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| Status |
Public on May 11, 2017 |
| Title |
DNA methylation analysis of fibroblasts isolated from 5- and 16-month Holstein cows |
| Organism |
Bos taurus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Background: Differences 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. Results: We 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 752 promoters 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. Conclusions: Our 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.
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| Overall design |
DNA methylation assessment of cultured fibroblasts isolated from cows at 5- and 16-months of age. Six cultures per age group. Paired samples - taken from the same animal at 2 different ages.
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| Contributor(s) |
Korkmaz FT, Kerr DE |
| Citation(s) |
28545453 |
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| Submission date |
Dec 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Filiz Korkmaz |
| E-mail(s) |
filiz.korkmaz@umassmed.edu
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| Phone |
413-885-6517
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| Organization name |
UMass Chan Medical School
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| Street address |
364 Plantation St.
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (1) |
| GPL15749 |
Illumina HiSeq 2000 (Bos taurus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA356857 |
| SRA |
SRP094839 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE91088_CpG_p_less_than_0.05.csv.gz |
526.2 Kb |
(ftp)(http) |
CSV |
| GSE91088_CpG_result_table.txt.gz |
19.9 Mb |
(ftp)(http) |
TXT |
| GSE91088_RAW.tar |
756.4 Mb |
(http)(custom) |
TAR (of BIGBED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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