Analysis of histone modifications and local interactions of DMRs. (a) Numbers of DMRs called between methylomes and their association with different genomic regions as indicated. A DMR is labelled as TSS if within 2 kb of an annotated transcriptional start. DMRs are labelled as intergenic if they are not within 2 kb of a refseq gene. DMRs that overlap with multiple genomic elements are counted in both categories. Top graph represents DMRs that show a decrease in DNA methylation upon differentiation, lower graph depicts the DMRs with an increase during differentiation. (b) Scatter plot displaying the absolute difference in DNA methylation of the DMRs (GFP_High - Villus) (X-axis) versus the difference in expression of the associated genes between GFP_high cells and the Villus (Y-axis) (GFP_High divided by Villus). (c-e) Chip-qPCR results for different histone modifications found in chromatin of Villus epithelium for eight individual DMRs. DMRs are labelled after their closest gene (as indicated), or after their chromosomal location. * P <0.05 (student t-test). $: 4C analysis shown in, Additional file 2, Figure S6. The control is a randomly chosen region close to the Sp5 TF.
Kaaij et al. Genome Biology 2013 14:R50 doi:10.1186/gb-2013-14-5-r50