ArticleGenes & development2016
S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation.
Article in Genes & development, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers, 2 of them syntheses that pooled it.
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Who cites it
190 citing papers in PubMed, 2 syntheses or guidelines pooled it, 286 citations in OpenAlex.
- An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops.Briefings in bioinformatics · 2022Pooled it
- Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.Nucleic acids research · 2022Pooled it
- RIAN-Seq: R-Loop Identification Assisted by Nuclease Digestion and High-Throughput Sequencing.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Genome-wide mapping reveals increased R-loops in topoisomerase III-beta-deficient human cells.iScience · 2026Article
- R-loops in colorectal cancer: mechanisms, mapping strategies, and therapeutic opportunities.Molecular biology reports · 2026Review
- Multi-omics dissection of R-loop dynamics in tumorigenesis: From transcription-replication conflict to therapeutic targets.Molecular therapy. Oncology · 2026Review
- Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases.bioRxiv : the preprint server for biology · 2026Article
- Stranded short nascent strand sequencing reveals the topology of DNA replication origins ineLife · 2026Article
- R-loops orchestrate RNAPII transcriptional reprogramming for the maternal-to-zygotic transition.Cell research · 2026Article
- Article
- An Orc1 initiator-specific motif (ISM)-related region limits ORC-ssDNA binding and promotes replication origin specificity in budding yeast.Frontiers in microbiology · 2026Article
- Emerging roles of RNA:DNA hybrid regulation by mammalian ribonuclease H2 in replication stress and cancer.Journal of cell science · 2025Review
- Evolutionary interplay between viruses and R-loops.FEBS letters · 2025Review
- Dual roles of DEAD-box RNA helicase Brr2 in genome stability regulation.Nature communications · 2025Article
- The paradox of R-loops: guardians of the genome or drivers of disease?Genome research · 2025Review
- The R-loop grammar predicts R-loop formation under different topological constraints.PLoS computational biology · 2025Article
- Update on R-loops in genomic integrity: Formation, functions, and implications for human diseases.Genes & diseases · 2025Review
- An improved cytological assay for R-loop detection in Saccharomyces cerevisiae utilizing a catalytically inactive RNase H.G3 (Bethesda, Md.) · 2025Article
- GPATCH4 functions as a regulator of nucleolar R-loops in hepatocellular carcinoma cells.Nucleic acids research · 2025Article
- High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations.Biomolecules · 2025Article
130 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.