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BMC Genomics

, 18:405

Non-human and non-rodent vertebrate genomics


BackgroundDifferences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 TLR4 pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide LPS. Age-dependent differences in IL-8 production are abolished by treatment with 5-aza-2-deoxycytidine and Trichostatin A AZA-TSA, suggesting epigenetic regulation of the innate response to LPS. In the current study, we performed reduced representation bisulfite sequencing RRBS on fibroblast cultures isolated from the same animals at 5- and 16-months of age to identify genes that exhibit variable methylation with age. To validate the role of methylation in gene expression, six innate response genes that were hyper-methylated in young animals were assessed by RT-qPCR in fibroblasts from animals at different ages and from different breeds.

ResultsWe identified 14,094 differentially methylated CpGs DMCs that differed between fibroblast cultures at 5- versus 16-months of age. Of the 5065 DMCs that fell within gene regions, 1117 were located within promoters, 1057 were within gene exons and 2891 were within gene introns and 67% were more methylated in young cultures. Transcription factor enrichment of the promoter regions hyper-methylated in young cultures revealed significant regulation by the key pro-inflammatory regulator, NF-κB. Additionally, five out of six chosen genes PIK3R1, FES, NFATC1, TNFSF13 and RORA that were more methylated in young cultures showed a significant reduction in expression post-LPS treatment in comparison with older cultures. Two of these genes, FES and NFATC1, were similarly down-regulated in Angus cultures that also exhibit a low LPS response phenotype.

ConclusionsOur study has identified immune-related loci regulated by DNA methylation in cattle that may contribute to differential cellular response to LPS, two of which exhibit an identical expression profile in both low-responding age and breed phenotypes. Methylation biomarkers of differential immunity may prove useful in developing selection strategies for replacement cows that are less susceptible to severe infections, such as coliform mastitis.

KeywordsDNA Methylation Innate Immunity LPS Inflammation RRBS AbbreviationsATFActivating transcription factor

AZA-TSA5-aza-2-deoxycytidine and Trichostatin A

CREBcAMP regulated binding protein

DAVIDDatabase for Annotation, Visualization, and Integrated Discovery

DMCDifferentially methylated CpG

DMRDifferentially methylated region

E. coliEscherichia coli

FESFeline sarcoma oncogene

GOGene Ontology



KEGGKyoto Encyclopedia for Genes and Genomes


MIRAMethylated CpG island recovery assay

MrMethylation ratio

NFATc1Nuclear factor of activated T-cells, calcineurin dependent 1

PAMPPathogen associated molecular pattern

PI3KPhosphoinositide 3-kinase

PIK3R1Phosphatidylinositol 3-kinase regulatory subunit alpha

PRRPattern recognition receptor

RORARetinoic acid related orphan receptor alpha

S. aureusStaphylococcus aureus

sAMLSecondary acute myeloid leukemia

SARASub-acute ruminal acidosis

TCF7Transcription factor 7

TFBSTranscription factor binding site

TLRToll-like receptor

TNFSF13Tumor Necrosis Factor Super Family 13

TSSTranscription start site

WGBSWhole genome bisulfite sequencing

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-017-3796-1 contains supplementary material, which is available to authorized users.

Autor: Filiz T. Korkmaz - David E. Kerr


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