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

https://doi.org/10.26508/lsa.202000762

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The sub‐nanomolar binding of DNA–RNA hybrids by the single‐chain Fv fragment of antibody S9.6

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Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer

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Characterization of monoclonal antibody to DNA · RNA and its application to immunodetection of hybrids

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

inferredcites →https://doi.org/10.1016/j.ccell.2019.07.003openalex-snapshot

Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation

inferredcites →https://doi.org/10.1016/j.cell.2005.06.008openalex-snapshot

Inactivation of the SR Protein Splicing Factor ASF/SF2 Results in Genomic Instability

inferredcites →https://doi.org/10.1016/j.celrep.2016.12.050openalex-snapshot

Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation

inferredcites →https://doi.org/10.1016/j.celrep.2018.04.025openalex-snapshot

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

inferredcites →https://doi.org/10.1016/j.celrep.2018.08.002openalex-snapshot

PRMT5 Regulates DNA Repair by Controlling the Alternative Splicing of Histone-Modifying Enzymes

inferredcites →https://doi.org/10.1016/j.jmb.2016.08.031openalex-snapshot

R Loops and Links to Human Disease

inferredcites →https://doi.org/10.1016/j.molcel.2008.12.013openalex-snapshot

Protein Arginine Methylation in Mammals: Who, What, and Why

inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.molcel.2011.04.026openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2011.10.017openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2012.01.017openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2014.01.011openalex-snapshot

Arginine Methylation Facilitates the Recruitment of TOP3B to Chromatin to Prevent R Loop Accumulation

inferredcites →https://doi.org/10.1016/j.molcel.2014.10.020openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2016.05.032openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2017.01.019openalex-snapshot

PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination

inferredcites →https://doi.org/10.1016/j.molcel.2018.04.001openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2019.01.024openalex-snapshot

R-Loops as Cellular Regulators and Genomic Threats

inferredcites →https://doi.org/10.1016/j.molcel.2019.07.037openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2019.10.002openalex-snapshot

R-Loops Promote Antisense Transcription across the Mammalian Genome

inferredcites →https://doi.org/10.1016/j.tig.2008.05.004openalex-snapshot

RNA-binding proteins in human genetic disease

inferredcites →https://doi.org/10.1016/j.tig.2016.10.002openalex-snapshot

Nascent Connections: R-Loops and Chromatin Patterning

inferredcites →https://doi.org/10.1016/j.tig.2020.05.008openalex-snapshot

Termination of Transcription by RNA Polymerase II: BOOM!

inferredcites →https://doi.org/10.1016/j.trecan.2019.08.006openalex-snapshot

R Loops and Their Composite Cancer Connections

inferredcites →https://doi.org/10.1016/s0092-8674(03)00934-6openalex-snapshot

Estrogen Receptor-α Directs Ordered, Cyclical, and Combinatorial Recruitment of Cofactors on a Natural Target Promoter

inferredcites →https://doi.org/10.1016/s1097-2765(01)00244-1openalex-snapshot

SMN, the Product of the Spinal Muscular Atrophy Gene, Binds Preferentially to Dimethylarginine-Containing Protein Targets

inferredcites →https://doi.org/10.1016/s1097-2765(01)00329-xopenalex-snapshot

DExD/H Box RNA Helicases

inferredcites →https://doi.org/10.1038/nature03032openalex-snapshot

Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination

inferredcites →https://doi.org/10.1038/nature03035openalex-snapshot

Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites

inferredcites →https://doi.org/10.1038/nature03041openalex-snapshot

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II

inferredcites →https://doi.org/10.1038/nature10730openalex-snapshot

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

inferredcites →https://doi.org/10.1038/nature13374openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature16469openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ncb1984openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ncomms15025openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ni919openalex-snapshot

R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nprot.2008.211openalex-snapshot

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

inferredcites →https://doi.org/10.1038/nrc3409openalex-snapshot

Protein arginine methyltransferases and cancer

inferredcites →https://doi.org/10.1038/nsmb.3395openalex-snapshot

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

inferredcites →https://doi.org/10.1038/onc.2009.261openalex-snapshot

The DEAD-box protein p72 regulates ERα-/oestrogen-dependent transcription and cell growth, and is associated with improved survival in ERα-positive breast cancer

inferredcites →https://doi.org/10.1038/s41467-018-06677-1openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41576-020-00302-yopenalex-snapshot

RNA-binding proteins in human genetic disease

inferredcites →https://doi.org/10.1038/s41580-019-0155-xopenalex-snapshot

The regulation, functions and clinical relevance of arginine methylation

inferredcites →https://doi.org/10.1073/pnas.0510310103openalex-snapshot

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

inferredcites →https://doi.org/10.1073/pnas.1419161111openalex-snapshot

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

inferredcites →https://doi.org/10.1073/pnas.1819476116openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1909047116openalex-snapshot

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

inferredcites →https://doi.org/10.1074/jbc.m112.383075openalex-snapshot

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

inferredcites →https://doi.org/10.1083/jcb.201703168openalex-snapshot

RECQ-like helicases Sgs1 and BLM regulate R-loop–associated genome instability

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/nar/gkh103openalex-snapshot

The UCSC Table Browser data retrieval tool

inferredcites →https://doi.org/10.1093/nar/gky955openalex-snapshot

GENCODE reference annotation for the human and mouse genomes

inferredcites →https://doi.org/10.1093/nar/gkz560openalex-snapshot

Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription

inferredcites →https://doi.org/10.1101/gad.1396306openalex-snapshot

The Drosophila P68 RNA helicase regulates transcriptional deactivation by promoting RNA release from chromatin

inferredcites →https://doi.org/10.1101/gad.242990.114openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.280834.116openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.300624.117openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.573310openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.237362.118openalex-snapshot

