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An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Source :
- Genome Research; 2023, Vol. 33 Issue: 10 p1848-1864, 17p
- Publication Year :
- 2023
-
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.
Details
- Language :
- English
- ISSN :
- 10889051 and 15495469
- Volume :
- 33
- Issue :
- 10
- Database :
- Supplemental Index
- Journal :
- Genome Research
- Publication Type :
- Periodical
- Accession number :
- ejs64444841
- Full Text :
- https://doi.org/10.1101/gr.277947.123