Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans.

ABSTRACT: DNA topology and alternative DNA structures are implicated in regulating diverse biological processes. Although biomechanical properties of these structures have been studied extensively in vitro, characterization in vivo, particularly in multicellular organisms, is limited. We devised new methods to map DNA supercoiling and single-stranded DNA in Caenorhabditis elegans embryos and diapause larvae. To map supercoiling, we quantified the incorporation of biotinylated psoralen into DNA using high-throughput sequencing. To map single-stranded DNA, we combined permanganate treatment with genome-wide sequencing of induced double-stranded breaks. We found high levels of negative supercoiling at transcription start sites (TSSs) in embryos. GC-rich regions flanked by a sharp GC-to-AT

SUBMITTER: Krassovsky K 

PROVIDER: S-EPMC8256864 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature