Resolution of R-loops by topoisomerase III-β (TOP3B) in coordination with the DEAD-box helicase DDX5

Mechanism for R-loop formation remote from the transcription start site: Topological issues and possible facilitation by dissociation of RNA polymerase

(2022) Boris P. Belotserkovskii et al.   DNA REPAIR

Human topoisomerases and their roles in genome stability and organization

(2022) Yves Pommier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution

(2021) Wei Yuan et al.   NUCLEIC ACIDS RESEARCH

Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods

(2021) Lionel A. Sanz et al.   Jove-Journal of Visualized Experiments

Thrap3 promotes R-loop resolution via interaction with methylated DDX5

(2021) Hyun Je Kang et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

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

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

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

The many lives of type IA topoisomerases

(2020) Anna H. Bizard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Direct observation of helicase–topoisomerase coupling within reverse gyrase

(2020) Xi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

(2020) Oscar D Villarreal et al.   Life Science Alliance

Origin matters: spontaneous DNA–RNA hybrids do not form in trans as a source of genome instability

(2020) Belén Gómez-González et al.   CURRENT GENETICS

DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks

(2020) Sourav Saha et al.   Cell Reports

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

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

DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation

(2019) Guanhui Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2019) Arianna Lockhart et al.   Cell Reports

Loss of TOP3B leads to increased R-loop formation and genome instability

(2019) Tao Zhang et al.   Open Biology

TOP3B: A Novel Candidate Gene in Juvenile Myoclonic Epilepsy?

(2018) Marwa Daghsni et al.   CYTOGENETIC AND GENOME RESEARCH

RNase H eliminates R‐loops that disrupt DNA replication but is nonessential for efficient DSB repair

(2018) Hongchang Zhao et al.   EMBO REPORTS

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

(2018) Christopher Grunseich et al.   MOLECULAR CELL

Arginine methylation of the C-terminus RGG motif promotes TOP3B topoisomerase activity and stress granule localization

(2018) Lifeng Huang et al.   NUCLEIC ACIDS RESEARCH

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

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

(2018) Hai Dang Nguyen et al.   CANCER RESEARCH

R-Loops in Motor Neuron Diseases

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

Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli

(2018) Julien Brochu et al.   PLoS Genetics

FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress

(2018) Yusuke Okamoto et al.   FEBS Journal

DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing

(2018) Prasun Chakraborty et al.   Nature Communications

Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila

(2018) Seung Kyu Lee et al.   Nature Communications

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

(2017) Chenlin Song et al.   GENES & DEVELOPMENT

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

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

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

Type IA topoisomerases can be “magicians” for both DNA and RNA in all domains of life

(2017) Muzammil Ahmad et al.   RNA Biology

Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism

(2017) Zheng Xing et al.   RNA

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

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

(2016) Stephan Hamperl et al.   CELL

Deletion of TOP3B Is Associated with Cognitive Impairment and Facial Dysmorphism

(2016) Carolyn S. Kaufman et al.   CYTOGENETIC AND GENOME RESEARCH

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

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

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

RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals

(2016) Muzammil Ahmad et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Jeremy D Amon et al.   eLife

Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters

(2016) Jessica Marinello et al.   PLoS One

Breaking bad: R-loops and genome integrity

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

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

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

(2014) Vaibhav Bhatia et al.   NATURE

R-Loops in Proliferating Cells but Not in the Brain: Implications for AOA2 and Other Autosomal Recessive Ataxias

(2014) Abrey J. Yeo et al.   PLoS One

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

(2014) Yujia A. Chan et al.   PLoS Genetics

The DEAD box proteins DDX5 (p68) and DDX17 (p72): Multi-tasking transcriptional regulators

(2013) Frances V. Fuller-Pace   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Coherence between Cellular Responses andin VitroSplicing Inhibition for the Anti-tumor Drug Pladienolide B and Its Analogs

(2013) Kerstin A. Effenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation

(2013) Dongyi Xu et al.   NATURE NEUROSCIENCE

Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders

(2013) Georg Stoll et al.   NATURE NEUROSCIENCE

A rapid and sensitive assay for DNA–protein covalent complexes in living cells

(2013) Kostantin Kiianitsa et al.   NUCLEIC ACIDS RESEARCH

Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation

(2013) Jessica Marinello et al.   NUCLEIC ACIDS RESEARCH

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

R-loops cause replication impairment and genome instability during meiosis

(2012) Maikel Castellano-Pozo et al.   EMBO REPORTS

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

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

The DEAD-box RNA Helicase Dbp2 Connects RNA Quality Control with Repression of Aberrant Transcription

(2012) Sara C. Cloutier et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

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

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

(2011) Anne Helmrich 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

Interfacial inhibitors: targeting macromolecular complexes

(2011) Yves Pommier et al.   NATURE REVIEWS DRUG DISCOVERY

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

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

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

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

Significance of topoisomerase IIIβ expression in breast ductal carcinomas: strong associations with disease-specific survival and metastasis

(2010) João Paulo Oliveira-Costa et al.   HUMAN PATHOLOGY

Mammalian Mitochondrial DNA Replication Intermediates Are Essentially Duplex but Contain Extensive Tracts of RNA/DNA Hybrid

(2010) Jaakko L.O. Pohjoismäki et al.   JOURNAL OF MOLECULAR BIOLOGY

Ataxia telangiectasia mutated activation by transcription- and topoisomerase I-induced DNA double-strand breaks

(2009) Olivier Sordet et al.   EMBO REPORTS

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

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Defective p53 engagement after the induction of DNA damage in cells deficient in topoisomerase 3β

(2008) Subhasis Mohanty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA