Global Mapping of H3K4me1 and H3K4me3 Reveals the Chromatin State-Based Cell Type-Specific Gene Regulation in Human Treg Cells
Figure 6
Prediction of enhancers and verification of activity for cell signature genes. Panel A
, UCSC hg18 genome browser views of H3K4me1 modifications of the cell signature gene FOXP3 loci (ChrX:48990000–49010000) in Treg and aTconv cells. The following tracks are shown (from top to bottom): genes' location; ChIP-Seq tag counts for H3K4me1 modifications in Treg cells; ChIP-Seq tag counts for H3K4me1 modifications in aTconv cells; UCSC genes based on RefSeq; mammalian consensus. The blue frames indicate the Treg cell-type specific H3K4me1 enriched regions. Panels B Functional analysis of enhancer candidates specific for Treg cells. These fragments are all enriched by H3K4me1 modifications except the FOXP3 (ChrX:49004128–49005080) fragment, which is H3K4me3 modified and identified as an enhancer in the published literatures. Panel C, Functional analysis of the enhancer candidates common in both Treg and aTconv cells, which are all H3K4me1 modified. All the selected enhancer candidates were cloned into the luciferase vector pGL3-Promoter, respectively. The indicated plasmids were transiently transfected into Jurkat T cells that were stimulated with or without PMA and ionomycin (PI) after transfection. Luciferase activity was normalized against the activity of a co-transfected Renilla construct. Mean values ± SEM are shown relative to the pGL3-promoter alone. * indicates a statistically significant difference between the cloned vs control plasmids (P<0.01; paired Student's t-test).