4C-seq analysis of a subset of DMRs. (a) Domainograms of interaction profiles of three DMRs looping to the TSS of a differentially expressed gene. Top panel: intragenic DMR (Eif2c2) looping to the host TSS. Middle panel: intergenic DMR looping to Tbx3. Bottom panel: intragenic DMR (Lars2) looping to a distant gene (Mosc2). Significant interactions are indicated in the domainogram using different colours, corresponding to different P values as indicated on the right. Above the domainogram normalized reads are plotted. Genes are shown as solid horizontal bars. The vertical arrows indicate the significant 4C interaction with a TSS. Significant differentially expressed genes P <0.01 (student t-test) are color-coded as indicated on the right. (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 gene, which it physically associates with based on 4C analysis, between GFP_High cells and the Villus (Y-axis) (GFP_High divided by Villus). Black circles indicate gene expression changes with P <0.01 (student t-test) and the red square P <0.05 (student t-test).
Kaaij et al. Genome Biology 2013 14:R50 doi:10.1186/gb-2013-14-5-r50