R-loops as Janus-faced modulators of DNA repair

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

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

(2021) Elodie Hatchi et al.   NATURE

Emerging roles for R-loop structures in the management of topological stress

(2020) Frederic Chedin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2020) Federico Ariel et al.   MOLECULAR CELL

The dark side of RNA:DNA hybrids

(2020) Alessandra Brambati et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

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

DNA dependent protein kinase (DNA-PK) enhances HIV transcription by promoting RNA polymerase II activity and recruitment of transcription machinery at HIV LTR

(2020) Sonia Zicari et al.   Oncotarget

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

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

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 protein A binds RNA and promotes R-loop formation

(2020) Olga M Mazina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleocytoplasmic shuttling of Gle1 impacts DDX1 at transcription termination sites

(2020) Manisha Sharma et al.   MOLECULAR BIOLOGY OF THE CELL

Looping the (R) Loop in DSB Repair via RNA Methylation

(2020) Belén Gómez-González et al.   MOLECULAR CELL

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

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

Location, Location, Location: The Role of Nuclear Positioning in the Repair of Collapsed Forks and Protection of Genome Stability

(2020) Jenna M. Whalen et al.   Genes

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

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

(2020) Gábor M. Harami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Damage Triggers a New Phase in Neurodegeneration

(2020) Fabio Pessina et al.   TRENDS IN GENETICS

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

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

Modifications and interactions at the R-loop

(2020) Miaomiao Li et al.   DNA REPAIR

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

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

RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

(2019) Pierre Collin et al.   MOLECULAR CELL

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

(2019) Viktor Posse et al.   PLoS Genetics

Single-molecule imaging of transcription at damaged chromatin

(2019) Alexandra C. Vítor et al.   Science Advances

Interplay between DNA sequence and negative superhelicity drives R-loop structures

(2019) Robert Stolz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Kaspar Burger et al.   NUCLEIC ACIDS RESEARCH

R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes

(2019) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

R-Loops as Cellular Regulators and Genomic Threats

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

High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing

(2019) Lionel A. Sanz et al.   Nature Protocols

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

PARP-1 Activation Directs FUS to DNA Damage Sites to Form PARG-Reversible Compartments Enriched in Damaged DNA

(2019) Anastasia S. Singatulina et al.   Cell Reports

The functional complexity of the RNA-binding protein Yra1: mRNA biogenesis, genome stability and DSB repair

(2019) Valentina Infantino et al.   CURRENT GENETICS

What causes an RNA-DNA hybrid to compromise genome integrity?

(2019) Ana G. Rondón et al.   DNA REPAIR

Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates?

(2019) Nadine Puget 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

Phase separation of 53 BP 1 determines liquid‐like behavior of DNA repair compartments

(2019) Sinan Kilic et al.   EMBO JOURNAL

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

(2019) Julieta Rivosecchi et al.   EMBO JOURNAL

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

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

A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair

(2019) Aline Marnef et al.   GENES & DEVELOPMENT

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

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

Bon voyage: A transcriptional journey around DNA breaks

(2019) Pierre Caron et al.   DNA REPAIR

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

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

(2019) Jun Tan et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

m6A RNA modification as a new player in R-loop regulation

(2019) Aline Marnef et al.   NATURE GENETICS

The Role of RNA in Biological Phase Separations

(2018) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals

(2018) Nilay Shah et al.   MOLECULAR CELL

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

(2018) Claudia Ribeiro de Almeida et al.   MOLECULAR CELL

Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin

(2018) Julien Brustel et al.   Scientific Reports

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

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

(2018) Takaaki Yasuhara et al.   CELL

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

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

(2018) Thomas Clouaire et al.   MOLECULAR CELL

53BP1–RIF1–shieldin counteracts DSB resection through CST- and Polα-dependent fill-in

(2018) Zachary Mirman et al.   NATURE

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan et al.   MOLECULAR CELL

Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks

(2018) Franziska Bonath et al.   NUCLEIC ACIDS RESEARCH

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

RAD52 is required for RNA-templated recombination repair in post-mitotic neurons

(2017) Starr Welty et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcription and DNA Damage: Holding Hands or Crossing Swords?

(2017) Giuseppina D'Alessandro et al.   JOURNAL OF MOLECULAR BIOLOGY

Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration

(2017) Matthias Groh 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

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

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

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

RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang 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

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

(2017) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

FANCM, BRCA1, and BLM cooperatively resolve the replication stress at the ALT telomeres

(2017) Xiaolei Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G9a coordinates with the RPA complex to promote DNA damage repair and cell survival

(2017) Qiaoyan Yang 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

A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

(2017) Fabio Iannelli et al.   Nature Communications

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

(2017) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2016) Corina Ohle et al.   CELL

Mechanism and regulation of DNA end resection in eukaryotes

(2016) Lorraine S. Symington   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

DNA repair by RNA: Templated, or not templated, that is the question

(2016) Chance Meers et al.   DNA REPAIR

Alternative lengthening of human telomeres is a conservative DNA replication process with features of break‐induced replication

(2016) Fani‐Marlen Roumelioti et al.   EMBO REPORTS

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

Break-induced telomere synthesis underlies alternative telomere maintenance

(2016) Robert L. Dilley et al.   NATURE

BMI1–UBR5 axis regulates transcriptional repression at damaged chromatin

(2016) Anthony Sanchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Interaction of BARD1 and HP1 Is Required for BRCA1 Retention at Sites of DNA Damage

(2015) W. Wu et al.   CANCER RESEARCH

RRP6/EXOSC10 is required for the repair of DNA double-strand breaks by homologous recombination

(2015) C. Marin-Vicente et al.   JOURNAL OF CELL SCIENCE

Transcriptional Elongation Factor ENL Phosphorylated by ATM Recruits Polycomb and Switches Off Transcription for DSB Repair

(2015) Ayako Ui 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

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system

(2015) Ruth Stuckey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose)

(2015) Matthias Altmeyer et al.   Nature Communications

Double strand break (DSB) repair in heterochromatin and heterochromatin proteins in DSB repair

(2014) Charlène Lemaître et al.   DNA REPAIR

A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response

(2014) Melanie Blasius et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

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

(2014) Julie Sollier et al.   MOLECULAR CELL

Requirement for PBAF in Transcriptional Repression and Repair at DNA Breaks in Actively Transcribed Regions of Chromatin

(2014) Andreas Kakarougkas et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki 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

DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal

(2014) Sébastien Britton et al.   NUCLEIC ACIDS RESEARCH

DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin

(2014) M. K. Ayrapetov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage

(2013) P. Richard et al.   GENES & DEVELOPMENT

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

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

(2013) Lamia Wahba et al.   eLife

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

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

(2012) Sofia Francia et al.   NATURE

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

(2012) M. Jinek et al.   SCIENCE

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

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

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

(2010) Niraj M. Shanbhag et al.   CELL