For the first time Zhuo Du et al. correlate mRNA and protein expression in C. elegans embryo to build the first embryo protein mapping.
After the generated single-cell mRNA expression atlas of Jonathan S. Packer (2019) in C. elegans embryo, a mapping of proteins expression to better understand biological processes, especially during embryogenesis of C. elegans, has been made by Zhuo Du et al.. A representation encompassing 266 transcription factors allows them to establish a regulatory hierarchy between many lineages, tissues and transcription factors in spatiotemporal fate patterning; also highlighting new functions of certain transcription factors. Since the protein level cannot be directly correlated to the expression of an mRNA.
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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 C. elegans 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.
- Zhuo DU et al., biorxiv.org (2020)