Conservation of cis-regulatory codes over half a billion years of evolution

Identifying homologous cell types across species is crucial in understanding cell type evolution. The retina is particularly suitable for comparative analysis because its six major cell classes' basic morphology, connectivity, and function have remained mainly unchanged since the earliest stages of vertebrate evolution. We conducted comparative single-nucleus chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas, which began to diverge over half a billion years ago, to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. Conservation appears as the clustering of multiple distinct high-affinity transcription factor (TF) binding sites toward the center of cell-class-specific open chromatin regions. Hierarchical clustering of machine-learning models of retinal cis-regulatory codes from various species reveals six clusters corresponding to the six retinal cell classes. Therefore, the retina’s cellular Bauplan is governed by cis-regulatory codes predating the divergence of extant vertebrates.This repository includes (1) cell metadata for single-nucleus chromatin accessibility (snATAC-seq), (2) hierarchical orthogroups, (3) genomic coordinates and nucleotide sequences of open chromatin regions, (4) evolutionarily conserved motifs (position probability matrices), and (5) gkm-SVM models. All raw single-cell sequencing data and processed data related to snATAC-seq are accessible through the Gene Expression Omnibus.