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

文献类型： 外文期刊

第一作者： Zhang, Zhe

作者： Zhang, Zhe;Chang, Lebin;Wang, Bingjie;Wei, Yilin;Li, Xinjian;Li, Xiuling;Wang, Kejun;Qiao, Ruimin;Yang, Feng;Yu, Tong;Han, Xuelei;Li, Xinjian;Zhang, Yongqian

作者机构：

关键词： ATAC-seq; RNA-seq; Backfat deposition; Regulatory mechanisms; Yunong Black Pig; Duroc Pig

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2024 年 25 卷 1 期

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收录情况： SCI

摘要： BackgroundBackfat 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.ResultsATAC-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).ConclusionsThis 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.

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