Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Background: A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. Results Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements, which were associated with tissue-relevant biological function. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible TEs. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle. Conclusions Our data provides a novel multi-tissue accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue specific and conserved biological function, as well as regulatory variants underlying variation in complex traits associated loci in pigs.