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Research article - Peer-reviewed, 2022

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

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


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.


ATAC-Seq; Sscrofa11; 1; RNA-Seq; frozen tissue; muscle

Published in

2022, volume: 12, number: 2, article number: jkab424

Authors' information

Salavati, Mazdak
University of Edinburgh
Woolley, Shernae A.
University of Edinburgh
Cortés Araya, Yennifer
University of Edinburgh
Halstead, Michelle M.
University of California Davis (UC Davis)
Stenhouse, Claire
University of Edinburgh
University of Edinburgh
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Ashworth, Cheryl J.
University of Edinburgh
Archibald, Alan L.
Univ Edinburgh
Donadeu, Francesc X.
University of Edinburgh
Hassan, Musa A.
University of Edinburgh
Clark, Emily L.
University of Edinburgh

UKÄ Subject classification

Genetics and Breeding

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