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.

中文翻译：

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鸡盲肠 DNA 甲基化组对肠炎沙门氏菌接种反应的改变


肠炎沙门氏菌（SE）是影响家禽生产的致病菌之一，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 甲基化参与基因表达、染色质结构和基因组印记等调控过程。为了了解鸡对 SE 接种反应的甲基化调控，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 甲基化谱。对照组有185,362,463个干净读数和126,098,724个独特读数，接种组有180,530,750个干净读数和126,782,896个独特读数。基因体内甲基化密度高于基因上下游区域。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信号通路以及多种代谢相关通路显着富集。 miRNA中差异甲基化胞嘧啶的密度最高。 HOX基因被广泛甲基化。分析了鸡对 SE 接种反应的全基因组 DNA 甲基化谱。 SE接种促进了鸡盲肠中的DNA甲基化，并引起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发挥重要作用。 本文的研究结果将加深对鸡 SE 接种反应中表观遗传调控的理解。