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Genome-Wide DNA Methylation and Its Effect on Gene Expression During Subclinical Mastitis in Water Buffalo

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Title Genome-Wide DNA Methylation and Its Effect on Gene Expression During Subclinical Mastitis in Water Buffalo
Not Available
 
Creator Varij Nayan
Kalpana Singh
Mir Asif Iquebal
Sarika Jaiswal
Anuradha Bhardwaj
Chhama Singh
Tanvi Bhatia
Sunil Kumar
Rakshita Singh
M. N. Swaroop
Rajesh Kumar
S. K. Phulia
Anurag Bharadwaj
T. K. Datta
Anil Rai
Dinesh Kumar
 
Subject water buffalo
subclinical mastitis
DNA methylation
gene expression
web resource
 
Description Not Available
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 Staphylococcus aureus 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.
Not Available
 
Date 2022-03-19T08:31:29Z
2022-03-19T08:31:29Z
2022-03-15
 
Type Research Paper
 
Identifier Nayan V, Singh K, Iquebal MA, Jaiswal S, Bhardwaj A, Singh C, Bhatia T, Kumar S, Singh R, Swaroop MN, Kumar R, Phulia SK, Bharadwaj A, Datta TK, Rai A and Kumar D (2022) Genome-Wide DNA Methylation and Its Effect on Gene Expression During Subclinical Mastitis in Water Buffalo. Front. Genet. 13:828292. doi: 10.3389/fgene.2022.828292
Not Available
http://krishi.icar.gov.in/jspui/handle/123456789/70367
 
Language English
 
Relation Not Available;
 
Publisher Not Available