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

Abstract

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

CLC Number:

S831.2

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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Study on Genome-wide Methylation Difference and Its Effect on Liver Transcriptome in Chickens During Pre-laying and Peak-laying Periods

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