Single-cell RNA counting at allele and isoform resolution using Smart-seq3

By Michael Hagemann-Jensen, C. Ziegenhain, Ping Chen, Daniel Ramsköld, Gert‐Jan Hendriks, Anton J. M. Larsson, O. Faridani, Rickard Sandberg. Nature Biotechnology, 2019

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Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states1. However, current short-read single-cell RNA-sequencing methods have limited ability to count RNAs at allele and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells2,3. Here we introduce Smart-seq3, which combines full-length transcriptome coverage with a 5′ unique molecular identifier RNA counting strategy that enables in silico reconstruction of thousands of RNA molecules per cell. Of the counted and reconstructed molecules, 60% could be directly assigned to allelic origin and 30–50% to specific isoforms, and we identified substantial differences in isoform usage in different mouse strains and human cell types. Smart-seq3 greatly increased sensitivity compared to Smart-seq2, typically detecting thousands more transcripts per cell. We expect that Smart-seq3 will enable large-scale characterization of cell types and states across tissues and organisms. Smart-seq3 enables isoform- and allele-specific reconstruction of RNA molecules.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7fbd585f910e0a3e7c787cf172372e1edc56a8c3