Abstract
DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlling their expression remain largely uncharacterized. To address this, we produced a multimodal resource and genomic regulatory map for the zebrafish community, which integrates single-cell combinatorial indexing assay for transposase-accessible chromatin with high-throughput sequencing (sci-ATAC-seq) with bulk histone PTMs and Hi-C data to achieve a genome-wide classification of the regulatory architecture determining transcriptional activity in the 24-h post-fertilization (hpf) embryo. We characterized the genome-wide chromatin architecture at bulk and single-cell resolution, applying sci-ATAC-seq on whole 24-hpf stage zebrafish embryos, generating accessibility profiles for ∼23,000 single nuclei. We developed a genome segmentation method, ScregSeg (single-cell regulatory landscape segmentation), for defining regulatory programs, and candidate CREs, specific to one or more cell types. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization and identified new regulatory principles between chromatin modalities prevalent during zebrafish development. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos identified novel cellular roles for this hematovascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work defines regulatory architecture and principles in the zebrafish embryo and establishes a resource of cell-type-specific genome-wide regulatory annotations and candidate CREs, providing a valuable open resource for genomics, developmental, molecular, and computational biology.
Highlights
The coordination of cis-regulatory elements (CREs) is essential to the tight regulation of gene expression programs that direct cell fate changes in embryonic development
We show that diverse cell types present in the 24-hpf embryo can be identified by their accessibility profiles and have identified complex patterns of CRE dynamics that reflect the combinatorial nature of transcriptional regulation
Using bulk ChIP-seq data for histone post-translational modifications (PTMs) known to occur at CREs, we provide the additional resource of a genome-wide classification for promoter- and enhancer-like chromatin states at the 24-hpf stage
Summary
The coordination of cis-regulatory elements (CREs) is essential to the tight regulation of gene expression programs that direct cell fate changes in embryonic development. The types of CREs include promoters, enhancers, insulators, and silencers, whose sequence and dynamic physical properties determine their function. The fundamental unit of a CRE is a nucleosome-depleted region (NDR), which acts as a binding platform for transcriptional regulators and can be highly dynamic across cell types due to. Mammalian NDRs often harbor divergently oriented core promoter sequence elements and transcription start sites (TSSs) and are flanked by well-positioned nucleosomes whose histone post-translational modifications (PTMs) reflect the activation state and/or class of CRE.[1,2] This complex architecture has been described as the regulatory interface between the genome and its functional output.[3]
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