ArticleNucleic acids research2019
The extruded non-template strand determines the architecture of R-loops.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids.The EMBO journal · 2026Article
- Type III CRISPR-Cas systems preferentially acquire spacers from early-expressed phage genes in a transcription-dependent manner.Nucleic acids research · 2026Article
- Evolutionary interplay between viruses and R-loops.FEBS letters · 2025Review
- Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery.Nucleic acids research · 2025Article
- Beyond the Synapse:International journal of molecular sciences · 2024Review
- Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding.PLoS computational biology · 2024Article
- DNA strand breaks at centromeres: Friend or foe?Seminars in cell & developmental biology · 2024Review
- Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures.DNA repair · 2023Review
- PARP1 associates with R-loops to promote their resolution and genome stability.Nucleic acids research · 2023Article
- Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids.Nature structural & molecular biology · 2023Article
- Unique properties of spacer acquisition by the type III-A CRISPR-Cas system.Nucleic acids research · 2022Article
- Article
- The role of B cells in the development, progression, and treatment of lymphomas and solid tumors.Advances in immunology · 2022Review
- Telomere Interacting Proteins and TERRA Regulation.Frontiers in genetics · 2022Review
- Article
- Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods.Journal of visualized experiments : JoVE · 2021Article
- Genome-wide mapping reveals R-loops associated with centromeric repeats in maize.Genome research · 2021Article
- Budding yeast Rap1, but not telomeric DNA, is inhibitory for multiple stages of DNA replication in vitro.Nucleic acids research · 2021Article
- Best practices for the visualization, mapping, and manipulation of R-loops.The EMBO journal · 2021Review
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Authors and funding
9 authors.
Funding
Abstract
Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.
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