猪背膘沉积相关的染色质可及性和基因表达的差异。

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

机构信息

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.

Sanya Institute, Hainan Academy of Agricultural Science, Sanya, 572025, China.

出版信息

BMC Genomics. 2024 Sep 30;25(1):902. doi: 10.1186/s12864-024-10805-1.

DOI:10.1186/s12864-024-10805-1

PMID:39349998

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11441165/

Abstract

BACKGROUND

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.

RESULTS

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).

CONCLUSIONS

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.

摘要

背景

背脂是猪重要的脂肪储备库，其过度积累会对猪的生长性能、养殖效率和猪肉质量产生不利影响。本研究旨在整合转座酶可及染色质与高通量测序（ATAC-seq）和 RNA 测序（RNA-seq），以探讨猪背脂沉积的分子机制。

结果

ATAC-seq 分析鉴定了 568 个基因，这些基因来源于 698 个差异可及区域，这些区域在脂肪细胞分化和脂质代谢相关途径中显著富集。此外，通过 motif 分析鉴定了总共 283 个转录因子（TFs）。RNA-seq 分析揭示了 978 个差异表达基因（DEGs），这些基因在与能量代谢、细胞周期和信号转导相关的途径中富集。ATAC-seq 和 RNA-seq 数据的整合表明，DEG 的表达水平与染色质可及性相关。这项综合研究强调了关键途径的参与，包括 Wnt 信号通路、Jak-STAT 信号通路和脂肪酸降解，在调节背脂沉积中的作用。通过严格的分析，我们鉴定了几个候选基因（LEP、CTBP2、EHHADH、OSMR、TCF7L2、BCL2、FGF1、UCP2、CCND1、TIMP1 和 VDR）作为潜在的背脂沉积的重要贡献者。此外，我们构建了 TF-TF 和 TF-靶基因调控网络，并鉴定了一系列与背脂沉积相关的潜在 TF（FOS、STAT3、SMAD3 和 ESR1）。