An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Genome Research Year : 2023

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 within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.

Dates and versions

hal-04562841 , version 1 (29-04-2024)

Identifiers

Cite

Can Yuan, Lijing Tang, Thomas Lopdell, Vyacheslav Petrov, Claire Oget-Ebrad, et al.. An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants. Genome Research, 2023, 33 (10), pp.1848-1864. ⟨10.1101/gr.277947.123⟩. ⟨hal-04562841⟩
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