2

(2022) Radhakrishnan Kanagaraj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proximity labeling identifies a repertoire of site-specific R-loop modulators

(2022) Qingqing Yan et al.   Nature Communications

DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes

(2022) Anna Maria Sole Giordano et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Best practices for the visualization, mapping, and manipulation of R‐loops

(2021) Frédéric Chédin et al.   EMBO JOURNAL

DDX41 regulates the expression and alternative splicing of genes involved in tumorigenesis and immune response

(2021) Kai Qin et al.   ONCOLOGY REPORTS

MRE11-RAD50-NBS1 Complex Is Sufficient to Promote Transcription by RNA Polymerase II at Double-Strand Breaks by Melting DNA Ends

(2021) Sheetal Sharma et al.   Cell Reports

Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability

(2021) Carlo Rinaldi et al.   Frontiers in Cell and Developmental Biology

RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination

(2021) Sijie Liu et al.   CELL

Excessive R-loops trigger an inflammatory cascade leading to increased HSPC production

(2021) Joshua T. Weinreb et al.   DEVELOPMENTAL CELL

BRCA2 promotes R‐loop resolution by DDX5 helicase at DNA breaks to facilitate their repair by homologous recombination

(2021) Gaetana Sessa et al.   EMBO JOURNAL

Emerging roles of centromeric RNAs in centromere formation and function

(2021) Qian Liu et al.   Genes & Genomics

RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors

(2021) Parasvi S. Patel et al.   JOURNAL OF CLINICAL INVESTIGATION

Nuclear sensing of breaks in mitochondrial DNA enhances immune surveillance

(2021) Marco Tigano et al.   NATURE

BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2–RAD52

(2021) Elodie Hatchi et al.   NATURE

NF-κB–induced R-loop accumulation and DNA damage select for nucleotide excision repair deficiencies in adult T cell leukemia

(2021) Yunlong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ADAR1 RNA editing enzyme regulates R-loop formation and genome stability at telomeres in cancer cells

(2021) Yusuke Shiromoto et al.   Nature Communications

Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

(2021) Kevin S. Lang et al.   Cell Reports

PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer

(2021) Roman M. Chabanon et al.   CANCER RESEARCH

PARP1-mediated PARylation of TonEBP prevents R-loop–associated DNA damage

(2021) Byeong Jin Ye et al.   DNA REPAIR

Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids

(2021) John A. Smolka et al.   JOURNAL OF CELL BIOLOGY

RNA transcripts stimulate homologous recombination by forming DR-loops

(2021) Jian Ouyang et al.   NATURE

R-loops as Janus-faced modulators of DNA repair

(2021) Aline Marnef et al.   NATURE CELL BIOLOGY

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

(2021) Aleix Bayona-Feliu et al.   NATURE GENETICS

Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions

(2021) Kiwon Park et al.   PLoS Genetics

ARID1A regulates R-loop associated DNA replication stress

(2021) Shuhe Tsai et al.   PLoS Genetics

Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations

(2021) Abigael Cheruiyot et al.   CANCER RESEARCH

The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair

(2021) Carel Fijen et al.   DNA REPAIR

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

(2021) Lisa Muniz et al.   EMBO JOURNAL

R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde

(2021) Sidrit Uruci et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA–DNA hybrid imaging

(2021) Magdalena P. Crossley et al.   JOURNAL OF CELL BIOLOGY

Aicardi-Goutières syndrome-associated mutation at ADAR1 gene locus activates innate immune response in mouse brain

(2021) Xinfeng Guo et al.   Journal of Neuroinflammation

Molecular mechanisms underlying nucleotide repeat expansion disorders

(2021) Indranil Malik et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution

(2021) Wei Yuan et al.   NUCLEIC ACIDS RESEARCH

The human nucleoporin Tpr protects cells from RNA-mediated replication stress

(2021) Martin Kosar et al.   Nature Communications

USP11 controls R-loops by regulating senataxin proteostasis

(2021) Mateusz Jurga et al.   Nature Communications

UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair

(2021) Greg H. P. Ngo et al.   Nature Communications

Harmful R-loops are prevented via different cell cycle-specific mechanisms

(2021) Marta San Martin-Alonso et al.   Nature Communications

The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

(2021) Evi Goulielmaki et al.   Nature Communications

BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance

(2021) Xavier Renaudin et al.   Cell Reports

Mitochondrial RNase H1 activity regulates R-loop homeostasis to maintain genome integrity and enable early embryogenesis in Arabidopsis

(2021) Lingling Cheng et al.   PLOS BIOLOGY

The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

(2021) Charanya Kumar et al.   eLife

DNA-RNA hybrids at DSBs interfere with repair by homologous recombination

(2021) Pedro Ortega et al.   eLife

Polθ reverse transcribes RNA and promotes RNA-templated DNA repair

(2021) Gurushankar Chandramouly et al.   Science Advances

The role of chromatin at transcription-replication conflicts as a genome safeguard

(2021) Aleix Bayona-Feliu et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

San1 deficiency leads to cardiomyopathy due to excessive R-loop-associated DNA damage and cardiomyocyte hypoplasia

(2021) Zhiheng Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Toxic R-loops: Cause or consequence of replication stress?

(2021) Samira Kemiha et al.   DNA REPAIR

Defining R-loop classes and their contributions to genome instability

(2021) Daisy Castillo-Guzman et al.   DNA REPAIR

A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress

(2021) Verena Hurst et al.   EMBO JOURNAL

An Aicardi-Goutières Syndrome–Causative Point Mutation in Adar1 Gene Invokes Multiorgan Inflammation and Late-Onset Encephalopathy in Mice

(2021) Maal Inoue et al.   JOURNAL OF IMMUNOLOGY

MYCN recruits the nuclear exosome complex to RNA polymerase II to prevent transcription-replication conflicts

(2021) Dimitrios Papadopoulos et al.   MOLECULAR CELL

The Protexin complex counters resection on stalled forks to promote homologous recombination and crosslink repair

(2021) Richard O. Adeyemi et al.   MOLECULAR CELL

Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ

(2021) Amelie Schellenbauer et al.   NUCLEIC ACIDS RESEARCH

R-loops trigger the release of cytoplasmic ssDNAs leading to chronic inflammation upon DNA damage

(2021) Ourania Chatzidoukaki et al.   Science Advances

Resolution of ROS‐induced G‐quadruplexes and R‐loops at transcriptionally active sites is dependent on BLM helicase

(2020) Jun Tan et al.   FEBS LETTERS

SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications

(2020) Shalini Singh et al.   LEUKEMIA

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

(2020) Federico Ariel et al.   MOLECULAR CELL

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Intrinsically disordered protein RBM14 plays a role in generation of RNA:DNA hybrids at double-strand break sites

(2020) Yumi Jang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

(2020) Shin Yen Chong et al.   Nature Communications

Checkpoint Defects Elicit a WRNIP1-Mediated Response to Counteract R-Loop-Associated Genomic Instability

(2020) Veronica Marabitti et al.   Cancers

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

(2020) Carmen Pérez-Calero et al.   GENES & DEVELOPMENT

Molecular mechanisms and cellular functions of cGAS–STING signalling

(2020) Karl-Peter Hopfner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RTEL1 suppresses G-quadruplex-associated R-loops at difficult-to-replicate loci in the human genome

(2020) Wei Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA:RNA hybrids form at DNA double-strand breaks in transcriptionally active loci

(2020) Aldo S. Bader et al.   Cell Death & Disease

The DNA secondary structures at telomeres and genome instability

(2020) Jun Tan et al.   Cell and Bioscience

Senataxin Ortholog Sen1 Limits DNA:RNA Hybrid Accumulation at DNA Double-Strand Breaks to Control End Resection and Repair Fidelity

(2020) Chetan C. Rawal et al.   Cell Reports

Replication Stress, DNA Damage, Inflammatory Cytokines and Innate Immune Response

(2020) Sandrine Ragu et al.   Genes

Lysyl-tRNA synthetase produces diadenosine tetraphosphate to curb STING-dependent inflammation

(2020) J. Guerra et al.   Science Advances

The MRE11 complex: A versatile toolkit for the repair of broken DNA

(2020) Giordano Reginato et al.   DNA REPAIR

A genome-wide and cotranscriptional suppressor of R loops

(2020) Jacob P. Matson et al.   GENES & DEVELOPMENT

Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution

(2020) Andrea Björkman et al.   GENES & DEVELOPMENT

R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities

(2020) Eduardo E Laverde et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation

(2020) Canfeng Zhang et al.   MOLECULAR CELL

RNA: a double-edged sword in genome maintenance

(2020) Dali Zong et al.   NATURE REVIEWS GENETICS

qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide

(2020) Magdalena P Crossley et al.   NUCLEIC ACIDS RESEARCH

Specificity of end resection pathways for double-strand break regions containing ribonucleotides and base lesions

(2020) James M. Daley et al.   Nature Communications

m5C modification of mRNA serves a DNA damage code to promote homologous recombination

(2020) Hao Chen et al.   Nature Communications

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

(2020) Alexy Promonet et al.   Nature Communications

Harmful DNA:RNA hybrids are formed in cis and in a Rad51-independent manner

(2020) Juan Lafuente-Barquero et al.   eLife

USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA–RNA helicase DHX9

(2020) Misaki Matsui et al.   Oncogenesis

XRN2 Links RNA:DNA Hybrid Resolution to Double Strand Break Repair Pathway Choice

(2020) Tuyen T. Dang et al.   Cancers

Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ

(2020) Chance Meers et al.   MOLECULAR CELL

RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops

(2020) Marianna Feretzaki et al.   NATURE

Replisome bypass of transcription complexes and R-loops

(2020) Jan-Gert Brüning et al.   NUCLEIC ACIDS RESEARCH

Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability

(2020) Lisa Prendergast et al.   Nature Communications

BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage

(2020) Fred C. Lam et al.   Nature Communications

The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress

(2020) Michael Bauer et al.   Nature Communications

Pathogenic mutations reveal a role of RECQ4 in mitochondrial RNA:DNA hybrid formation and resolution

(2020) Chou-Wei Chang et al.   Scientific Reports

CDCA7 and HELLS suppress DNA:RNA hybrid-associated DNA damage at pericentromeric repeats

(2020) Motoko Unoki et al.   Scientific Reports

BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation

(2020) Drake S. Edwards et al.   Cell Reports

Causes and consequences of RNA polymerase II stalling during transcript elongation

(2020) Melvin Noe Gonzalez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution

(2020) Hyun Je Kang et al.   NUCLEIC ACIDS RESEARCH

Replisome bypass of a protein-based R-loop block by Pif1

(2020) Grant D. Schauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions

(2020) Panagiotis Kotsantis et al.   Cell Reports

WDR82/PNUTS-PP1 Prevents Transcription-Replication Conflicts by Promoting RNA Polymerase II Degradation on Chromatin

(2020) Helga B. Landsverk et al.   Cell Reports

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage

(2020) Marta Giannini et al.   PLoS Genetics

ATM pathway activation limits R-loop-associated genomic instability in Werner syndrome cells

(2019) Veronica Marabitti et al.   NUCLEIC ACIDS RESEARCH

RNase H1 directs origin-specific initiation of DNA replication in human mitochondria

(2019) Viktor Posse et al.   PLoS Genetics

Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks

(2019) Kaspar Burger et al.   NUCLEIC ACIDS RESEARCH

Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase

(2019) Steffi Herold et al.   NATURE

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

BRCA1-associated R-loop affects transcription and differentiation in breast luminal epithelial cells

(2019) Huai-Chin Chiang et al.   NUCLEIC ACIDS RESEARCH

Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation

(2019) Luigi Alfano et al.   NUCLEIC ACIDS RESEARCH

The mitochondrial R-loop

(2019) Ian J Holt   NUCLEIC ACIDS RESEARCH

Transcriptional responses to DNA damage

(2019) Erica Silva et al.   DNA REPAIR

RNases H: Structure and mechanism

(2019) Malwina Hyjek et al.   DNA REPAIR

Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids

(2019) Sofiane Y Mersaoui et al.   EMBO JOURNAL

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

(2019) Sonia Barroso et al.   EMBO REPORTS

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

FANCM limits ALT activity by restricting telomeric replication stress induced by deregulated BLM and R-loops

(2019) Bruno Silva et al.   Nature Communications

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks

(2019) Judit Domingo-Prim et al.   Nature Communications

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

(2019) Jessica L. Feldman et al.   Cell Reports

Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors

(2019) Fabio Pessina et al.   NATURE CELL BIOLOGY

Dual Processing of R-Loops and Topoisomerase I Induces Transcription-Dependent DNA Double-Strand Breaks

(2019) Agnese Cristini et al.   Cell Reports

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

(2019) Diana Zatreanu et al.   MOLECULAR CELL

R-Loops Promote Antisense Transcription across the Mammalian Genome

(2019) Sue Mei Tan-Wong et al.   MOLECULAR CELL

ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop

(2019) Dominick A. Matos et al.   MOLECULAR CELL

Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops

(2019) Nagaraja Chappidi et al.   MOLECULAR CELL

MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading

(2019) Axel Delamarre et al.   MOLECULAR CELL

An R-loop-initiated CSB–RAD52–POLD3 pathway suppresses ROS-induced telomeric DNA breaks

(2019) Jun Tan et al.   NUCLEIC ACIDS RESEARCH

ZPR1 prevents R-loop accumulation, upregulates SMN2 expression and rescues spinal muscular atrophy

(2019) Annapoorna Kannan et al.   BRAIN

The molecular landscape of ETMR at diagnosis and relapse

(2019) Sander Lambo et al.   NATURE

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

FANCM suppresses DNA replication stress at ALT telomeres by disrupting TERRA R-loops

(2019) Xiaolei Pan et al.   Scientific Reports

From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond

(2018) Flavia Michelini et al.   CHEMICAL REVIEWS

Mitochondrial DNA replication in mammalian cells: overview of the pathway

(2018) Maria Falkenberg   Essays in Biochemistry

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations

(2018) Liang Chen et al.   MOLECULAR CELL

Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters

(2018) Christopher Grunseich et al.   MOLECULAR CELL

Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer

(2018) Quan Zhu et al.   MOLECULAR CELL

RNA–DNA hybrids promote the expansion of Friedreich's ataxia (GAA)n repeats via break-induced replication

(2018) Alexander J Neil et al.   NUCLEIC ACIDS RESEARCH

DDX41 Recognizes RNA/DNA Retroviral Reverse Transcripts and Is Critical for In Vivo Control of Murine Leukemia Virus Infection

(2018) Spyridon Stavrou et al.   mBio

Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair

(2018) Wei-Ting Lu et al.   Nature Communications

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

(2018) Sarah Cohen et al.   Nature Communications

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

(2018) Agnese Cristini et al.   Cell Reports

BRCA2 Regulates Transcription Elongation by RNA Polymerase II to Prevent R-Loop Accumulation

(2018) Mahmud K.K. Shivji et al.   Cell Reports

Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes

(2018) Hai Dang Nguyen et al.   CANCER RESEARCH

Human Rad52 Promotes XPG-Mediated R-loop Processing to Initiate Transcription-Associated Homologous Recombination Repair

(2018) Takaaki Yasuhara et al.   CELL

Mrc1 and Rad9 cooperate to regulate initiation and elongation of DNA replication in response to DNA damage

(2018) Julien Bacal et al.   EMBO JOURNAL

Human proteins that interact with RNA/DNA hybrids

(2018) Isabel X. Wang et al.   GENOME RESEARCH

Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

(2018) Lorenzo Costantino et al.   MOLECULAR CELL

R-Loops in Motor Neuron Diseases

(2018) Martina G. L. Perego et al.   MOLECULAR NEUROBIOLOGY

EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma

(2018) Aparna Gorthi et al.   NATURE

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

(2018) Morgane Macheret et al.   NATURE

SAMHD1 acts at stalled replication forks to prevent interferon induction

(2018) Flavie Coquel et al.   NATURE

ATR-Mediated Global Fork Slowing and Reversal Assist Fork Traverse and Prevent Chromosomal Breakage at DNA Interstrand Cross-Links

(2018) Karun Mutreja et al.   Cell Reports

The CMG Helicase Bypasses DNA-Protein Cross-Links to Facilitate Their Repair

(2018) Justin L. Sparks et al.   CELL

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

(2018) Saša Šviković et al.   EMBO JOURNAL

Helicase Subunit Cdc45 Targets the Checkpoint Kinase Rad53 to Both Replication Initiation and Elongation Complexes after Fork Stalling

(2018) Geylani Can et al.   MOLECULAR CELL

Transcription shapes DNA replication initiation and termination in human cells

(2018) Yu-Hung Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication

(2018) Ina Klusmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability

(2018) Sonia Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB

(2018) Yaqun Teng et al.   Nature Communications

BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment

(2018) Giuseppina D’Alessandro et al.   Nature Communications

Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

(2018) Nodar Makharashvili et al.   eLife

SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability

(2017) Chenlin Song et al.   GENES & DEVELOPMENT

RECQ-like helicases Sgs1 and BLM regulate R-loop–associated genome instability

(2017) Emily Yun-Chia Chang et al.   JOURNAL OF CELL BIOLOGY

R Loops and Links to Human Disease

(2017) Patricia Richard et al.   JOURNAL OF MOLECULAR BIOLOGY

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

(2017) Hai Dang Nguyen et al.   MOLECULAR CELL

Histone Mutants Separate R Loop Formation from Genome Instability Induction

(2017) Desiré García-Pichardo et al.   MOLECULAR CELL

Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair

(2017) Olga M. Mazina et al.   MOLECULAR CELL

cGAS surveillance of micronuclei links genome instability to innate immunity

(2017) Karen J. Mackenzie et al.   NATURE

Mitotic progression following DNA damage enables pattern recognition within micronuclei

(2017) Shane M. Harding et al.   NATURE

Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

(2017) Flavia Michelini et al.   NATURE CELL BIOLOGY

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

(2017) Alessandra Brambati et al.   NUCLEIC ACIDS RESEARCH

And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break

(2017) P. Christopher Caridi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cytosine deamination and base excision repair cause R-loop–induced CAG repeat fragility and instability inSaccharomyces cerevisiae

(2017) Xiaofeng A. Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

(2017) Mohini Jangi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability

(2017) Francisco García-Benítez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids

(2017) Shira Sagie et al.   Nature Communications

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis

(2017) Xiaowen Zhang et al.   Nature Communications

Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation

(2017) Sreerama Chaitanya Sridhara et al.   Cell Reports

The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

(2017) Juan Lafuente-Barquero et al.   PLoS Genetics

Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

(2016) Corina Ohle et al.   CELL

Conflict Resolution in the Genome: How Transcription and Replication Make It Work

(2016) Stephan Hamperl et al.   CELL

Ribonuclease H2 mutations induce a cGAS/STING‐dependent innate immune response

(2016) Karen J Mackenzie et al.   EMBO JOURNAL

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

(2016) Jérôme Poli et al.   GENES & DEVELOPMENT

RECQ5 helicase promotes resolution of conflicts between replication and transcription in human cells

(2016) Vaclav Urban et al.   JOURNAL OF CELL BIOLOGY

DEAD Box 1 Facilitates Removal of RNA and Homologous Recombination at DNA Double-Strand Breaks

(2016) Lei Li et al.   MOLECULAR AND CELLULAR BIOLOGY

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

ViableRNaseH1knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function

(2016) Walt F. Lima et al.   NUCLEIC ACIDS RESEARCH

Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

(2016) Gokhan Akman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased global transcription activity as a mechanism of replication stress in cancer

(2016) Panagiotis Kotsantis et al.   Nature Communications

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Promotion of RAD51-Mediated Homologous DNA Pairing by the RAD51AP1-UAF1 Complex

(2016) Fengshan Liang et al.   Cell Reports

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

(2016) Julio C. Morales et al.   PLoS Genetics

RNase H enables efficient repair of R-loop induced DNA damage

(2016) Jeremy D Amon et al.   eLife

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

(2016) Caroline Townsend Stork et al.   eLife

Innate Immune Pattern Recognition: A Cell Biological Perspective

(2015) Sky W. Brubaker et al.   Annual Review of Immunology

A new model to study neurodegeneration in ataxia oculomotor apraxia type 2

(2015) Olivier J. Becherel et al.   HUMAN MOLECULAR GENETICS

RNA Polymerase III Regulates Cytosolic RNA:DNA Hybrids and Intracellular MicroRNA Expression

(2015) Christine Xing'er Koo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription

(2015) Rebekka A. Schwab et al.   MOLECULAR CELL

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

(2015) Christopher O. Barnes et al.   MOLECULAR CELL

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

DNA damage during the G0/G1 phase triggers RNA-templated, Cockayne syndrome B-dependent homologous recombination

(2015) Leizhen Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative lengthening of telomeres renders cancer cells hypersensitive to ATR inhibitors

(2015) R. L. Flynn et al.   SCIENCE

Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX

(2015) David Clynes et al.   Nature Communications

Genome-Derived Cytosolic DNA Mediates Type I Interferon-Dependent Rejection of B Cell Lymphoma Cells

(2015) Yu J. Shen et al.   Cell Reports

The Fanconi Anemia Pathway Protects Genome Integrity from R-loops

(2015) María L. García-Rubio et al.   PLoS Genetics

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome

(2015) Yoong Wearn Lim et al.   eLife

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

(2014) Min Gao et al.   CELL RESEARCH

Cytosolic RNA:DNA hybrids activate the cGAS–STING axis

(2014) Arun K Mankan et al.   EMBO JOURNAL

RNA:DNA hybrids are a novel molecular pattern sensed by TLR9

(2014) R. E. Rigby et al.   EMBO JOURNAL

RNA polymerase II contributes to preventing transcription-mediated replication fork stalls

(2014) I. Felipe-Abrio et al.   EMBO JOURNAL

ATR checkpoint kinase and CRL1 TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks

(2014) J.-S. Im et al.   GENES & DEVELOPMENT

DNA2 Cooperates with the WRN and BLM RecQ Helicases to Mediate Long-range DNA End Resection in Human Cells

(2014) Andreas Sturzenegger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

Arginine Methylation Facilitates the Recruitment of TOP3B to Chromatin to Prevent R Loop Accumulation

(2014) Yanzhong Yang et al.   MOLECULAR CELL

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

(2014) Aaron R. Haeusler et al.   NATURE

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

(2014) Vaibhav Bhatia et al.   NATURE

Transcript-RNA-templated DNA recombination and repair

(2014) Havva Keskin et al.   NATURE

Processing of double-R-loops in (CAG)·(CTG) and C9orf72 (GGGGCC)·(GGCCCC) repeats causes instability

(2014) Kaalak Reddy et al.   NUCLEIC ACIDS RESEARCH

Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome

(2014) D. Colak et al.   SCIENCE

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

(2014) Rajika Arora et al.   Nature Communications

Out of Balance: R-loops in Human Disease

(2014) Matthias Groh et al.   PLoS Genetics

R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome

(2014) Matthias Groh et al.   PLoS Genetics

Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

(2014) Erick W. Loomis et al.   PLoS Genetics

A Novel Mechanism Inducing Genome Instability in Kaposi's Sarcoma-Associated Herpesvirus Infected Cells

(2014) Brian R. Jackson et al.   PLoS Pathogens

The DNA Translocase FANCM/MHF Promotes Replication Traverse of DNA Interstrand Crosslinks

(2013) Jing Huang et al.   MOLECULAR CELL

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

R-loop formation atSnord116mediates topotecan inhibition ofUbe3a-antisenseand allele-specific chromatin decondensation

(2013) Weston T. Powell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing

(2013) Olivier J. Becherel et al.   PLoS Genetics

The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

(2013) Lamia Wahba et al.   eLife

Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

(2012) Amaya Alzu et al.   CELL

Senataxin, Defective in the Neurodegenerative Disorder Ataxia with Oculomotor Apraxia 2, Lies at the Interface of Transcription and the DNA Damage Response

(2012) O. Yuce et al.   MOLECULAR AND CELLULAR BIOLOGY

Playing the End Game: DNA Double-Strand Break Repair Pathway Choice

(2012) J. Ross Chapman et al.   MOLECULAR CELL

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

(2012) Stéphane Larochelle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes

(2011) Prasun Chakraborty et al.   DNA REPAIR

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

(2011) Belén Gómez-González et al.   EMBO JOURNAL

BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair

(2011) A. V. Nimonkar et al.   GENES & DEVELOPMENT

R-loop-mediated genomic instability is caused by impairment of replication fork progression

(2011) W. Gan et al.   GENES & DEVELOPMENT

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability

(2011) Lamia Wahba et al.   MOLECULAR CELL

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

(2010) Niraj M. Shanbhag et al.   CELL

Pattern Recognition Receptors and Inflammation

(2010) Osamu Takeuchi et al.   CELL

Competition between the RNA Transcript and the Nontemplate DNA Strand during R-Loop Formation In Vitro: a Nick Can Serve as a Strong R-Loop Initiation Site

(2009) D. Roy et al.   MOLECULAR AND CELLULAR BIOLOGY

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

Genome instability: a mechanistic view of its causes and consequences

(2008) Andrés Aguilera et al.   NATURE REVIEWS GENETICS