The regulatory landscape of optic fissure closure in the vertebrate eye

Purpose Optic fissure closure (OFC) is a critical tissue fusion event in normal eye development and its failure results in ocular coloboma (OC), an inferonasal ocular tissue defect that persists throughout life. Most OC cases lack a genetic diagnosis, reflecting limited understanding of the genes and pathways that regulate OFC. We aimed to determine if OFC gene expression is regulated by the non-coding genome and identify novel candidate loci for OFC/OC.

Using the embryonic chicken eye, we performed integrated profiling of accessible chromatin and gene expression patterns during OFC. Matched RNA-seq and ATAC-seq from distinct spatial and temporal eye tissues were utilised with bioinformatic tools to identify regulatory genomic elements and infer gene regulatory networks, and to map synonymous loci in the human genome.

We revealed domains of accessible chromatin during active fusion and the broader ventral retina that were distinct from those in the dorsal retina, implicating these loci for gene regulation during development and fusion of the optic fissure. In silico analysis using de novo motif enrichment and transcription factor (TF) foot-printing revealed TEAD, ZIC, and SOX TF activity during OFC, and retinoic acid signalling related TF activity in the dorsal eye. A subset of chicken OFC-specific peaks mapped to human cis-regulatory elements near known coloboma genes and OFC candidate genes identified in this study.

This provides the first evidence for dynamic cis-regulatory activity during OFC, identifies candidate loci for future mutational analysis, and offers new genetic leads for OC cases without a genetic diagnosis. Competing Interest Statement The authors have declared no competing interest. Footnotes Funding: J.R. was supported by a UKRI Future leaders Fellowship (MR/S033165/1). B.H.C.C., J.P. and J.R. were supported by the Biotechnology and Biological Sciences Research Council (BBS/E/D/10002071). M.M. was funded by The Wellcome Trust (205174/Z/16/Z), Moorfields Eye Charity. J.R., B.H.C.C., and M.M. are supported by Medical Research Foundation and Moorfields Eye Charity grant MRF-JF-EH-23-123. Competing interests. The authors declare that they have no competing interests.