Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.

ABSTRACT: The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approac

SUBMITTER: Yamada N 

PROVIDER: S-EPMC7672471 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature