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Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.

ABSTRACT: Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.

PROVIDER: PRJNA292881 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2163190.fastq.gz	Fastqsanger.gz
	SRR2163200.fastq.gz	Fastqsanger.gz
	SRR2163220.fastq.gz	Fastqsanger.gz
	SRR2163191.fastq.gz	Fastqsanger.gz
	SRR2163201.fastq.gz	Fastqsanger.gz

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Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.

Project description:BackgroundWe have previously found substantial animal-to-animal and age-dependent variation in the response of Holstein fibroblast cultures challenged with LPS. To expand on this finding, fibroblast cultures were established from dairy (Holstein) and beef (Angus) cattle and challenged with LPS to examine breed-dependent differences in the innate immune response. Global gene expression was measured by RNA-Seq, while an epigenetic basis for expression differences was examined by methylated CpG island recovery assay sequencing (MIRA-Seq) analysis.ResultsThe Holstein breed displayed a more robust response to LPS than the Angus breed based on RNA-Seq analysis of cultures challenged with LPS for 0, 2, and 8 h. Several immune-associated genes were expressed at greater levels (FDR < 0.05) in Holstein cultures including TLR4 at all time points and a number of pro-inflammatory genes such as IL8, CCL20, CCL5, and TNF following LPS exposure. Despite extensive breed differences in the transcriptome, MIRA-Seq unveiled relatively similar patterns of genome-wide DNA methylation between breeds, with an overall hypomethylation of gene promoters. However, by examining the genome in 3Kb windows, 49 regions of differential methylation were discovered between Holstein and Angus fibroblasts, and two of these regions fell within the promoter region (-2500 to +500 bp of the transcription start site) of the genes NTRK2 and ADAMTS5.ConclusionsFibroblasts isolated from Holstein cattle display a more robust response to LPS in comparison to cultures from Angus cattle. Different selection strategies and management practices exist between these two breeds that likely give rise to genetic and epigenetic factors contributing to the different immune response phenotypes.

| S-EPMC4806443 | biostudies-literature

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.

Project description:This SuperSeries is composed of the SubSeries listed below.

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Transcript abundances associated with fertility in a case-control design including Angus and Holstein heifers

Project description:We carried out an experiment to test the hypothesis that differences in gene transcript abundance due to fertility fitness would be shared between heifers of different breeds. We produced transcriptome data from peripheral white blood cells from 22 heifers (purebred Angus heifers (n=12), purebred Holstein (n=10) heifers). We identified two genes whose transcript abundance differed (eFDR ≤ 0.002) between the two groups (Fertile and Sub-Fertile), namely Adipocyte Plasma Membrane Associated Protein (APMAP, 1.16 greater abundance in the Fertile group) and Dynein Axonemal Intermediate Chain 7 (DNAI7, 1.23 greater abundance in the Sub-Fertile group).

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Breed-dependent differences in transcriptomic response of dermal fibroblasts to lipopolysaccharide

Project description:We report the breed-dependent differences in the innate immune response of dermal fibroblasts following exposure to lipopolysaccharide (LPS). Skin biopsies were collected from Angus (a beef breed) and Holstein (a dairy breed) animals and isolated fibroblasts were exposed to LPS to investigate differences in gene expression between these two cattle breeds.

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Project description:Transcript abundances associated with fertility in a case-control design including Angus and Holstein heifers

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