Main menu

Nanopore sequencing accurately resolves alternatively spliced transcripts


Short-read sequencing technologies struggle with transcripts of genes with multiple isoforms, due to difficulties in measuring exon connectivity where many exons are located further away from each other than the maximum read length1, 2. Bolisetty et al.1 used nanopore sequencing and the Drosophila model system for a transcriptomic analysis of genes famous for having a large number of isoforms (Dscam1, Rdl, MRP, Mhc).

The team detected a total of 7,899 full-length isoforms for these four genes using a gene-specific RT-PCR approach. Dscam1 is the most abundantly alternatively spliced gene known and it has the potential to generate a total of 38,016 isoforms (115 exons, 95 of which are alternatively spliced, forming 4 clusters)3. For the purpose of the study, the authors focused on the region covering exons 3–10 (19,008 potential isoforms). They were able to reliably resolve 7,874 Dscam1 isoforms with an average identity of >90% for full-length alignments, despite the fact that the exons within each cluster shared 80% nucleotide identity with each other (Figure 1).

Bolisetty et al.1 demonstrated that long nanopore reads are particularly suited for the characterisation of multipleisoform transcripts, even in cases where exons have significant similarity to one another.

A total of 7,874 Dscam1 isoforms, with an average identity of >90% for full-length alignments, were reliably resolved.

Figure 1: Nanopore sequencing of Dscam1 isoforms. Exon cluster variants (top) and the isoform connectivity of two highly expressed Dscam1 isoforms (bottom). Image taken with permission from Professor Brenton Graveley, University of Connecticut Health Center, Farmington, Connecticut, USA; image originally part of a figure from an article1 published by BioMed Central.
  1. Bolisetty, M. T., Rajadinakaran, G. & Graveley, B. R. Determining exon connectivity in complex mRNAs by nanopore sequencing. Genome Biol. 16, 204 (2015).
  2. Clark, M. Elucidating the expression and splicing patterns of neuropsychiatric disease genes in human brain. Presentation. Available at: [Accessed: 22 October 2019]
  3. Schmucker, D. et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101(6):671-84 (2000).

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

纳米孔技术

订阅 Nanopore 更新 资源库及发表刊物 什么是 Nanopore 社区

关于 Oxford Nanopore

新闻 公司历程 可持续发展 领导团队 媒体资源和联系方式 投资者 合作者 在 Oxford Nanopore 工作 职位空缺 商业信息 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag