A Transcriptional Lineage of the Early C. elegans Embryo

Abstract

SUMMARY During embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell’s fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify genome-wide mRNA abundance in each cell of the C. elegans embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify genes that were previously unappreciated as being critical for development. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fate of each cell, describes at a cellular resolution the mRNA landscape that guides development.

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism

“…We estimated the amount of mRNA in the two-cell stage C. elegans embryos at ~2,000,000 transcripts from published transcriptome-level RNA-seq data (Osborne Nishimura et al, 2015). While we used smFISH-based linear regression to calibrate the published RNA-seq data, an independent study used an alternate approach of calibration using spike-in control RNA probes (Tintori et al, 2016). Our estimate of the amount of mRNA transcripts is close to the findings of this independent study.…”

A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization

“…By analyzing single cells, it becomes possible to understand cellular heterogeneity, to make measurements with improved spatial and temporal resolution, and to study processes for which it is impossible or impractical to collect sufficient material for bulk assays. Single-cell sequencing approaches have been widely used (Wang and Navin, 2015), including in C. elegans (Hashimshony et al, 2012; Osborne Nishimura et al, 2015; Tintori et al, 2016); and single-cell enzyme activity measurements have been pioneered (Guillaume-Gentil et al, 2016; Kovarik and Allbritton, 2011). Here, we presented a single-cell approach for measuring protein-protein interactions at the single molecule level in individual, staged C. elegans embryos.…”

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

“…Using RNA-seq, a whole-embryo time series was produced (Boeck et al 2016), which provides temporal data from the early embryo to late in embryonic development, but the data set lacks cell-type-specificity. Expression data sets with single-cell resolution (Hashimshony et al 2012(Hashimshony et al , 2015Tintori et al 2016;Cao et al 2017) are promising in terms of refined temporal and spatial information but suffer from sparse sampling of the transcripts per cell. Many single-cell RNA-seq methods also rely on the end sequencing of cDNA molecules and thus largely fail to capture alternative splicing events.…”