Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs

• Published in: BMC genomics 2024-09, Vol.25 (1), p.902-13, Article 902
• Main Authors: Zhang, Zhe, Chang, Lebin, Wang, Bingjie, Wei, Yilin, Li, Xinjian, Li, Xiuling, Zhang, Yongqian, Wang, Kejun, Qiao, Ruimin, Yang, Feng, Yu, Tong, Han, Xuelei
• Format: Article
• Language: English
• Subjects: Accessibility; Adipocytes; Adipose Tissue - metabolism; Amino acids; Analysis; Animal husbandry; Animals; ATAC-seq; Backfat deposition; Bcl-2 protein; Bioinformatics; Body fat; Cell cycle; Cellular signal transduction; Chromatin; Chromatin - genetics; Chromatin - metabolism; Deposition; Diseases; DNA binding proteins; Duroc Pig; Energy metabolism; Epigenetics; ESR1 protein; Fatty acids; Fibroblast growth factor 1; Fibroblast growth factors; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Gene regulation; Gene sequencing; Genes; Genetic transcription; Genomes; High-Throughput Nucleotide Sequencing; Hogs; Lipid metabolism; Lipids; Livestock breeding; Meat quality; Mitochondrial uncoupling protein 2; Molecular modelling; Next-generation sequencing; Pork; Quality control; Regulatory mechanisms; Ribonucleic acid; RNA; RNA sequencing; RNA-Seq; Signal transduction; Smad3 protein; Software; Stat3 protein; Statistical significance; Swine; Swine - genetics; Tissue inhibitor of metalloproteinase 1; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transposase; Wnt protein; Yunong Black Pig
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10805-1

Backfat serves as a vital fat reservoir in pigs, and its excessive accumulation will adversely impact pig growth performance, farming efficiency, and pork quality. The aim of this research is to integrate assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to explore the molecular mechanisms underlying porcine backfat deposition. ATAC-seq analysis identified 568 genes originating from 698 regions exhibiting differential accessibility, which were significantly enriched in pathways pertinent to adipocyte differentiation and lipid metabolism. Besides, a total of 283 transcription factors (TFs) were identified by motif analysis. RNA-seq analysis revealed 978 differentially expressed genes (DEGs), which were enriched in pathways related to energy metabolism, cell cycle and signal transduction. The integration of ATAC-seq and RNA-seq data indicates that DEG expression levels are associated with chromatin accessibility. This comprehensive study highlights the involvement of critical pathways, including the Wnt signaling pathway, Jak-STAT signaling pathway, and fatty acid degradation, in the regulation of backfat deposition. Through rigorous analysis, we identified several candidate genes (LEP, CTBP2, EHHADH, OSMR, TCF7L2, BCL2, FGF1, UCP2, CCND1, TIMP1, and VDR) as potentially significant contributors to backfat deposition. Additionally, we constructed TF-TF and TF-target gene regulatory networks and identified a series of potential TFs related to backfat deposition (FOS, STAT3, SMAD3, and ESR1). This study represents the first application of ATAC-seq and RNA-seq, affording a novel perspective into the mechanisms underlying backfat deposition and providing invaluable resources for the enhancement of pig breeding programs.