The rise of single‐cell transcriptomics in yeast

Abstract

The field of single‐cell omics has transformed our understanding of biological processes and is constantly advancing both experimentally and computationally. One of the most significant developments is the ability to measure the transcriptome of individual cells by single‐cell RNA‐seq (scRNA‐seq), which was pioneered in higher eukaryotes. While yeast has served as a powerful model organism in which to test and develop transcriptomic technologies, the implementation of scRNA‐seq has been significantly delayed in this organism, mainly because of technical constraints associated with its intrinsic characteristics, namely the presence of a cell wall, a small cell size and little amounts of RNA. In this review, we examine the current technologies for scRNA‐seq in yeast and highlight their strengths and weaknesses. Additionally, we explore opportunities for developing novel technologies and the potential outcomes of implementing single‐cell transcriptomics and extension to other modalities. Undoubtedly, scRNA‐seq will be invaluable for both basic and applied yeast research, providing unique insights into fundamental biological processes.

Gene transcription in yeasts: From molecules to integrated processes

“…However, two main facts come to mind, particularly in view of the papers published in this Special Issue. First, the more we use advanced technologies to dig into the transcription process, the more we uncover an unsuspected diversity in the features of transcriptomes, as highlighted by native elongating transcript sequencing (Xi et al, 2024), long-read sequencing (Koster et al, 2024), single-cell transcriptomics (Brettner et al, 2024;Nadal-Ribelles et al, 2024) or live imaging (Kindongo et al, 2024). Second, it is now obvious that transcription must be envisioned in a broader picture since it is tightly intertwined with other nuclear processes, that is, downstream events in RNA metabolism such as RNA processing (Albihlal et al, 2024;Struhl, 2023), localization and turnover, but also several DNAdependent transactions, including chromatin organization (Georis et al, 2023;Yague-Sanz, 2024), replication and repair (Piguet & Houseley, 2024).…”