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

Author

Listed:
  • Ashley Byrne

    (Cell, and Developmental Biology, University of California-Santa Cruz
    UC Santa Cruz Genomics Institute)

  • Anna E. Beaudin

    (University of California-Santa Cruz
    Present address: Department of Molecular and Cell Biology, School of Natural Sciences, University of California-Merced, 5200 Lake Rd, Merced, California 95343, USA)

  • Hugh E. Olsen

    (UC Santa Cruz Genomics Institute
    University of California-Santa Cruz)

  • Miten Jain

    (UC Santa Cruz Genomics Institute
    University of California-Santa Cruz)

  • Charles Cole

    (UC Santa Cruz Genomics Institute
    University of California-Santa Cruz)

  • Theron Palmer

    (University of California-Santa Cruz)

  • Rebecca M. DuBois

    (University of California-Santa Cruz)

  • E. Camilla Forsberg

    (University of California-Santa Cruz
    Institute for the Biology of Stem Cells, University of California-Santa Cruz)

  • Mark Akeson

    (UC Santa Cruz Genomics Institute
    University of California-Santa Cruz)

  • Christopher Vollmers

    (UC Santa Cruz Genomics Institute
    University of California-Santa Cruz)

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.

Suggested Citation

  • Ashley Byrne & Anna E. Beaudin & Hugh E. Olsen & Miten Jain & Charles Cole & Theron Palmer & Rebecca M. DuBois & E. Camilla Forsberg & Mark Akeson & Christopher Vollmers, 2017. "Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms16027
    DOI: 10.1038/ncomms16027
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    Cited by:

    1. Shuyao Zhang & Yuhua Xiao & Xinzhi Mo & Xu Chen & Jiawei Zhong & Zheyao Chen & Xu Liu & Yuanhui Qiu & Wangxuan Dai & Jia Chen & Xishan Jin & Guoping Fan & Youjin Hu, 2024. "Simultaneous profiling of RNA isoforms and chromatin accessibility of single cells of human retinal organoids," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Ashley Byrne & Daniel Le & Kostianna Sereti & Hari Menon & Samir Vaidya & Neha Patel & Jessica Lund & Ana Xavier-Magalhães & Minyi Shi & Yuxin Liang & Timothy Sterne-Weiler & Zora Modrusan & William S, 2024. "Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Angeles Arzalluz-Luque & Pedro Salguero & Sonia Tarazona & Ana Conesa, 2022. "acorde unravels functionally interpretable networks of isoform co-usage from single cell data," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Zhuo-Xing Shi & Zhi-Chao Chen & Jia-Yong Zhong & Kun-Hua Hu & Ying-Feng Zheng & Ying Chen & Shang-Qian Xie & Xiao-Chen Bo & Feng Luo & Chong Tang & Chuan-Le Xiao & Yi-Zhi Liu, 2023. "High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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