(A) Enrichment of human genome tiles that receive a top 0.1% bin score using a zGPAE-trained classifier at enhancers active in the indicated cell type, as revealed by ChIP-seq to chromatin marks in the Roadmap Epigenomics project (Visel et al., 2008). -Such tiles are significantly enriched within a variety of epithelial enhancers. [E05: H1 BMP4 Derived Trophoblast Cultured Cells; E027: Breast Myoepithelial Primary Cells; E028: Breast variant Human Mammary Epithelial Cells; E057, E058: Foreskin Keratinocyte Primary Cells; E079: Esophagus; E091: Placenta; E099: Placenta amnion; E119, Mammary Epithelial Primary Cells (HMEC); E127:NHEK-Epidermal Keratinocyte Primary Cells]. (B) Average density of H3K27Ac ChIP-seq signal in NHEK and GM12878 cells (Visel et al., 2008) at top 0.1% tiles using a zGPAE-trained classifier. (C) Genome browser view focused on IRF6-9.7, also known as IRF6 multispecies conserved sequence 9.7 (MCS9.7) (hg19 chr1:209989050–209989824). A SNP within it, rs642961 (chr1: 209989270), is associated with risk for non-syndromic orofacial cleft. Brazil mutation refers to a rare mutation reported in a patient with Van der Woude syndrome (Fakhouri et al., 2012). This element has peaks of H3K27Ac, IRF6, TP63, and KLF4 ChIP-seq in normal human keratinocytes. Multiz Alignments of 100 vertebrate species shows it is conserved among mammals but not in zebrafishNonetheless it possesses tiles in the top 1.0-1.5% and 0.2% bins using a zGPAE-trained classifier (D) Genome browser view focused on ZNF750-37 (hg19 chr17:80832267–80835105). This element has similar ChIP-seq signature as IRF6-9.7, and like it is not overtly conserved to fish but posseses high-scoring tiles using the zGPAE-trained classifier. (E) GFP expression pattern of Tg(IRF6-9.7:gfp; krt4:Tomato) at five dpf. (F) GFP expression pattern of Tg(ZNF750-37:gfp; krt4:Tomato) at five dpf. Both of these human non-coding elements have periderm enhancer activity in zebrafish embryos.
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