The regulatory landscape of optic fissure closure in the vertebrate eye

The process of optic fissure closure (OFC) is a critical tissue fusion event in eye development. Failure of OFC results in coloboma, a persistent gap in the eye that can significantly affect vision. Most coloboma cases do not have a genetic diagnosis, reflecting poor understanding of the genes required for OFC and how these are regulated and their impact on cell behaviours. The chicken is a good model for interrogating developmental gene expression and regulatory networks, and the embryonic chicken eye develops similarly to humans. Results: Here we performed integrated profiling of accessible chromatin and gene expression during OFC in the chicken embryonic eye. This revealed domains of accessible chromatin during active fusion and in the broader ventral retina that were distinct from the dorsal retina, implicating these as active during fusion of the optic fissure and important for gene regulation in this distinct region of the developing vertebrate eye. Open chromatin elements could be linked by proximity and TAD boundaries to adjacent genes that have distinct spatial and temporal expression profiles during optic fissure closure. Using a combination of de novo motif enrichment and transcription factor (TF) foot-printing occupancy analyses in silico, we found evidence for TEAD/ZIC/SOX activity during OFC, and retinoic-acid related TF activity in the developing dorsal eye. We were able to map a sub-set of chicken OFC specific peaks to cis-regulatory elements in the human genome and identified loci proximity to known human coloboma genes or in coloboma candidate genes identified by our analyses in chicken. Conclusions: This study leverages eye development in the chicken embryo to deliver the first evidence for dynamic cis-regulatory activity of gene expression during OFC and identifies candidate loci for future mutational and activity analyses, providing the first genetic clues to identify non-coding loci as candidates for coloboma. Overall design: ATAC-seq samples of bulk-dissected fissure and dorsal retina tissue from Hamburger-Hamilton (HH) stage 30 and 34 chicken embryos respectively. There are three biological replicates per condition, and each replicate is prepared from pooled dissected retinal tissues of 10 embyos.