2024/10/19 by Yang Joon Kim, Shruthi VijayKumar, Benjamin Giovanni Iovino +16 · 2 voices · 5 citations
Biochemistry, Genetics and Molecular Biology · #Genetics, Bioinformatics, and Biomedical Research #Zebrafish Biomedical Research Applications #Bioinformatics and Genomic Networks
paper · pdf · doi:10.1101/2024.10.18.618987
During embryonic development, gene regulatory networks (GRNs) drive molecular differentiation of cell types. However, the temporal dynamics of these networks remain poorly understood. Here, we present Zebrahub-Multiome, a single-cell multiomic atlas that captures chromatin accessibility and gene expression from 94,562 cells across six stages of zebrafish embryogenesis (10-24 hours post-fertilization), capturing key developmental stages from the end of gastrulation to the onset of organogenesis. By measuring regulatory element activity alongside transcriptional output from the same cells, we identify 640,000 cis-regulatory elements organized into 402 hierarchically structured modules corresponding to specific developmental pathways. Early embryonic stages employ broadly shared regulatory programs that progressively fragment into lineage-specific modules. Timeresolved gene regulatory network inference reveals that transcription factors undergo functional transitions – from multilineage regulators to specialized, lineage-committed factors. These quantitative measurements reveal the regulatory network rewiring that drives cell fate specification. Our interactive web portal ( zebrahub.org/epigenomics ) enables exploration of gene dynamics, regulatory networks, and perturbation predictions, providing a quantitative framework for understanding vertebrate developmental regulation.