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

A temporally resolved scATAC-seq atlas of ~95,000 zebrafish brain and retina nuclei defines 213 chromatin states and reveals extensive cell type- and region-specific remodeling across larval, juvenile, and adult stages.

• Why it matters: Neural cis-regulatory programs are thought to integrate transcription factor activity with chromatin accessibility, but how these programs are organized and remodeled during post-embryonic development is unclear.
• What they did: The study generated a single-cell chromatin accessibility resource across developmental stages, then integrated scATAC-seq with transcriptomic data to link motif accessibility to transcription factor expression and identify regulatory stability versus remodeling patterns.
• The result: Using the atlas, the authors systematically identify and functionally validate candidate enhancers in vivo, including compact, combinatorial enhancer modules at the slc1a3b locus in radial glia with candidate regulatory inputs shared with human SLC1A3.

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