ArticleeLife2021
A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 46 citations in OpenAlex.
- Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.Nucleic acids research · 2022Pooled it
- Thymine DNA glycosylase binds to R-loops and excises 5-formyl and 5-carboxyl cytosine from DNA/RNA hybrids.The Journal of biological chemistry · 2026Article
- Integrative Analysis Reveals Conserved R-Loop Features in Mouse Embryonic Stem Cells.Epigenomes · 2026Article
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- The paradox of R-loops: guardians of the genome or drivers of disease?Genome research · 2025Review
- Genome-wide in vivo and ex vivo mapping of R-loops using engineered N-terminal hybrid-binding domain of RNase H3 (enDR3).Nucleic acids research · 2025Article
- Update on R-loops in genomic integrity: Formation, functions, and implications for human diseases.Genes & diseases · 2025Review
- TASOR expression in naive embryonic stem cells safeguards their developmental potential.Cell reports · 2024Article
- RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility.Nucleic acids research · 2024Article
- R-loops' m6A modification and its roles in cancers.Molecular cancer · 2024Review
- Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases.iScience · 2024Article
- Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization.Nature cell biology · 2024Review
- Approaches for Mapping and Analysis of R-loops.Current protocols · 2024Review
- ZFP281 controls transcriptional and epigenetic changes promoting mouse pluripotent state transitions via DNMT3 and TET1.Developmental cell · 2024Article
- TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk.Cell reports · 2024Article
- Review
- G-quadruplexes associated with R-loops promote CTCF binding.Molecular cell · 2023Article
- Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin.iScience · 2022Article
- spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity.Science advances · 2022Article
- TERRA regulates DNA G-quadruplex formation and ATRX recruitment to chromatin.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
R-loops are three-stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation is associated with genome instability and is observed in neurodevelopmental diseases and cancers. Genome-wide profiling of R-loops in normal and diseased cells can help identify locations of pathogenic R-loops and advance efforts to attenuate them. We present an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce genome-wide profiles that retain strand information. BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. In mouse embryonic stem cells, we apply BisMapR to find that gene promoters form R-loops in both directions and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.
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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.