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

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

(2021) Frédéric Chédin et al.   EMBO JOURNAL

Tracking break-induced replication shows that it stalls at roadblocks

(2021) Liping Liu et al.   NATURE

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

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

Replication dynamics of recombination-dependent replication forks

(2021) Karel Naiman et al.   Nature Communications

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

(2021) Jianming Wang et al.   Cell Reports

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

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

ARID1A regulates R-loop associated DNA replication stress

(2021) Shuhe Tsai et al.   PLoS Genetics

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

(2021) Evi Goulielmaki et al.   Nature Communications

Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae

(2020) Rani Yeung et al.   GENETICS

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

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

The dark side of RNA:DNA hybrids

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

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

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

Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication

(2020) Romain Forey et al.   MOLECULAR CELL

Rad53 limits CMG helicase uncoupling from DNA synthesis at replication forks

(2020) Sujan Devbhandari et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

(2020) Alexy Promonet et al.   Nature Communications

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

(2020) Tuyen T. Dang et al.   Cancers

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

INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins

(2020) Salih Topal et al.   Cell Reports

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

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

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

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

R-Loops as Cellular Regulators and Genomic Threats

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

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

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

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

(2019) Sonia Barroso et al.   EMBO REPORTS

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

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

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

Checkpoint inhibition of origin firing prevents DNA topological stress

(2019) Esther C. Morafraile et al.   GENES & DEVELOPMENT

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

MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription–replication conflicts

(2019) Emily Yun-Chia Chang et al.   Nature Communications

Fork pausing complex engages topoisomerases at the replisome

(2019) Maksym Shyian et al.   GENES & DEVELOPMENT

Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide

(2019) Olivier Brison et al.   Nature Communications

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

Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts

(2018) Alba Duch et al.   Nature Communications

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

(2018) Julien Bacal et al.   EMBO JOURNAL

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

(2018) Morgane Macheret et al.   NATURE

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

(2018) Saša Šviković et al.   EMBO JOURNAL

Noncoding transcription influences the replication initiation program through chromatin regulation

(2018) Julien Soudet et al.   GENOME RESEARCH

Transcription shapes DNA replication initiation and termination in human cells

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

Transcription-dependent regulation of replication dynamics modulates genome stability

(2018) Marion Blin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Pervasive transcription fine-tunes replication origin activity

(2018) Tito Candelli et al.   eLife

Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration

(2017) Matthias Groh et al.   JOURNAL OF MOLECULAR BIOLOGY

The impact of replication stress on replication dynamics and DNA damage in vertebrate cells

(2017) Hervé Técher et al.   NATURE REVIEWS GENETICS

Mechanisms of DNA replication termination

(2017) James M. Dewar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spatial and Temporal Control of Evolution through Replication–Transcription Conflicts

(2017) Houra Merrikh   TRENDS IN MICROBIOLOGY

PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes

(2017) Phong Lan Thao Tran et al.   Nature Communications

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

(2016) Stephan Hamperl et al.   CELL

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

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

The nuclear pore complex: understanding its function through structural insight

(2016) Martin Beck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

(2016) Joseph S Osmundson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nascent Connections: R-Loops and Chromatin Patterning

(2016) Frédéric Chédin   TRENDS IN GENETICS

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

Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

(2016) Joseph S Osmundson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans

(2016) Ehsan Pourkarimi et al.   eLife

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

(2016) Caroline Townsend Stork et al.   eLife

The Causes and Consequences of Topological Stress during DNA Replication

(2016) Andrea Keszthelyi et al.   Genes

INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation

(2015) Anne Lafon et al.   MOLECULAR CELL

Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA

(2015) Julien Gros et al.   MOLECULAR CELL

Replication fork reversal in eukaryotes: from dead end to dynamic response

(2015) Kai J. Neelsen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability

(2015) Stephanie A. Schalbetter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability

(2014) Fei-Long Meng et al.   CELL

Temporal separation of replication and transcription during S-phase progression

(2014) Matthieu Meryet-Figuiere et al.   CELL CYCLE

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

The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts

(2014) E. Herrera-Moyano et al.   GENES & DEVELOPMENT

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

(2014) Julie Sollier et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Out of Balance: R-loops in Human Disease

(2014) Matthias Groh et al.   PLoS Genetics

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

(2013) Jacqueline H. Barlow et al.   CELL

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

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

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

(2012) Amaya Alzu et al.   CELL

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

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

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

(2012) G. I. Dellino et al.   GENOME RESEARCH

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

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

Coordinated control of replication and transcription by a SAPK protects genomic integrity

(2012) Alba Duch et al.   NATURE

Topoisomerase I poisoning results in PARP-mediated replication fork reversal

(2012) Arnab Ray Chaudhuri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Replication Checkpoint Protects Fork Stability by Releasing Transcribed Genes from Nuclear Pores

(2011) Rodrigo Bermejo et al.   CELL

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

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

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

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

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

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

(2011) C. Cayrou et al.   GENOME RESEARCH

Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes

(2011) Anne Helmrich et al.   MOLECULAR CELL

Co-directional replication–transcription conflicts lead to replication restart

(2011) Houra Merrikh et al.   NATURE

Genome Instability and Transcription Elongation Impairment in Human Cells Depleted of THO/TREX

(2011) María S. Domínguez-Sánchez et al.   PLoS Genetics

Topoisomerase I regulates open chromatin and controls gene expression in vivo

(2010) Mickaël Durand-Dubief et al.   EMBO JOURNAL

Epigenetic Instability due to Defective Replication of Structured DNA

(2010) Peter Sarkies et al.   MOLECULAR CELL

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome

(2010) Matthew D Sekedat et al.   Molecular Systems Biology

Replication stress checkpoint signaling controls tRNA gene transcription

(2010) Vesna C Nguyen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity

(2010) S. Ide et al.   SCIENCE

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

(2010) R. T. Pomerantz et al.   SCIENCE

Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription

(2009) Rodrigo Bermejo et al.   CELL

The S-Phase Checkpoint Is Required To Respond to R-Loops Accumulated in THO Mutants

(2009) B. Gomez-Gonzalez 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

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces cerevisiae

(2009) Anna Azvolinsky et al.   MOLECULAR CELL

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

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics