Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

Abstract

There is very little species-specific information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-seq)’ to profile regions of open chromatin in flash frozen pig muscle tissue samples. This protocol has allowed us to identify putative regulatory regions in semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. The ATAC-Seq data were mapped to Sscrofa11.1 with Bowtie2 and Genrich were used for post-alignment peak-calling. Of the 4661 putative regions of accessible chromatin identified, >50% were within 1 kb of known transcription start sites. The size of each open chromatin region varied according to the developmental time point. At day 90 of gestation, we investigated chromatin openness relative to foetal piglet size. In parallel we measured genome-wide gene expression and allele-specific expression using RNA-Seq analysis of the same muscle samples. We found regions of open chromatin associated with down regulation of genes involved in muscle development in small sized foetal piglets. The dataset that we have generated here provides: i) a resource for studies of genome regulation in pigs, and ii) contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes. Future work could leverage the ATAC-Seq data with very large datasets of genetic variants from phenotyped pigs. This approach could inform chromatin aware genomic prediction models and determine whether regions of open chromatin are enriched for trait-linked variants, and especially for muscle and meat traits.