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

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

Solution to the 50-year-old Okazaki-fragment problem

(2019) Peter M. Burgers   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The extruded non-template strand determines the architecture of R-loops

(2019) Yeraldinne Carrasco-Salas et al.   NUCLEIC ACIDS RESEARCH

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

(2019) Wei Yuan et al.   Science Advances

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

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

(2019) Julieta Rivosecchi et al.   EMBO JOURNAL

Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding

(2019) Chi-Fu Chen et al.   GENETICS

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

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

R-Loops Promote Antisense Transcription across the Mammalian Genome

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

RNase H1 and H2 Are Differentially Regulated to Process RNA-DNA Hybrids

(2019) Arianna Lockhart et al.   Cell Reports

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

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

R-loops: targets for nuclease cleavage and repeat instability

(2018) Catherine H. Freudenreich   CURRENT GENETICS

Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

(2018) María García-Rubio et al.   GENES & DEVELOPMENT

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

(2018) Christopher Grunseich et al.   MOLECULAR CELL

Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers

(2018) Vladimir A Kuznetsov et al.   NUCLEIC ACIDS RESEARCH

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

PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to sites of DNA damage controls H2A.Z loading

(2018) Gergely Rona et al.   eLife

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

(2018) Takaaki Yasuhara et al.   CELL

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

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

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

Ribonucleotide incorporation enables repair of chromosome breaks by nonhomologous end joining

(2018) John M. Pryor et al.   SCIENCE

CRISPR-Cas guides the future of genetic engineering

(2018) Gavin J. Knott et al.   SCIENCE

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells

(2018) Alessio De Magis 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

Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion

(2018) Emma Briggs et al.   PLoS Genetics

Divergent lncRNA GATA3-AS1 Regulates GATA3 Transcription in T-Helper 2 Cells

(2018) Hunter R. Gibbons et al.   Frontiers in Immunology

Histone demethylase KDM5A regulates the ZMYND8–NuRD chromatin remodeler to promote DNA repair

(2017) Fade Gong 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

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

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

DNA–RNA hybrids: the risks of DNA breakage during transcription

(2017) Andrés Aguilera et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

DNA–RNA hybrids: the risks of DNA breakage during transcription

(2017) Andrés Aguilera et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

(2017) Jason G Dumelie 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

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

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

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation

(2016) Sara C. Cloutier et al.   MOLECULAR CELL

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

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin

(2016) Pavel Savitsky et al.   Cell Reports

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

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

The Yin and Yang of R-loop biology

(2015) Lorenzo Costantino et al.   CURRENT OPINION IN CELL BIOLOGY

GADD45a physically and functionally interacts with TET1

(2015) Sabine Kienhöfer et al.   DIFFERENTIATION

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination

(2015) Dorothy Yanling Zhao et al.   NATURE

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

TERRA and the state of the telomere

(2015) Karsten Rippe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gadd45a promotes DNA demethylation through TDG

(2015) Zheng Li et al.   NUCLEIC ACIDS RESEARCH

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

(2015) Raquel Boque-Sastre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Telomere elongation chooses TERRA ALTernatives

(2015) Rajika Arora et al.   RNA Biology

Breaking bad: R-loops and genome integrity

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

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

(2015) Julie Nadel et al.   Epigenetics & Chromatin

TERRA and the state of the telomere

(2015) Karsten Rippe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribonucleotides in DNA: Origins, repair and consequences

(2014) Jessica S. Williams et al.   DNA REPAIR

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

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

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

Long Noncoding RNA TARID Directs Demethylation and Activation of the Tumor Suppressor TCF21 via GADD45A

(2014) Khelifa Arab 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

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

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

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

(2014) Rajika Arora et al.   Nature Communications

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

Polycomb repressive complex 2 contributes to DNA double-strand break repair

(2013) Stuart Campbell et al.   CELL CYCLE

The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening

(2013) Verena Pfeiffer et al.   EMBO JOURNAL

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

Telomeric Noncoding RNA TERRA Is Induced by Telomere Shortening to Nucleate Telomerase Molecules at Short Telomeres

(2013) Emilio Cusanelli et al.   MOLECULAR CELL

Ribonucleotides Misincorporated into DNA Act as Strand-Discrimination Signals in Eukaryotic Mismatch Repair

(2013) Medini Manohar Ghodgaonkar et al.   MOLECULAR CELL

Ribonucleotides Are Signals for Mismatch Repair of Leading-Strand Replication Errors

(2013) Scott A. Lujan et al.   MOLECULAR CELL

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

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

Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence

(2013) Bettina Balk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation

(2013) Felipe C. Beckedorff 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

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

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

DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation

(2012) Mina Nakama et al.   GENES TO CELLS

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

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks

(2012) Tibor Pankotai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) M. Jinek et al.   SCIENCE

BMI1 Is Recruited to DNA Breaks and Contributes to DNA Damage-Induced H2A Ubiquitination and Repair

(2011) V. Ginjala et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) Lamia Wahba et al.   MOLECULAR CELL

Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

(2011) Hannah E. Mischo 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

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

(2010) Niraj M. Shanbhag et al.   CELL

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

(2010) A. El Hage et al.   GENES & DEVELOPMENT

BMI1-mediated histone ubiquitylation promotes DNA double-strand break repair

(2010) Ismail Hassan Ismail et al.   JOURNAL OF CELL BIOLOGY

Molecular Dissection of Telomeric Repeat-Containing RNA Biogenesis Unveils the Presence of Distinct and Multiple Regulatory Pathways

(2010) A. Porro et al.   MOLECULAR AND CELLULAR BIOLOGY

Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

(2010) B. P. Belotserkovskii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases

(2010) S. A. Nick McElhinny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE