3,211 results found
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

    Jason G Dumelie, Samie R Jaffrey
    Genome-wide profiling of R-loops at near single-nucleotide resolution reveals distinct R-loop boundaries depending on the presence and location of the first exon-intron junction.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops

    Inigo Urrutia-Irazabal et al.
    RNA polymerase recruits the PcrA DNA helicase via a conserved interaction motif in order to remove R-loops and prevent conflicts with replication.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide

    Phillip Wulfridge, Kavitha Sarma
    BisMapR reveals strand-specific R-loops with high resolution at small-scale genomic features including bidirectionally transcribed promoters and enhancers.
    1. Chromosomes and Gene Expression

    Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

    Caroline Townsend Stork et al.
    The transcriptional response elicited by the hormone estrogen leads to DNA double-strand breaks by promoting R-loop formation in breast cancer cells.
    1. Biochemistry and Chemical Biology

    CRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks

    Joshua C Cofsky et al.
    The DNA flanks on either side of an R-loop differ in stability, and CRISPR-Cas12 enzymes form double-strand breaks by targeting the more unstable flank with their single DNase active site.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

    Charanya Kumar et al.
    Reconstitution of orientation-specific R-loop-replisome collisions with purified proteins reveals the differential impact of R-loop-associated RNA:DNA hybrids and G-quadruplexes on replication fork progression.
    1. Chromosomes and Gene Expression

    RNase H enables efficient repair of R-loop induced DNA damage

    Jeremy D Amon, Douglas Koshland
    In addition to causing DNA damage, R-loops cause genomic instability by interfering with DNA repair.
    1. Structural Biology and Molecular Biophysics

    Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA

    Ruobo Zhou et al.
    Analyzing single molecules reveals that Pif1 family helicases periodically patrol DNA, which may explain this enzyme's ability to suppress genome instability at G-quadruplex motifs and transcriptional RNA-DNA hybrids (R-loops).
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

    Nodar Makharashvili et al.
    The CtIP DNA repair enzyme is required for the removal of transcription-associated lesions in eukaryotic cells.
    1. Chromosomes and Gene Expression

    High-resolution, genome-wide mapping of positive supercoiling in chromosomes

    Monica S Guo et al.
    GapR-seq enables the global mapping of positive supercoiling in bacteria and yeast, revealing positive supercoils downstream of highly expressed genes and, in yeast, associated with centromeres, pericentromeres, telomeres, replication origins, and R-loops.

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