Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford, OX3 7FY, UK.
Sci Rep. 2019 Feb 6;9(1):1510. doi: 10.1038/s41598-018-37618-z.
DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33-66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
DNA 甲基化在各种哺乳动物生物学过程中对基因表达模式的调控起着关键作用。牛肺泡巨噬细胞（bAM）转录组因感染牛分枝杆菌（M. bovis）而发生的改变已有大量文献记载；然而，这种细胞内病原体对 bAM 表观基因组的影响尚未确定。本研究采用全基因组亚硫酸氢盐测序（WGBS）来评估 M. bovis 感染对 bAM DNA 甲基化组的影响。将感染 M. bovis 的 bAM 与未感染的 bAM 在感染后 24 小时（hpi）的甲基化组进行比较。未观察到 DNA 甲基化（CpG 或非 CpG）的差异。对近端启动子区域的 DNA 甲基化分析揭示了 >250 个具有中等甲基化（IM）启动子的基因（平均甲基化率为 33-66%）。针对低、中、高甲基化启动子基因的基因本体论分析显示，具有 IM 启动子的基因富含与免疫相关的 GO 类别；而在高或低甲基化组中未观察到这种富集。对 IM 类基因的靶向分析证实了 WGBS 的观察结果。本研究是首次在牛中以单核苷酸分辨率检测重要的牛细胞宿主-病原体相互作用模型中的全基因组 DNA 甲基化，为 bAM 中的 IM 启动子甲基化提供了证据。
