Pig fetal skeletal muscle development is associated with genome-wide DNA hypomethylation and corresponding alterations in transcript and microRNA expression.

Publisher: Canadian Science Publishing Country of Publication: Canada NLM ID: 8704544 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1480-3321 (Electronic) Linking ISSN: 08312796 NLM ISO Abbreviation: Genome Subsets: MEDLINE

Publication: 2011- : Ottawa, ON : Canadian Science Publishing
Original Publication: Ottawa, Canada : National Research Council of Canada, c1987-

DNA Methylation* ; MicroRNAs*/genetics; Swine/genetics ; Animals ; Epigenesis, Genetic ; DNA ; Muscle Development/genetics

Fetal myogenesis represents a critical period of porcine skeletal muscle development and requires coordinated expression of thousands of genes. Epigenetic mechanisms, including DNA methylation, drive transcriptional regulation during development; however, these processes are understudied in developing porcine tissues. We performed bisulfite sequencing to assess DNA methylation in pig longissimus dorsi muscle at 41- and 70-days gestation (dg), as well as RNA- and small RNA-sequencing to identify coordinated changes in methylation and expression between myogenic stages. We identified 45 739 differentially methylated regions (DMRs) between stages, and the majority ( N  = 34 232) were hypomethylated at 70 versus 41 dg. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression. Differential miRNA methylation was significantly negatively correlated with abundance, and dynamic expression of assayed miRNAs persisted postnatally. Motif analysis revealed significant enrichment of myogenic regulatory factor motifs among hypomethylated regions, suggesting that DNA hypomethylation may function to increase accessibility of muscle-specific transcription factors. We show that developmental DMRs are enriched for GWAS SNPs for muscle- and meat-related traits, demonstrating the potential for epigenetic processes to influence phenotypic diversity. Our results enhance understanding of DNA methylation dynamics of porcine myogenesis and reveal putative cis -regulatory elements governed by epigenetic processes.

Keywords: longissimus dorsi muscle; DNA methylation; WGBS; microRNA; pig

0 (MicroRNAs)
9007-49-2 (DNA)

Date Created: 20230306 Date Completed: 20230404 Latest Revision: 20230404

20250114

10.1139/gen-2022-0008

36876850