Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Ashley Byrne, Anna E. Beaudin, Hugh E. Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M. DuBois, E. Camilla Forsberg, Mark Akeson and Christopher Vollmers ()
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Ashley Byrne: Cell, and Developmental Biology, University of California-Santa Cruz
Anna E. Beaudin: University of California-Santa Cruz
Hugh E. Olsen: UC Santa Cruz Genomics Institute
Miten Jain: UC Santa Cruz Genomics Institute
Charles Cole: UC Santa Cruz Genomics Institute
Theron Palmer: University of California-Santa Cruz
Rebecca M. DuBois: University of California-Santa Cruz
E. Camilla Forsberg: University of California-Santa Cruz
Mark Akeson: UC Santa Cruz Genomics Institute
Christopher Vollmers: UC Santa Cruz Genomics Institute

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: Abstract Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After benchmarking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level.

Date: 2017
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DOI: 10.1038/ncomms16027

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