Fig. 3: Strong craniofacial-specific enhancers target Gini genes.

a Expression values versus CFSEs number modeled by linear loess smoothing for embryonic craniofacial (blue), embryonic heart (red), fetal brain (green), and all tissues in GTEx (gray). b Histogram plot of distance for closest craniofacial (blue bars) Gini gene to CFSEs compared to a randomly picked Gini gene from all other tissues (gray bars). The median and standard deviation were calculated from 1000 iterations. Each line is an interpolation for craniofacial Gini genes (orange) and for the maximum and minimum random Gini genes (dark gray dashed). c Gini gene enrichment for genes with bivalent promoters in craniofacial tissue. The pink bars are bivalent genes conserved between human and mouse, and the purple bars are bivalent regions spanning DNA-binding genes. The bars for the expected overlap represent the median and lines represent the standard deviation calculated from 1000 iterations of randomly selected genes from the gini analysis (n = 33,073). d Genome browser shot of EBF3 locus showing 25-state ChromHMM segmentation from culture model of CNCCs, and CS13 through CS20 of primary human craniofacial tissue. EBF3 has a bivalent promoter in these samples (dark purple). Above the segmentation tracks is the active and novel CFSE track shown in orange, which includes strong enhancer ChromHMM states 13–15. Below are RNA-seq bigwig signal tracks for human embryonic stem cells (ESC), CNCCs, and CS13 through CS22.