Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

作     者：Mengqi Wang Nathalie Bissonnette Mario Laterriere Pier‑Luc Dudemaine David Gagne Jean‑Philippe Roy Xin Zhao Marc‑Andre Sirard Eveline M.Ibeagha‑Awemu Mengqi Wang;Nathalie Bissonnette;Mario Laterrière;Pier-Luc Dudemaine;David Gagné;Jean-Philippe Roy;Xin Zhao;Marc-André Sirard;Eveline M.Ibeagha-Awemu

作者机构：Sherbrooke Research and Development CentreAgriculture and Agri-Food CanadaSherbrookeQuebecCanada Department of Animal ScienceLaval UniversityQuebecQuebecCanada Quebec Research and Development CentreAgriculture and Agri-Food CanadaQuebecQuebecCanada Department of Clinical SciencesUniversite de MontrealSt‑HyacintheQuebecCanada Department of Animal ScienceMcGill UniversitySte‑Anne‑De‑BellevueQuebecCanada. 

出 版 物：《Journal of Animal Science and Biotechnology》 (畜牧与生物技术杂志（英文版）)

年 卷 期：2023年第14卷第2期

页      面：593-613页

核心收录：

学科分类：090603[农学-临床兽医学] 09[农学] 0906[农学-兽医学] 

基　　金：provided by Agriculture and Agri-Food Canada 

主　　题：Discriminant biomarkers Gene expression Genome‑wide DNA methylation pattern Immune processes and pathways Methylation haplotype block Milk somatic cell Streptococcus uberis Subclinical mastitis 

摘      要：Background:Mastitis caused by different pathogens including Streptococcus uberis(***)is responsible for huge economic losses to the dairy *** order to investigate the potential genetic and epigenetic regulatory mecha‑nisms of subclinical mastitis due to ***,the DNA methylome(whole genome DNA methylation sequencing)and transcriptome(RNA sequencing)of milk somatic cells from cows with naturally occurring *** subclinical mastitis and healthy control cows(n=3/group)were ***:Globally,the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and *** DNA methylation levels at the promoter,first exon and first intron regions were nega‑tively correlated with the expression level of genes at a whole‑genome‑wide *** general,DNA methylation level was lower in ***‑positive group(SUG)than in the control group(CTG).A total of 174,342 differentially methylated cytosines(DMCs)(FDR0.05)were identified between SUG and CTG,including 132,237,7412 and 34,693 DMCs in the context of CpG,CHG and CHH(H=A or T or C),***,101,612 methylation haplotype blocks(MHBs)were identified,including 451 MHBs that were significantly different(dMHB)between the two groups.A total of 2130 differentially expressed(DE)genes(1378 with up‑regulated and 752 with down‑regulated expression)were found in *** of methylome and transcriptome data with MethGET program revealed 1623 genes with signifi‑cant changes in their methylation levels and/or gene expression changes(MetGDE genes,MethGET P‑value0.001).Functional enrichment of genes harboring≥15 DMCs,DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to *** infection,especially cytokine ***,discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers,including 6 DE genes,15 CpG‑DMCs and 5 dMHBs that discrimina