Human proteins that interact with RNA/DNA hybrids

inferredcites →https://doi.org/10.1128/mcb.00415-16openalex-snapshot

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

inferredcites →https://doi.org/10.1128/mcb.01458-13openalex-snapshot

Purification and Identification of p68 RNA Helicase Acting as a Transcriptional Coactivator Specific for the Activation Function 1 of Human Estrogen Receptor α

inferredcites →https://doi.org/10.1158/2159-8290.cd-12-0116openalex-snapshot

DDX5 Regulates DNA Replication and Is Required for Cell Proliferation in a Subset of Breast Cancer Cells

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-018-1478-1openalex-snapshot

DNA Topoisomerase I differentially modulates R-loops across the human genome

inferredcites →https://doi.org/10.1261/rna.060335.116openalex-snapshot

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

inferredcites →https://doi.org/10.1261/rna.067249.118openalex-snapshot

The DEAD-box protein Dbp2p is linked to noncoding RNAs, the helicase Sen1p, and R-loops

inferredcites →https://doi.org/10.1371/journal.pgen.1006107openalex-snapshot

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

inferredcites →https://doi.org/10.15252/embj.201695131openalex-snapshot

An ATR‐dependent function for the Ddx19 RNA helicase in nuclear R‐loop metabolism

inferredcites →https://doi.org/10.15252/embj.2018100986openalex-snapshot

Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids

inferredcites →https://doi.org/10.2174/1875036201307010001openalex-snapshot

Comparison of Sequencing Utility Programs

inferredcites →https://doi.org/10.7554/elife.17548openalex-snapshot

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.2139/ssrn.4175592openalex-extracted

THOC5 Complexes With DDX5, DDX17 and CDK12 Are Essential in Primitive Cell Survival to Regulate R Loop Structures and Transcription Elongation Rate

inferred← citeshttps://doi.org/10.1002/1873-3468.14947openalex-snapshot

Looping forward: exploring R‐loop processing and therapeutic potential

inferred← citeshttps://doi.org/10.1002/1878-0261.13431openalex-snapshot

Hypoxia‐mediated regulation of DDX5 through decreased chromatin accessibility and post‐translational targeting restricts R‐loop accumulation

inferred← citeshttps://doi.org/10.1002/cam4.71396openalex-snapshot

ZC3H12D and DDX5 Antagonistically Regulate Cyclin D1 mRNA Stability and Cell Cycle Progression in Breast Cancer

inferred← citeshttps://doi.org/10.1002/cpz1.1037openalex-snapshot

Approaches for Mapping and Analysis of R‐loops

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R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors

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Deletion of RBMX RGG/RG motif in Shashi-XLID syndrome leads to aberrant p53 activation and neuronal differentiation defects

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

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Cancer synthetic vulnerabilities to protein arginine methyltransferase inhibitors

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Building an integrated view of R-loops, transcription, and chromatin

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THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate

inferred← citeshttps://doi.org/10.1016/j.isci.2025.112408openalex-snapshot

The NONO protein regulates nonclassical DNA structure: Effects on circadian genes and DNA damage

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Helicases in R-loop Formation and Resolution

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Characterization of R-Loop–Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression

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Cellular pathways influenced by protein arginine methylation: Implications for cancer

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Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis

inferred← citeshttps://doi.org/10.1016/j.tcb.2023.03.001openalex-snapshot

DDX47 untangles R-loops with only certain other helicases

inferred← citeshttps://doi.org/10.1016/j.tibs.2021.01.009openalex-snapshot

Reciprocal Links between Pre-messenger RNA 3′-End Processing and Genome Stability

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DDX5 mRNA-targeting antisense oligonucleotide as a new promising therapeutic in combating castration-resistant prostate cancer

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Thrap3 promotes R-loop resolution via interaction with methylated DDX5

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APOBEC3C coordinates DDX5 in R-loop resolution and dynamic control of Chk1-mediated stress-responsive circuitry as a prerequisite for gemcitabine resistance in p53-deficient cells

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RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation

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Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes

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APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer

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Gene regulation by convergent promoters

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Resolution of R-loops and transcription–replication conflicts by SETX–BRCA1–BARD1 complex

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MCM8 interacts with DDX5 to promote R-loop resolution

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p53 activates circASCC3 to repress R-loops and enhance resistance to chemotherapy

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Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression

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R-loops: emerging key regulators in plants

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R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation

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Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions

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Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion

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RNA helicase-dependent gene looping impacts messenger RNA processing

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PARP1 associates with R-loops to promote their resolution and genome stability

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RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells

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DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions

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R-loops, type I topoisomerases and cancer

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The human HELQ helicase and XRN2 exoribonuclease cooperate in R-loop resolution

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R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B

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Cell-type-specific aberrant R-loop accumulation regulates target gene and confers cell-specificity

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XRN2 Is Required for Cell Motility and Invasion in Glioblastomas

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RNA helicase DEAD-box-5 is involved in R-loop dynamics of preimplantation embryos

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LSm4 biomolecular condensates drive XRN2-mediated RNA decay at DNA double-strand breaks to facilitate repair

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The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids

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Rôle multifacette de la SUMOylation dans le maintien de la biologie du centromère et la régulation du redémarrage des fourches de réplication chez Schizosaccharomyces pombe

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