Fig. 2: Human and dog coloboma-linked mutations found within validated Ihh enhancers.

a The genomic landscape of NHEJ1 and IHH from the UCSC Genome Browser. The tracks presented are publicly available ones associated with cis-regulatory elements: histone marks (H3K4me1), the open chromatin state (DNaseI hypersensitivity), and the evolutionary conservation, as well as other data from GeneHancer and ENCODE, are given in detail in Sup. Fig. 3. In yellow, the nine Ihh enhancers tested in mice by Will et al.; In red- the approximate location of the 7.8 kb deletion found in dogs (by Parker et al.) as the likely causal variant for Collie Eye Anomaly (corresponding to “macular colobomas” in humans). UCSC’s BLAT was used to locate the enhancers and the 7.8 kb deletion in dogs on the human genome (hg19). In light blue- the variant found in the present study. b Zoom-in on the proximal end of one of Ihh’s distal enhancers- ‘i8’ (name termed by Will et al.), presented with evolutionary conservation track. In light blue- the variant found in the present study. c Sanger sequencing demonstrating the single nucleotide substitution- NHEJ1 (NM_024782.2): c.588+18131 A > G, found in all available affected individuals in our study. WT unaffected homozygous wild-type individual; Het. obligatory heterozygous carrier; Mut. affected homozygous mutant individual. d Conserved PAX4 binding site (in blue), found using rVista, in the Human and the Chicken genomic sequences.