Single-Cell Protein Atlas of Transcription Factors Reveals the Combinatorial Code for Spatiotemporal Patterning theC. elegansEmbryo

Abstract

<jats:title>SUMMARY</jats:title><jats:p>A high-resolution protein atlas is essential for understanding the molecular basis of biological processes. Using protein-fusion reporters and imaging-based single-cell analyses, we present a protein expression atlas of <jats:italic>C. elegans</jats:italic> embryogenesis encompassing 266 transcription factors (TFs) in nearly all (90%) lineage-resolved cells. Single-cell analysis reveals a combinatorial code and cascade that elucidate the regulatory hierarchy between a large number of lineage-, tissue-, and time-specific TFs in spatiotemporal fate patterning. Guided by expression, we identify essential functions of CEH-43/DLX, a lineage-specific TF, and ELT-1/GATA3, a well-known skin fate specifier, in neuronal specification; and M03D4.4 as a pan-muscle TF in converging muscle differentiation in the body wall and pharynx. Finally, systems-level analysis of TF regulatory state uncovers lineage- and time-specific kinetics of fate progression and widespread detours of the trajectories of cell differentiation. Collectively, our work reveals a single-cell molecular atlas and general principles underlying the spatiotemporal patterning of a metazoan embryo.</jats:p>

The anterior Hox geneceh-13andelt-1/GATAactivate the posterior Hox genesnob-1andphp-3to specify posterior lineages in theC. elegansembryo

“…Finally, while elt-1 has a well-defined known role in epidermal fate specification(57), our work shows that it is also required for nob-1 enhancer activity. This is consistent with other recent work identifying defects in cell division patterns and the expression of the neurogenic TF lin-32 in elt-1 mutants(58). The ability of developmental transcription factors to “moonlight’ is likely facilitated by complex regulation by multiple enhancers as seen for nob-1/php-3 , and ceh- 13 (30, 31) since enhancer evolution can enable genes to be expressed at different locations and times in development(59, 60).…”

Single‐cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos

“…An intriguing question is when and how equivalent chromatin activity landscape is precisely specified in early progenitor cells that are not lineage-related. Since progenitor cells from different cell lineages generally exhibit divergent chromatin activity and gene expression programs (Packer et al, 2019;Ma et al, 2020), the specification of equivalent chromatin activity would be a regulated process. In rare cases, L-R symmetric cells exhibit functional asymmetry (Hobert, 2014).…”

“…Given that cells of a tissue derive from different lineages, we tested whether lineage origin accounts for this intra-tissue chromatin heterogeneity. Our recent finding using cellular protein expression of transcription factors has revealed that many tissue-specific TFs show lineagerestricted expression, contributing to a lineage-dependent intratissue heterogeneity in gene expression (Ma et al, 2020). Here, we further tested whether chromatin changes underlie this pattern.…”

“…A similar result was obtained (Fig EV5A ), confirming that the lineage effects on intra-tissue chromatin heterogeneity were also present in mature cells. This finding then led to the question of whether lineage-dependent chromatin heterogeneity results in heterogeneity in global gene expression in addition to transcription factors (Ma et al, 2020). Using scRNA-seq data, we found that the transcriptome divergences between intra-tissue cells increased with cell lineage distances not only at the 350-cell stage but also at the 600-cell stage, when most cells have almost completed embryonic differentiation (Fig EV5B and C).…”