Project description:The vertebrate retina is patterned along its dorsal-ventral (DV) axis by signaling centers that provide each domain with distinct molecular and functional properties, including differential photoreceptor composition and opsin expression. 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. Comparative genomics showed that this architecture is deeply conserved: the efnb2-slc10a2 synteny and TAD boundaries are maintained from human to zebrafish. To enable functional testing of this long regulatory interval, we strategically turned to Tetraodon nigroviridis, a species with one of the most compact vertebrate genomes, allowing nearly the entire orthologous enhancer cluster (~13 kb) to be cloned intact. Transgenic assays in both zebrafish and mouse demonstrated that this Tetraodon enhancer cluster drives dorsal retina-specific eGFP expression, underscoring the deep conservation of its regulatory function across vast phylogenetic distances. Together, these results highlight how a multi-species approach leveraging complementary strengths of model and non-model organisms can illuminate ancient regulatory mechanisms underlying vertebrate eye patterning.

			Action	DRS
	2i_ChIP.dedupe_trimmed.aligned_mouse.uniq.sort.bam	Bam
	2i_ChIP.dedupe_trimmed.aligned_mouse.uniq.sort.bam.bai	Bam
	12h_ChIP.dedupe_trimmed.aligned_mouse.uniq.sort.bam	Bam
	12h_ChIP.dedupe_trimmed.aligned_mouse.uniq.sort.bam.bai	Bam
	18h_ChIP.dedupe_trimmed.aligned_mouse.uniq.sort.bam	Bam

Dataset Information

Genetic dissection of the Fgf5 enhancer cluster

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