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

Can Yuan, Lijing Tang, Thomas Lopdell, Vyacheslav A Petrov, Claire Oget-Ebrad, Gabriel Costa Monteiro Moreira, José Luis Gualdrón Duarte, Arnaud Sartelet, Zhangrui Cheng, Mazdak Salavati, D Claire Wathes, Mark A Crowe, Wouter Coppieters, Mathew Littlejohn, Carole Charlier, Tom Druet, Michel Georges*, Haruko Takeda, GplusE Consortium

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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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.

Original languageEnglish
Pages (from-to)1848-1864
Number of pages17
JournalGenome Research
Issue number10
Early online date26 Sept 2023
Publication statusPrint publication - Oct 2023
Externally publishedYes

Bibliographical note

© 2023 Yuan et al.; Published by Cold Spring Harbor Laboratory Press.


  • Animals
  • Cattle/genetics
  • Chromatin Immunoprecipitation Sequencing
  • High-Throughput Nucleotide Sequencing
  • Sequence Analysis, DNA
  • Chromatin/genetics
  • Regulatory Sequences, Nucleic Acid


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