Single-cell chromatin profiling reveals dynamic regulatory logic and enhancer elements in brain and retina development

However, how these regulatory programs are organized and remodeled during post-embryonic neural development remains poorly understood. We generate a temporally resolved single-cell chromatin accessibility atlas of ~95,000 zebrafish brain and retina nuclei spanning larval, juvenile, and adult stages.

We define 212 discrete chromatin states and uncover widespread, cell type-specific chromatin reorganization across development. By integrating with transcriptomic data, we link motif accessibility to transcription factor expression and identify regulatory programs that are either maintained or reconfigured during post-embryonic development of each cell type. Leveraging this atlas, we systematically identify and functionally validate candidate enhancers in vivo.