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

Autor:	Yuan C; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Tang L; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Lopdell T; Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand., Petrov VA; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Oget-Ebrad C; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Moreira GCM; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Gualdrón Duarte JL; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Sartelet A; Clinical Department of Ruminant, University of Liège, 4000 Liège, Belgium., Cheng Z; Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom., Salavati M; Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom., Wathes DC; Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom., Crowe MA; School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland., Coppieters W; GIGA Genomics platform, GIGA Institute, University of Liège, 4000 Liège, Belgium., Littlejohn M; Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand., Charlier C; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Druet T; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium., Georges M; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; michel.georges@uliege.be., Takeda H; Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.
Jazyk:	angličtina
Zdroj:	Genome research [Genome Res] 2023 Oct; Vol. 33 (10), pp. 1848-1864. Date of Electronic Publication: 2023 Sep 26.
DOI:	10.1101/gr.277947.123
Abstrakt:	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. (© 2023 Yuan et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
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