Table2_Genome-Wide DNA Methylation Profile in Jejunum Reveals the Potential Genes Associated With Paratuberculosis in Dairy Cattle.XLSX

Paratuberculosis in cattle causes substantial economic losses to the dairy industry. Exploring functional genes and corresponding regulatory pathways related to resistance or susceptibility to paratuberculosis is essential to the breeding of disease resistance in cattle. Co-analysis of genome-wide DNA methylation and transcriptome profiles is a critically important approach to understand potential regulatory mechanism underlying the development of diseases. In this study, we characterized the profiles of DNA methylation of jejunum from nine Holstein cows in clinical, subclinical, and healthy groups using whole-genome bisulfite sequencing (WGBS). The average methylation level in functional regions was 29.95% in the promoter, 29.65% in the 5’ untranslated region (UTR), 68.24% in exons, 71.55% in introns, and 72.81% in the 3’ UTR. A total of 3,911, 4,336, and 4,094 differentially methylated genes (DMGs) were detected in clinical vs. subclinical, clinical vs. healthy, and subclinical vs. healthy comparative group, respectively. Gene ontology (GO) and analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DMGs were significantly enriched in specific biological processes related to immune response, such as Th1 and Th2 cell differentiation, wnt, TNF, MAPK, ECM-receptor interaction, cellular senescence, calcium, and chemokine signaling pathways (q value <0.05). The integration of information about DMGs, differentially expressed genes (DEGs), and biological functions suggested nine genes CALCRL, TNC, GATA4, CD44, TGM3, CXCL9, CXCL10, PPARG, and NFATC1 as promising candidates related to resistance/susceptibility to Mycobacterium avium subspecies paratuberculosis (MAP). This study reports on the high-resolution DNA methylation landscapes of the jejunum methylome across three conditions (clinical, subclinical, and healthy) in dairy cows. Our investigations integrated different sources of information about DMGs, DEGs, and pathways, enabling us to find nine functional genes that might have potential application in resisting paratuberculosis in dairy cattle.

牛副结核病对乳制品行业造成了巨额经济损失。探索与牛副结核病抗性或易感性相关的功能基因及其调控通路，对于开展牛抗病育种工作至关重要。全基因组DNA甲基化与转录组联合分析，是解析疾病发生潜在调控机制的关键手段。本研究采用全基因组亚硫酸氢盐测序（whole-genome bisulfite sequencing, WGBS）技术，对临床型、亚临床型及健康三组共9头荷斯坦奶牛的空肠组织DNA甲基化谱进行了表征分析。功能区域的平均甲基化水平分别为：启动子区29.95%、5'非翻译区（5' untranslated region, UTR）29.65%、外显子区68.24%、内含子区71.55%以及3'非翻译区（3' UTR）72.81%。在临床型vs亚临床型、临床型vs健康型、亚临床型vs健康型三个比较组中，分别检测到3911、4336和4094个差异甲基化基因（differentially methylated genes, DMGs）。基因本体（Gene Ontology, GO）及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析结果显示，这些差异甲基化基因显著富集于与免疫应答相关的特定生物学过程，包括Th1与Th2细胞分化、Wnt、TNF、MAPK、细胞外基质-受体相互作用、细胞衰老、钙信号及趋化因子信号通路等（q值<0.05）。通过整合差异甲基化基因、差异表达基因（differentially expressed genes, DEGs）及生物学功能相关信息，本研究筛选出CALCRL、TNC、GATA4、CD44、TGM3、CXCL9、CXCL10、PPARG及NFATC1这9个基因，它们均为与鸟分枝杆菌副结核亚种（Mycobacterium avium subspecies paratuberculosis, MAP）感染的抗性/易感性相关的潜在候选基因。本研究构建了奶牛空肠甲基化组在三种状态（临床型、亚临床型及健康型）下的高分辨率DNA甲基化图谱。本研究通过整合差异甲基化基因、差异表达基因及信号通路的多源信息，最终筛选出9个功能基因，其在奶牛抗副结核病育种中具备潜在应用价值。