Defining R-loop classes and their contributions to genome instability

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

(2021) Frédéric Chédin et al.   EMBO JOURNAL

Efficient RNA polymerase II pause release requires U2 snRNP function

(2021) Livia Caizzi et al.   MOLECULAR CELL

Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis

(2021) Elena A Kouzminova et al.   NUCLEIC ACIDS RESEARCH

Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M

(2021) Jianming Wang et al.   Cell Reports

A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide

(2021) Phillip Wulfridge et al.   eLife

PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer

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

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

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

(2021) Rui Sousa-Luís et al.   MOLECULAR CELL

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

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

Take Your PIC

(2021) Alexis Verger et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Ultra-Deep Coverage Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

(2020) Maika Malig et al.   JOURNAL OF MOLECULAR BIOLOGY

The R-loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli

(2020) Wei Xu et al.   PLANT CELL

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2

(2020) Célia Alecki et al.   Nature Communications

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

(2020) Alexy Promonet et al.   Nature Communications

Replisome bypass of transcription complexes and R-loops

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

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

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

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

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

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Transcription-mediated replication hindrance: a major driver of genome instability

(2019) Belén Gómez-González et al.   GENES & DEVELOPMENT

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

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

(2019) Sonia Barroso et al.   EMBO REPORTS

R-loop-dependent replication and genomic instability in bacteria

(2019) Marc Drolet et al.   DNA REPAIR

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

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

(2019) Diana Zatreanu et al.   MOLECULAR CELL

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach

(2019) Qingqing Yan et al.   Cell Reports

Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA

(2019) Morimoto et al.   Genes

Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing

(2018) Tassa Saldi et al.   GENES & DEVELOPMENT

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

(2018) Stella R. Hartono et al.   JOURNAL OF MOLECULAR BIOLOGY

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

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

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

(2018) Sarah Cohen et al.   Nature Communications

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

(2018) Hai Dang Nguyen et al.   CANCER RESEARCH

R-loop generation during transcription: Formation, processing and cellular outcomes

(2018) Boris P. Belotserkovskii et al.   DNA REPAIR

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

(2018) Aparna Gorthi 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

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

Regulation of ATR activity via the RNA polymerase II associated factors CDC73 and PNUTS-PP1

(2018) Helga B Landsverk et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine–homopyrimidine sequence localized in the vicinity of the promoter

(2017) Boris P. Belotserkovskii et al.   NUCLEIC ACIDS RESEARCH

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

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

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

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

(2016) Lamia Wahba et al.   GENES & DEVELOPMENT

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

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

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability

(2016) Peter Zeller et al.   NATURE GENETICS

Transcription–replication conflicts: how they occur and how they are resolved

(2016) Tatiana García-Muse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

(2016) Yves Pommier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nascent Connections: R-Loops and Chromatin Patterning

(2016) Frédéric Chédin   TRENDS IN GENETICS

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

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

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

(2016) Caroline Townsend Stork et al.   eLife

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

Breaking bad: R-loops and genome integrity

(2015) Julie Sollier et al.   TRENDS IN CELL BIOLOGY

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

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

(2014) Julie Sollier et al.   MOLECULAR CELL

Mechanisms of genome instability induced by RNA-processing defects

(2014) Yujia A. Chan et al.   TRENDS IN GENETICS

RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes

(2014) Pénélope Legros et al.   PLoS Genetics

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

(2014) Aziz El Hage et al.   PLoS Genetics

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

(2014) Iris Jonkers et al.   eLife

Control of Transcriptional Elongation

(2013) Hojoong Kwak et al.   Annual Review of Genetics

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

Replication of theEscherichia colichromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics

(2013) Nkabuije Z. Maduike et al.   MOLECULAR MICROBIOLOGY

Causes and consequences of replication stress

(2013) Michelle K. Zeman et al.   NATURE CELL BIOLOGY

R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli

(2013) Hallie Wimberly et al.   Nature Communications

R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants

(2012) P. C. Stirling et al.   GENES & DEVELOPMENT

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

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

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Biological validation that SF3b is a target of the antitumor macrolide pladienolide

(2011) Akira Yokoi et al.   FEBS Journal

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives

(2010) Kenneth N Kreuzer et al.   Virology Journal

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

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