yeastDrop-Seq – a yeast-optimized scRNA-Seq method

Stochastic gene expression leads to inherent variability in expression outcomes even in isogenic single-celled organisms grown in the same environment. The Drop-Seq technology facilitates transcriptomic studies of individual mammalian cells, and it has had transformative effects on the characterization of cell identity and function based on single-cell transcript counts. However, application of this technology to organisms with different cell size and morphology characteristics has been challenging.

Yale University researchers have developed yeastDrop-Seq, a yeast-optimized platform for quantifying the number of distinct mRNA molecules in a cell-specific manner in individual yeast cells. Using yeastDrop-Seq, we measured the transcriptomic impact of the lifespan-extending compound mycophenolic acid and its epistatic agent guanine. Each treatment condition had a distinct transcriptomic footprint on isogenic yeast cells as indicated by distinct clustering with clear separations among the different groups. The yeastDrop-Seq platform facilitates transcriptomic profiling of yeast cells for basic science and biotechnology applications.

A schematic of the single-cell mRNA sequencing workflow
for transcriptomic analysis of yeast cells

Fig. 1

The yeastDrop-Seq solution containing chemicals for cell-wall digestion and cell lysis is mixed with barcoded microbeads, and the mixture is flown through one inlet of a microfluidic device. Yeast cells with intact cell walls and oil are flown through the second and third inlet of the microfluidic device, respectively. Encapsulated cells are then incubated to allow for cell-wall breakage and lysis. mRNA molecules hybridize to the barcoded microbeads via their polyA tails, droplets are broken, and reverse transcription occurs. cDNA is PCR-amplified and the cDNA libraries are prepared and submitted for sequencing.

Urbonaite G, Lee JTH, Liu P et al. (2021) A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Commun Biol 4, 822. [article]

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