Wang Yuanmei, Liu Liying, Li Min, Lin Lili, Su Pengcheng, Tang Hui, Fan Xinzhong, Li Xianyao
College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
College of Life Science, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
BMC Genomics. 2020 Nov 23;21(1):814. doi: 10.1186/s12864-020-07174-w.
Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study.
There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8946 differentially methylated genes (3639 hypo-methylated genes, 5307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated.
The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.
肠炎沙门氏菌（SE）是一种病原菌，影响家禽生产并对公众健康构成严重威胁。鸡肉和鸡蛋是人类沙门氏菌病的主要来源。DNA甲基化参与包括基因表达、染色质结构和基因组印记在内的调控过程。为了解鸡对SE接种反应中的甲基化调控，本研究通过全基因组亚硫酸氢盐测序分析了SE接种后的全基因组DNA甲基化图谱。
对照组有185,362,463条clean reads和126,098,724条唯一reads，接种组有180,530,750条clean reads和126,782,896条唯一reads。基因体内的甲基化密度高于基因上游和下游区域。接种组和对照组之间获得了8946个差异甲基化基因（3639个低甲基化基因，5307个高甲基化基因）。甲基化基因主要富集在免疫相关的基因本体（GO）术语和代谢过程术语中。细胞因子-细胞因子受体相互作用、TGF-β信号通路、FoxO信号通路、Wnt信号通路和几个代谢相关通路显著富集。miRNA中差异甲基化胞嘧啶的密度最高。HOX基因广泛甲基化。
分析了鸡对SE接种反应中的全基因组DNA甲基化图谱。SE接种促进了鸡盲肠中的DNA甲基化，并导致免疫和代谢相关基因的甲基化改变。Wnt信号通路、miRNA和HOX基因家族可能在鸡SE接种的甲基化调控中起关键作用。本文的研究结果将加深对鸡对SE接种反应中表观遗传调控的理解。
