Creatic isletsThe clinical characteristics of the 53 male and 34 female donors of
Creatic isletsThe clinical characteristics of the 53 male and 34 female donors of human pancreatic islets are shown in Table 1.We next evaluated if there are epigenetic differences CI-1011 cost between sexes in human pancreatic islets. The genome-wide DNA methylation pattern was analyzed with the Infinium HumanMethylation450 BeadChip array. After quality control, DNA methylation data were obtained for a total of 482,954 sites, excluding data on the Y chromosome. We next performed an unsupervised clustering of the islet DNA methylation data for all 87 donors. Figure 1A clearly shows that the genome-wide DNA methylation data in human islets cluster based on sex. However, after removing the X chromosome methylation data (11,150 sites) from the data set we could no longer detect any clustering based on sex (Figure 1B). We then tested if the average degree of DNA methylation of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25962748 all analyzed sites differed between males and females. There were no differences in the average degree of methylation between the sexes when analyzing the DNA methylation sites on all chromosomes (females 48.5 ?1.2 versus males 48.3 ?1.1 , P = 0.48) or when analyzing the DNA methylation sites on the autosomal chromosomes separately (females 48.5 ?1.2 versus males 48.5 ?1.1 , P = 1.0) (Figure 2A). However, when analyzing the average degree of DNA methylation of all analyzed sites on the X chromosome, females exhibited a higher degree of methylation compared with males (females 48.9 ?1.5 versus males 41.0 ?1.1 , P = 4.7 ?10-15) (Figure 2A). To further dissect the impact of sex on DNA methylation in human pancreatic islets, we calculated the average DNA methylation levels of the analyzed sites based on either their functional genomic annotation (TSS1500 (theHall et al. Genome Biology 2014, 15:522 http://genomebiology.com/2014/15/12/Page 3 ofFigure 1 Females and males cluster separately based on DNA methylation in human pancreatic islets. (A) An unsupervised clustering analysis of the genome-wide DNA methylation data for all analyzed sites that passed quality control in human islets of 53 male and 34 female donors, after batch correction. The clustering includes 482,954 sites. Females are indicated with red color and (F), and males are indicated with blue color and (M). (B) An unsupervised clustering analysis of the genome-wide DNA methylation data including only autosomal data that passed quality control in human islets from 53 male and 34 female donors, after batch correction. Removal of X-chromosome DNA methylation data makes females and males cluster together. The clustering includes 471,804 sites. Females are indicated with red color and (F), and males are indicated with blue color and (M).region 200 to 1,500 nucleotides upstream of the transcription start site (TSS)), TSS200 (the 200 nucleotides immediately upstream of the TSS), 5 untranslated region (UTR), first exon, body, 3 UTR or intergenic) or the CpG content and neighborhood context [22]. This was done for the autosomal chromosomes and X chromosome separately. The average DNA methylation level of the studied genome regions did not differ significantly between males and females for the autosomal chromosomes (Figure 2B,C). For the X chromosome, however, all studied genome regions differed significantly between the sexes with false discovery rate (FDR) less than 5 (q <0.05) (Figure 2D,E). While the TSS1500, TSS200, 5 UTR, first exon, body and intergenic regions had higher average methylation levels in females compared wit.