Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations

Abstract

Single-cell RNA sequencing has revealed extensive cellular heterogeneity within many organisms, but few methods have been developed for microbial clonal populations. The yeast genome displays unusually dense transcript spacing, with interleaved and overlapping transcription from both strands, resulting in a minuscule but complex pool of RNA that is protected by a resilient cell wall. Here, we have developed a sensitive, scalable and inexpensive yeast single-cell RNA-seq (yscRNA-seq) method that digitally counts transcript start sites in a strand- and isoform-specific manner. YscRNA-seq detects the expression of low-abundance, noncoding RNAs and at least half of the protein-coding genome in each cell. In clonal cells, we observed a negative correlation for the expression of sense–antisense pairs, whereas paralogs and divergent transcripts co-expressed. By combining yscRNA-seq with index sorting, we uncovered a linear relationship between cell size and RNA content. Although we detected an average of ~3.5 molecules per gene, the number of expressed isoforms is restricted at the single-cell level. Remarkably, the expression of metabolic genes is highly variable, whereas their stochastic expression primes cells for increased fitness towards the corresponding environmental challenge. These findings suggest that functional transcript diversity acts as a mechanism that provides a selective advantage to individual cells within otherwise transcriptionally heterogeneous populations.

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Fig. 1: Absolute transcriptome quantification of single yeast cells using yscRNA-seq.
Fig. 2: yscRNA-seq as a tool to quantitatively profile transcriptional architectures and TSS variation.
Fig. 3: yscRNA-seq reveals a high-resolution map of the transcriptional heterogeneity within clonal yeast populations.
Fig. 4: Functional consequences of stochastic gene expression.

Code availability

Custom code generated in this study can be downloaded from http://steinmetzlab.embl.de/yscRNASeq/.

Data availability

All data generated in this study has been uploaded to Gene Expression Omnibus under accession number GSE122392.

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Acknowledgements

The authors would like to thank S. Linnarsson for providing reagents during the initial tests with yscRNA-seq. We thank the Protein Expression and Purification Core Facility at EMBL, B. Hennig and L. Velten for providing in-house purified Tn5. We thank R. Böttcher for fruitful discussions. We thank D. Caetano-Anollés for editing and refining the manuscript. M.N.-R. was a recipient of an EMBO long-term fellowship (Stanford University) and later of a Maria de Maeztu Postdoctoral Fellowship (Doctores Banco de Santander-María de Maeztu at Universitat Pompeu Fabra). P.L. is a recipient of a FI Predoctoral Fellowship (Generalitat de Catalunya). This work was supported by the National Institutes of Health and a European Research Council Advanced Investigator Grant (grant no. AdG-294542 to L.M.S.) and the National Key Research and Development Program of China (grant no. 2017YFC0908405 to W.W.). The study was also supported by grants from the Spanish Ministry of Economy and Competitiveness (grant nos BFU2015-64437-P, FEDER, BFU2014-52125-REDT and BFU2014-51672-REDC to F.P.; BFU2017-85152-P and FEDER to E.d.N.), the Catalan Government (grant no. 2017 SGR 799), the Fundación Botín, the Banco Santander through its Santander Universities Global Division to F.P. and the Unidad de Excelencia Maria de Maeztu, grant no. MDM-2014-0370. F.P. is a recipient of an ICREA Acadèmia (Generalitat de Catalunya).

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Contributions

M.N.-R., S.I., W.W. and L.M.S. conceived the project. M.N.-R., S.I., W.W., P.L. and M.N. developed the protocol and performed the analyses. M.N.-R., S.I. and M.N. performed the experiments. W.W. and P.L. performed the computational analyses. M.N.-R., S.I., P.L., W.W., E.d.N., F.P. and L.M.S. participated in experimental design, data analysis and writing the manuscript. E.d.N., F.P. and L.M.S. supervised the work. All authors read and edited the manuscript.

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Correspondence to Lars M. Steinmetz.

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Supplementary information

Supplementary Information

Supplementary Figures 1–4, and Supplementary Tables 1 and 2.

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Supplementary Table 3

Raw expression BY4741 yscRNA-seq libraries after applying the quality filter criteria (total of 127 cells). Table contains raw number of molecules for each gene (rows) for each cell (rows).

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Nadal-Ribelles, M., Islam, S., Wei, W. et al. Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nat Microbiol 4, 683–692 (2019). https://doi.org/10.1038/s41564-018-0346-9

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