Multi-tissue regulatory atlas maps sheep non-coding genome and links it to domestication traits

Researchers have posted a preprint on bioRxiv describing SheepEpimap, a comprehensive multi-tissue epigenomic resource for sheep (Ovis aries). The atlas integrates 516 CUT&Tag histone modification datasets, ATAC-seq chromatin accessibility profiling, and RNA-seq transcriptomic data across 43 adult tissues.

The resource annotates 2.93 million cis-regulatory elements — genomic regions outside protein-coding sequences that control when and where genes are active — and identifies 557,441 enhancer–gene pairs and 145,407 variants with allele-specific effects on regulatory activity. The team also trained a sequence-to-function deep-learning model to decode the base-pair-level determinants of chromatin accessibility, enabling prediction of the regulatory impact of sequence variants not directly measured in the atlas.

The authors apply the resource to questions of domestication genetics and economically important complex traits in sheep, linking specific non-coding variants and regulatory elements to phenotypes relevant to livestock production and breeding. The approach mirrors similar multi-tissue regulatory atlases developed for humans (GTEx, ENCODE) and cattle, extending this class of resource to a commercially significant small ruminant species.

SheepEpimap will be of primary interest to researchers in livestock genomics, comparative epigenomics, regulatory genomics, and the genetics of domestication. The work remains a preprint and has not yet undergone peer review.