A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina

Although the key DV patterning genes are well studied, the cisregulatory mechanisms that establish and maintain these territories remain poorly understood. To explore this regulatory landscape, we turned to the four-eyed fish Anableps anableps, whose large, protruding eyes and expanded ventral retina facilitate precise dissection of dorsal and ventral halves for spatially resolved genomics.

Bulk RNA-seq of the Anableps dorsal and ventral retina regions recovered canonical DV markers, while bulk ATAC-seq revealed dorsally enriched ATAC-seq peaks residing within a low-genedensity region between efnb2a and gtpbp8. These putative cis-regulatory elements located to a 29 kb interval forming a contiguous enhancer cluster. Via Hi-C analysis, we identified a topologically associating domain (TAD) encompassing efnb2a, gtpbp8, and slc10a2, with a dorsal-enriched chromatin contact linking the enhancer cluster to the efnb2a promoter.