Prediction of essential liver transcription factors in response to fat deposition in pigs based on changes in transposase-accessible chromatin signals

Abstract

Pigs have been altered throughout the decades to increase the meat content in their carcasses. However, this has led to a reduction in fat levels in subcutaneous, visceral, and intramuscular fats, where intramuscular fat is crucial for flavor. The current study used combined RNA-assay for transposase-accessible chromatin (ATAC) sequencing analysis to identify key transcription factors (TFs) that might regulate important molecular mechanisms associated with fat deposition in the livers of pigs. In this study, two native Złotnicka White pig groups were used that significantly differed in terms of their fat content. RNA-seq identified 272 genes as being differentially expressed (showing >1.2 fold change) and ATAC-seq identified 6333 significant peaks (differentially accessible regions [DARs]) in the transcription start site (TSS) flanking region. Ninety-eight genes overlapped between the RNA and ATAC seq results, and these differentially expressed genes–DARs were included in a subsequent motif analysis. The TRRUST and MEME tools were used to identify crucial TFs, which predicted possible binding TF motifs based on TSS ATAC peaks. The candidate TFs suggested in the present study for fat deposition in pigs are SREBP1, ATF4, KLF11, RORA, and MYC, whose DNA-binding motif sequence was enriched in DAR overlapping TSS. Moreover, for MYC, ATF4, and KLF11 TFs, DARs were identified within the TSS flanking regions. The present study aimed to pinpoint the key liver TFs that are indirectly related to fat deposition in pigs.