Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos

• Published in: Cell genomics Vol. 2; no. 1; p. 100083
• Main Authors: McGarvey, Alison C., Kopp, Wolfgang, Vučićević, Dubravka, Mattonet, Kenny, Kempfer, Rieke, Hirsekorn, Antje, Bilić, Ilija, Gil, Marine, Trinks, Alexandra, Merks, Anne Margarete, Panáková, Daniela, Pombo, Ana, Akalin, Altuna, Junker, Jan Philipp, Stainier, Didier Y.R., Garfield, David, Ohler, Uwe, Lacadie, Scott Allen
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12-01-2022; Elsevier
• Subjects: chromatin; cis regulatory element; enhancer; Hi-C; npas4l; promoter; single-cell ATAC-seq; zebrafish; npas4l; enhancer; single-cell ATAC-seq; Hi-C; promoter; zebrafish; chromatin; cis regulatory element
• ISSN: 2666-979X; 2666-979X
• DOI: 10.1016/j.xgen.2021.100083

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.
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•Single-cell DNA accessibility defines 17 cell types from the 24-hpf zebrafish embryo•Machine learning with ScregSeg classifies complex regulatory programs genome-wide•Integrating sc and bulk chromatin data reveals cross-modal regulatory principles•sci-ATAC profiling of npas4l mutants exposes unexpected changes in cell composition
Accessibility measurements at single-cell resolution define cell states in the highly heterogeneous zebrafish embryo and reveal unexpected cellular phenotypes in genetic mutants. Genome-wide classification of complex cross-cell-type regulatory programs using machine learning provides a solid resource for future studies with immediate direct effects on transgenic reporter gene design, candidate identification for perturbation studies, and regulatory sequence annotation for the advancement of predictive models. Integrating single-cell data with bulk chromatin measurements reveals principled relationships between transcriptional regulatory mechanisms.