产蛋前期和产蛋高峰期鸡全基因组甲基化差异及其对肝脏转录组影响的研究

doi:10.11843/j.issn.0366-6964.2022.09.007

摘要/Abstract

摘要： 旨在通过对产蛋前期和产蛋高峰期鸡肝全基因组甲基化差异进行分析，解析基因组甲基化对不同发育阶段肝中基因表达差异的影响。本研究采用全基因组重亚硫酸盐测序（WGBS）技术对产蛋前期（20周龄）和产蛋高峰期（30周龄，各3只DNA混池）卢氏绿壳蛋鸡肝全基因组的甲基化水平进行检测，并与已有的肝mRNA转录组数据进行整合分析，探讨基因组甲基化对不同生理阶段基因表达差异的影响。结果表明，全基因组范围约有4%的胞嘧啶（C）发生了甲基化（mC）；两个生理阶段的总体甲基化水平基本一致。共检测到670个差异甲基化区域（DMRs）和356个差异甲基化基因（DMGs）。基因本体（GO）和相关信号通路（KEGG）分析发现，超甲基化DMGs显著富集在发育的正向调控、细胞形态改变的调控、VEGF信号通路、肌动蛋白细胞骨架的调控、粘着斑及间隙连接等相关过程，低甲基化DMGs显著富集在胚胎消化道形态的发生、间充质细胞增殖的正向调控、淀粉和蔗糖代谢及Wnt信号通路等相关过程。基因不同功能区域甲基化水平与基因表达水平有关，启动子（promoter）及基因体（gene body）区域甲基化水平与基因表达水平呈显著负相关，其他区域（内含子、3'UTR）的甲基化水平与基因的表达水平无明显关系。其中，与肝脂质代谢相关的候选基因RASD1、HAO1、UBE2O、MSRB3受甲基化调控。本研究绘制了不同生理时期卢氏绿壳蛋鸡全基因组甲基化图谱，结合mRNA转录组数据阐述了DNA甲基化在基因表达方面的调控作用，并鉴定出了不同生理时期受甲基化调控的基因，为深入研究表观遗传调控在不同生理时期蛋鸡肝代谢中的作用机制提供参考。

关键词: 卢氏绿壳蛋鸡, 肝, 全基因组甲基化, 转录组, 脂质代谢

Abstract: The objective of this study was to investigate the effect of genomic methylation on the difference of gene expression in liver at different developmental stages through the analysis of the genome-wide methylation difference in liver between pre-laying and peak-laying hens. In this study, genomic DNA (DNA pools of 3 in each group) isolated from livers of Lushi blue-shelled hens in pre-laying (20-week-old) and peak-laying (30-week-old) were scanned by whole genome bisulfite sequencing (WGBS) method for genome-wide methylation analysis. Integrative analysis of pre-existing liver mRNA transcriptome data and the WGBS data were conducted to explore the effect of genomic methylation on gene expression differences at different physiological stages. The results showed that about 4% cytosine (C) were methylated(mC) in the whole genome. The overall methylation level of two physiological stages was basically the same. A total of 670 differentially methylated regions (DMRs) and 356 related differentially methylated genes (DMGs) were detected. The gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses revealed that hypermethylated DMGs were significantly enriched in positive regulation of growth, regulation of cell morphogenesis, VEGF signaling pathway, regulation of actin cytoskeleton, focal adhesion and gap junction etc, while hypomethylated DMGs were significantly enriched in embryonic digestive tract morphogenesis, positive regulation of mesenchymal cell proliferation, starch and sucrose metabolism, Wnt signaling pathway etc. The methylation levels in different functional regions of genes were correlated with gene expression levels. The methylation levels in the promoter and gene body regions of genes were significantly negatively correlated with gene expression levels, the methylation levels in the other regions (intron, 3' UTR) of genes were not obviously correlated with gene expression levels. In addition, 4 candidate genes, RASD1, HAO1, UBE2O and MSRB3, related to liver lipid metabolism were regulated by methylation. This study provided the genome-wide methylation atlas of Lushi blue-shelled hens at different physiological periods. The role of DNA methylation in regulating gene expression was illustrated with mRNA transcriptome data, and genes regulated by methylation in different physiological periods were identified. The results provided reference information for the epigenetic regulation mechanism on liver metabolism at different physiological stages in laying hens.

Key words: Lushi blue-shelled hens, liver, genome-wide methylation, transcriptome, lipid metabolism

中图分类号:

S831.2

郭玉龙, 职毅豪, 李欣妍, 董佳佳, 李转见, 田亚东, 李红, 刘小军. 产蛋前期和产蛋高峰期鸡全基因组甲基化差异及其对肝脏转录组影响的研究[J]. 畜牧兽医学报, 2022, 53(9): 2888-2899.

GUO Yulong, ZHI Yihao, LI Xinyan, DONG Jiajia, LI Zhuanjian, TIAN Yadong, LI Hong, LIU Xiaojun. Study on Genome-wide Methylation Difference and Its Effect on Liver Transcriptome in Chickens During Pre-laying and Peak-laying Periods[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2888-2899.

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