Dynamic changes in chromatin accessibility and gene expression involved in fetal myogenesis of Min pigs

Abstract

Objective: Chinese fat-type pig breeds possess good meat quality, but their growth rate and lean meat percentage are not dominant. Investigating the dynamic transcriptional regulation of skeletal muscle development could help improve meat yield in these breeds. However, little is known about chromatin accessibility and its association with gene expression during prenatal skeletal muscle development in these pigs. Methods: ATAC-seq and RNA-seq were performed to profile chromatin accessibility and transcriptome in skeletal muscle at 45, 70, and 100 days post-coitus (E45, E75, and E100) from two male and two female full-sib fetuses of Min pig. Results: This study demonstrated that the majority of ATAC-seq peak signals were located within 3 kb of transcription start sites. Notably, a greater number of genes associated with differential peaks were observed in the E100 vs. E45 comparison, relative to the E70 vs. E45 and E100 vs. E75 comparisons. This finding was consistent with the RNA-seq data, where the E100 vs. E45 comparison also exhibited the highest number of differentially expressed genes. Gene Ontology analysis of the RNA-seq data demonstrated that genes involved in skeletal muscle contraction, muscle fiber development, and energy metabolism were up-regulated during fetal development, while those associated with cell cycle regulation and proliferation were down-regulated. Integration of ATAC-seq and RNA-seq data identified a few differentially expressed genes associated with chromatin accessibility, with the overlapping genes primarily related to cell proliferation in the early fetal stage and metabolism in later stages. Conclusion: This study provides significant insights into the molecular mechanisms underlying fetal skeletal muscle development in Min pigs.