Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans

A protocol to transform a fluorescent reporter from a nuclear to a cytoplasmic location

To facilitate cell identification for expression pattern analysis in C. elegans , an SL2::GFP::H2B fluorescent reporter cassette has become a popular and widely used choice to generate nuclear localized reporter alleles by CRISPR/Cas9 genome engineering. When added at the 3' end of a locus of interest, this cassette concentrates GFP into the nucleus and permits the identification of expressing cells, for example with the help of the NeuroPAL tool. However, there are instances in which it is desirable to visualize the complete morphology of a cell that expresses an SL2::GFP::H2B reporter cassette. We describe here a CRISPR/Cas9-engineering strategy to transform an endogenous SL2::GFP::H2B tag into a cytosolic tag by insertion of the self-cleaving T2A tag in between GFP and H2B.

A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types

During embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay are less well-understood. Here we directly measured spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA-sequencing. This allowed us to calculate mRNA half-lives within specific cell types and developmental stages and identify differentially regulated mRNA decay throughout embryonic development. We identified transcript features that are correlated with mRNA stability and found that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that, on average, mRNA is more stable in the germline compared to in the soma and in later embryonic stages compared to in earlier stages. This work suggests that differential mRNA decay across cell states and time helps to shape developmental gene expression, and it provides a valuable resource for studies of mRNA turnover regulatory mechanisms.