Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids

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

(2021) Frédéric Chédin et al.   EMBO JOURNAL

qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide

(2020) Magdalena P Crossley et al.   NUCLEIC ACIDS RESEARCH

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

The mitochondrial R-loop

(2019) Ian J Holt   NUCLEIC ACIDS RESEARCH

RNases H: Structure and mechanism

(2019) Malwina Hyjek 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

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

(2019) Sonia Barroso et al.   EMBO REPORTS

CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing’s sarcoma

(2019) Nathan T. Ross et al.   Nature Chemical Biology

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

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

Dynamic regulation of nucleolar architecture

(2018) Attila Németh et al.   CURRENT OPINION IN CELL BIOLOGY

Spliceosomal components protect embryonic neurons from R-loop-mediated DNA damage and apoptosis

(2018) Shelly Sorrells et al.   Disease Models & Mechanisms

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

Interplay between RNASEH2 and MOV10 controls LINE-1 retrotransposition

(2018) Jongsu Choi et al.   NUCLEIC ACIDS RESEARCH

Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis

(2018) Mikael S. Lindström et al.   ONCOGENE

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

Human proteins that interact with RNA/DNA hybrids

(2018) Isabel X. Wang et al.   GENOME RESEARCH

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability

(2018) Sonia Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

(2017) Hai Dang Nguyen et al.   MOLECULAR CELL

Dynamic nucleoplasmic and nucleolar localization of mammalian RNase H1 in response to RNAP I transcriptional R-loops

(2017) Wen Shen et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Lilian Kabeche et al.   SCIENCE

Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin

(2017) Aleix Bayona-Feliu et al.   Nature Communications

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

(2017) Sreerama Chaitanya Sridhara et al.   Cell Reports

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

Nascent Connections: R-Loops and Chromatin Patterning

(2016) Frédéric Chédin   TRENDS IN GENETICS

RNA Polymerase III Regulates Cytosolic RNA:DNA Hybrids and Intracellular MicroRNA Expression

(2015) Christine Xing'er Koo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

RNA:DNA hybrids are a novel molecular pattern sensed by TLR9

(2014) R. E. Rigby et al.   EMBO JOURNAL

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

Human Eukaryotic Initiation Factor 2 (eIF2)-GTP-Met-tRNAiTernary Complex and eIF3 Stabilize the 43 S Preinitiation Complex

(2014) Masaaki Sokabe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

(2014) Vaibhav Bhatia et al.   NATURE

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

Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

(2014) Erick W. Loomis et al.   PLoS Genetics

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

(2013) Damilola D. Phillips et al.   JOURNAL OF MOLECULAR RECOGNITION

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

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

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

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL

SGNP: An Essential Stress Granule/Nucleolar Protein Potentially Involved in 5.8s rRNA Processing/Transport

(2008) Chun-Hong Zhu et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY