An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.

ABSTRACT: We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate withi

SUBMITTER: Yuan C 

PROVIDER: S-EPMC10691486 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature