Nayan Varij, Singh Kalpana, Iquebal Mir Asif, Jaiswal Sarika, Bhardwaj Anuradha, Singh Chhama, Bhatia Tanvi, Kumar Sunil, Singh Rakshita, Swaroop M N, Kumar Rajesh, Phulia S K, Bharadwaj Anurag, Datta T K, Rai Anil, Kumar Dinesh
ICAR-Central Institute for Research on Buffaloes, Hisar, India.
Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India.
Front Genet. 2022 Mar 15;13:828292. doi: 10.3389/fgene.2022.828292. eCollection 2022.
Subclinical mastitis (SCM) in buffalo is one of the most challenging paradoxes for the dairy sector with very significant milk production losses and poses an imminent danger to milch animal's milk-producing ability. We present here the genome-wide methylation specific to SCM in water buffalo and its consequential effect on the gene expression landscape for the first time. Whole-genome DNA methylation profiles from peripheral blood lymphocytes and gene expression profiles from milk somatic cells of healthy and SCM cases were catalogued from the MeDIP-Seq and RNA-Seq data. The average methylation in healthy buffaloes was found to be higher than that in the SCM-infected buffaloes. DNA methylation was abundant in the intergenic region followed by the intronic region in both healthy control and SCM groups. A total of 3,950 differentially methylated regions (DMRs) were identified and annotated to 370 differentially methylated genes (DMGs), most of which were enriched in the promoter region. Several important pathways were activated due to hypomethylation and belonged to the infection, Th17 cell differentiation, and antigen processing and presentation pathways along with others of defense responses. DNA methylome was compared with transcriptome to understand the regulatory role of DNA methylation on gene expression specific to SCM in buffaloes. A total of 4,778 significant differentially expressed genes (DEGs) were extracted in response to SCM, out of which 67 DMGs were also found to be differentially expressed, suggesting that during SCM, DNA methylation could be one of the epigenetic regulatory mechanisms of gene expression. Genes like CSF2RB, LOC102408349, C3 and PZP like, and CPAMD8 were found to be downregulated in our study, which are known to be involved in the immune response to SCM. Association of DNA methylation with transposable elements, miRNAs, and lncRNAs was also studied. The present study reports a buffalo SCM web resource (BSCM2TDb) available at http://webtom.cabgrid.res.in/BSCM2TDb that catalogues all the mastitis-related information of the analyses results of this study in a single place. This will be of immense use to buffalo researchers to understand the host-pathogen interaction involving SCM, which is required in endeavors of mastitis control and management.
水牛亚临床型乳腺炎（SCM）是乳制品行业最具挑战性的难题之一，会造成非常严重的产奶量损失，并对泌乳动物的产奶能力构成迫在眉睫的威胁。我们首次在此展示了水牛SCM特有的全基因组甲基化及其对基因表达图谱的后续影响。从甲基化DNA免疫沉淀测序（MeDIP-Seq）和RNA测序（RNA-Seq）数据中梳理出健康和SCM病例外周血淋巴细胞的全基因组DNA甲基化谱以及乳体细胞的基因表达谱。发现健康水牛的平均甲基化水平高于感染SCM的水牛。在健康对照组和SCM组中，基因间区域的DNA甲基化最为丰富，其次是内含子区域。共鉴定出3950个差异甲基化区域（DMR），并注释到370个差异甲基化基因（DMG），其中大部分富集在启动子区域。由于低甲基化激活了几个重要途径，这些途径属于感染、Th17细胞分化、抗原加工和呈递途径以及其他防御反应途径。将DNA甲基化组与转录组进行比较，以了解DNA甲基化对水牛SCM特异性基因表达的调控作用。共提取出4778个响应SCM的显著差异表达基因（DEG），其中67个DMG也被发现差异表达，这表明在SCM期间，DNA甲基化可能是基因表达的表观遗传调控机制之一。在我们的研究中，发现CSF2RB、LOC102408349、C3和PZP样以及CPAMD8等基因表达下调，已知它们参与对SCM的免疫反应。还研究了DNA甲基化与转座元件、微小RNA（miRNA）和长链非编码RNA（lncRNA）的关联。本研究报告了一个水牛SCM网络资源（BSCM2TDb），可在http://webtom.cabgrid.res.in/BSCM2TDb获取，该资源将本研究分析结果中所有与乳腺炎相关的信息集中编目在一处。这将对水牛研究人员深入了解涉及SCM的宿主-病原体相互作用有极大帮助，而这在乳腺炎控制和管理工作中是必需的。
