Multi-modal characterization of chromatin architecture from 24 hpf whole zebrafish embryos

DNA accessibility of cis regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. To obtain a more comprehensive view of CRE dynamics, we applied single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq) to whole 24hpf stage zebrafish embryos thereby measuring DNA accessibility in ~23,000 single cells. We developed two solutions to computational challenges in analyzing single-cell accessibility maps: 1) selection of informative genome segments, and 2) genome-wide classification of both cell-type-specific and multi-cell-type accessibility dynamics. We validated the sci-ATAC-seq results with bulk measurements for histone post-translational modifications and 3D genome organization, recovering known relationships between chromatin modalities and providing additional regulatory classifications. Furthermore, we applied sci-ATAC-seq to cloche/npas4l mutant embryos which revealed known and novel cellular roles for the hemato-vascular transcriptional master regulator, and suggested an intricate network regulating its expression. These data and their extensive analysis constitute a valuable developmental, molecular, and computational resource for future studies. ChIP-seq for 5 histone post-translational modifications with two replicates each and input controls; in situ Hi-C sequenced across three lanes; two replicates of chromatin-associated RNA-seq; and single-cell combinatorial indexing ATAC-seq performed twice on wild-type embryos and once on mixed embryos wild-type, heterozygous, and homozygous npas4lbns297