In average DNA methylation in the palmitate-treated islets for all gene
In average DNA methylation in the palmitate-treated islets for all gene and CpG island regions except TSS200, 1st Exon and CpG islands (Figure 6 and Additional file 9: Table S9). We next evaluated if palmitate also Sodium lasalocid web affects the level of DNA methylation of individual CpG sites in human islets. Genome-wide DNA methylation array data were successfully generated for 483,844 sites in islets of 13 donors. Palmitate exposure changed the degree of DNA methylation of 46,977 sites at P <0.05, which is almost double the expected number with P <0.05 and significantly more than expected based on a chi-squared test (P <0.0001, Additional file 10: Table S10). However, no individual methylation site had q <0.05 based on a FDR analysis and the lowest P-value was 5.7 ?10-6. Out of those, 4,690 sites had an absolute difference in DNA methylation greater than 3 in palmitate-treated versus control islets. This cut-off was set to increase the biological relevance of the results. Among the 4,690 sites with an absolute difference in methylation greater than 3 and P <0.05, 4,561 sites displayed increased DNA methylation due to palmitate treatment, corresponding to 2,753 unique genes and 1,429 intergenic sites. Moreover, 129 sites showed decreased DNA methylation dueHall et al. BMC Medicine 2014, 12:103 7 ofabcFigure 3 Gene set analysis of differentially expressed genes in human islets exposed to palmitate. Results of KEGG pathway analysis using a) all differentially expressed genes, b) down-regulated genes only and c) up-regulated genes only in human islets exposed to palmitate. Numbers in brackets indicate the total number of genes in the corresponding palmitate exposure out of which 99 were located in 94 unique genes, and 30 were intergenic sites. The fold change for PubMed ID: the 46,977 differentially methylated DNA methylation sites (P <0.05), calculated as DNA methylation of palmitate-treated islets/DNA methylation of control treated islets, ranged from 0.54 to 1.84. This corresponds to changes in DNA methylation from a 46 decrease to an 84 increase.Overlapping changes in mRNA expression and DNA methylation in palmitate-treated human isletsEpigenetic modifications may regulate mRNA expression [3-5] and we therefore tested if any of the genes thatexhibit differential mRNA expression also exhibit differential DNA methylation in islets exposed to palmitate. Significant mRNA expression data (q <0.05) were merged with DNA methylation sites with P <0.05 and an absolute difference in DNA methylation 3 . We found 290 individual genes with differential mRNA expression (q <0.05) and a corresponding change in DNA methylation (in total, 371 DNA methylation sites) (Figure 1b and Additional file 11: Table S11). Out of these 290 genes, 213 had decreased mRNA expression together with altered DNA methylation (269 DNA methylation sites, whereof 264 sites had increased and 5 sites had decreased DNA methylation) in response to palmitate treatment. Additionally, 77 uniqueHall et al. BMC Medicine 2014, 12:103 8 ofFigure 4 Differential mRNA expression of genes in enriched KEGG pathways in palmitate-exposed human islets. a) Differentially downregulated genes in the glycolysis/gluconeogenesis pathway. b) Differentially expressed genes in the glutathione metabolism pathway. c) Differentially expressed genes in the insulin signaling pathway. d) Differentially expressed genes in the bio.

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