ArticleScience advances2022
spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity.
Article in Science advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 24 citations in OpenAlex.
- R-loops in colorectal cancer: mechanisms, mapping strategies, and therapeutic opportunities.Molecular biology reports · 2026Review
- R-loops and D-loops: a delicate balance in genomic stability and instability.Cell communication and signaling : CCS · 2026Review
- R-loop homeostasis at transposable elements safeguards transcriptional silencing in replication-quiescent oocytes.Nature communications · 2026Article
- Emerging roles of RNA:DNA hybrid regulation by mammalian ribonuclease H2 in replication stress and cancer.Journal of cell science · 2025Review
- The paradox of R-loops: guardians of the genome or drivers of disease?Genome research · 2025Review
- Tandem ssDNA in neutrophil extracellular traps binds thrombin and regulates immunothrombosis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- N 2-Alkyl-dG lesions elicit R-loop accumulation in the genome.Nucleic acids research · 2024Article
- Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq.Nature communications · 2024Article
- Nono induces Gadd45b to mediate DNA repair.Life science alliance · 2024Article
- Article
- Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization.Nature cell biology · 2024Review
- Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts.Nucleic acids research · 2024Article
- Exploring transient global transcriptional changes induced by ascorbic acid revealed via atKAS-seq profiling.Functional & integrative genomics · 2024Article
- Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics.Nucleic acids research · 2023Article
- Detection of alternative DNA structures and its implications for human disease.Molecular cell · 2023Review
- Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.The Journal of biological chemistry · 2023Review
- Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease.Life science alliance · 2023Article
- KAS-Analyzer: a novel computational framework for exploring KAS-seq data.Bioinformatics advances · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
R-loops affect transcription and genome stability. Dysregulation of R-loops is related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive ribonuclease H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq) to map R-loops by taking advantage of the presence of a ssDNA in the triplex structure. We show that spKAS-seq detects R-loops and their dynamics at coding sequences, enhancers, and other intergenic regions with as few as 50,000 cells. A joint analysis of R-loops and chromatin-bound RNA binding proteins (RBPs) suggested that R-loops can be RBP binding hotspots on the chromatin.
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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.