Determining exon connectivity in complex mRNAs by nanopore sequencing

Genome Biol. 2015 Sep 30:16:204. doi: 10.1186/s13059-015-0777-z.

Abstract

Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length. Here, we use the Oxford Nanopore MinION sequencer to identify 7,899 'full-length' isoforms expressed from four Drosophila genes, Dscam1, MRP, Mhc, and Rdl. These results demonstrate that nanopore sequencing can be used to deconvolute individual isoforms and that it has the potential to be a powerful method for comprehensive transcriptome characterization.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP-Binding Cassette Transporters / genetics
  • Animals
  • Cell Adhesion Molecules
  • Drosophila
  • Drosophila Proteins / genetics
  • Exons / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Myosins / genetics
  • Nanopores*
  • Neural Cell Adhesion Molecules / genetics
  • Protein Isoforms / genetics
  • RNA, Messenger / genetics*
  • Receptors, GABA-A / genetics
  • Transcriptome / genetics

Substances

  • ATP-Binding Cassette Transporters
  • Cell Adhesion Molecules
  • Drosophila Proteins
  • Dscam1 protein, Drosophila
  • MRP protein, Drosophila
  • Neural Cell Adhesion Molecules
  • Protein Isoforms
  • RNA, Messenger
  • Rdl protein, Drosophila
  • Receptors, GABA-A
  • myosin-18, Drosophila
  • Myosins