TY  - JOUR
A1  - Yuan, Can
A1  - Tang, Lijing
A1  - Lopdell, Thomas
A1  - Petrov, Vyacheslav A.
A1  - Oget-Ebrad, Claire
A1  - Moreira, Gabriel Costa Monteiro
A1  - Gualdrón Duarte, José Luis
A1  - Sartelet, Arnaud
A1  - Cheng, Zhangrui
A1  - Salavati, Mazdak
A1  - Wathes, D. Claire
A1  - Crowe, Mark A.
A1  - GplusE Consortium
A1  - Coppieters, Wouter
A1  - Littlejohn, Mathew
A1  - Charlier, Carole
A1  - Druet, Tom
A1  - Georges, Michel
A1  - Takeda, Haruko
T1  - An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
Y1  - 2023/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1848 
EP  - 1864 
DO  - 10.1101/gr.277947.123 
VL  - 33 
IS  - 10 
UR  - http://genome.cshlp.org/content/33/10/1848.abstract 
N2  - 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. 
ER  -