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

Salavati, Mazdak and Woolley, Shernae A. and Cortés Araya, Yennifer and Halstead, Michelle M. and Stenhouse, Claire and Johnsson, Martin and Ashworth, Cheryl J. and Archibald, Alan L. and Donadeu, Francesc X. and Hassan, Musa A. and Clark, Emily L. (2022). Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3. 12 :2 , jkab424
[Research article]

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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.

Authors/Creators:Salavati, Mazdak and Woolley, Shernae A. and Cortés Araya, Yennifer and Halstead, Michelle M. and Stenhouse, Claire and Johnsson, Martin and Ashworth, Cheryl J. and Archibald, Alan L. and Donadeu, Francesc X. and Hassan, Musa A. and Clark, Emily L.
Title:Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
Series Name/Journal:G3
Year of publishing :2022
Volume:12
Number:2
Article number:jkab424
Number of Pages:18
Publisher:OXFORD UNIV PRESS INC
ISSN:2160-1836
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:ATAC-Seq, Sscrofa11, 1, RNA-Seq, frozen tissue, muscle
URN:NBN:urn:nbn:se:slu:epsilon-p-115140
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115140
Additional ID:
Type of IDID
DOI10.1093/g3journal/jkab424
Web of Science (WoS)000768242900012
ID Code:27711
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:05 May 2022 14:25
Metadata Last Modified:05 May 2022 14:31

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