The Atoh7 shadow enhancer provides transcriptional robustness during retinal ganglion cell development

The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis. ATOH7 transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of the ATOH7 human SE causes non-syndromic congenital retinal non-attachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reduces Atoh7 mRNA >5-fold, but does not recapitulate optic nerve loss; however, SEdel/KO (knockout) trans heterozygotes have thin optic nerves. By analyzing Atoh7 mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show how the SE ensures robust Atoh7 transcriptional output. Combining SE deletion, KO and wild-type alleles in a genotypic series, we determined the amount of Atoh7 needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions in Atoh7 dosage. Together these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism hard-wired in the machinery of vertebrate retinal ganglion cell genesis. Overall design: ATAC-seq open chromatin profiling of E14.5 wild type and Atoh7 shadow enhancer mutant retinas. There were 3 biological replicates per genotype, which consisted of pooled retinal pairs from individual animals and 50,000 cells from each pair per replicate.