SynthesisNucleic acids research2022
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.
Synthesis in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Resolution of R-loops and transcription-replication conflicts by SETX-BRCA1-BARD1 complex.Nature structural & molecular biology · 2026Article
- Epitranscriptomic control of telomere maintenance.Molecular biology reports · 2026Review
- Integrative Analysis Reveals Conserved R-Loop Features in Mouse Embryonic Stem Cells.Epigenomes · 2026Article
- Alternative nucleic acid structures in microbial biology: regulatory functions and antimicrobial opportunities.Frontiers in cellular and infection microbiology · 2026Review
- Lamin A/C loss promotes R-loop-mediated genomic instability and poor survival in small-cell lung cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- 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
- An improved cytological assay for R-loop detection in Saccharomyces cerevisiae utilizing a catalytically inactive RNase H.G3 (Bethesda, Md.) · 2025Article
- Analysis of R-loop forming regions identifies RNU2-2 and RNU5B-1 as neurodevelopmental disorder genes.Nature genetics · 2025Article
- Enhancing R-loop prediction with high-throughput sequencing data.NAR genomics and bioinformatics · 2025Article
- Lamin A/C Deficiency Drives Genomic Instability and Poor Survival in Small-Cell Lung Cancer through Increased R-loop Accumulation.bioRxiv : the preprint server for biology · 2025Article
- Methods for constructing and evaluating consensus genomic interval sets.Nucleic acids research · 2024Article
- Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases.iScience · 2024Article
- Approaches for Mapping and Analysis of R-loops.Current protocols · 2024Review
- Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation.Communications biology · 2023Article
- Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization.Nucleic acids research · 2023Article
- Exploration and analysis of R-loop mapping data with RLBase.Nucleic acids research · 2023Article
- RLSuite: An Integrative R-Loop Bioinformatics Framework.Journal of bioinformatics and systems biology : Open access · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
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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.