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

Mazdak Salavati,Alan L Archibald,Shernae A Woolley,Claire Stenhouse,Martin Johnsson,Emily L Clark,Michelle M Halstead,Francesc X Donadeu,Cheryl J Ashworth,Musa A Hassan,Yennifer Cortés Araya,J Holland

doi:10.1093/g3journal/jkab424

Abstract

There is very little 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 programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen 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. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.

Highlights

The domestic pig (Sus scrofa) is a hugely important farmed animal species globally, contributing a source of healthy animal protein to feed the growing human population
Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites
We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation

Summary

Introduction

The domestic pig (Sus scrofa) is a hugely important farmed animal species globally, contributing a source of healthy animal protein to feed the growing human population. There is very little species-specific information about how the genome is regulated in domestic pigs. This lack of knowledge hinders efforts to identify causative variants for complex traits, and a better knowledge of genome regulation might improve genomic prediction in breeding programs. To address this knowledge gap, we aim to identify regulatory sequences in the pig genome, starting with regions of open chromatin

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