Prospects for the use of third generation sequencers for quantitative profiling of transcriptome

  • S.P. Radko Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • L.K. Kurbatov Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • K.G. Ptitsyn Adzhinomoto-Genetika,1 Dorozhny 1-st Road, Moscow, 117545 Russia
  • Y.Y. Kiseleva Russian Scientific Center of Roentgenoradiology, 86 Profsoyuznaya str., Moscow, 117997 Russia
  • E.A. Ponomarenko Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • A.V. Lisitsa Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • A.I. Archakov Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
Keywords: third generation sequencing; transcriptome; quantitative profiling

Abstract

Transcriptome profiling is widely employed to analyze transcriptome dynamics when studying various biological processes at the cell and tissue levels. Unlike the second generation sequencers, which sequence relatively short fragments of nucleic acids, the third generation DNA/RNA sequencers developed by biotechnology companies “PacBio” and “Oxford Nanopore Technologies” allow one to sequence transcripts as single molecules and may be considered as potential molecular counters capable to measure the number of copies of each transcript with high throughput, sensitivity, and specificity. In the present review, the features of single molecule sequencing technologies offered by “PacBio” and “Oxford Nanopore Technologies” are considered alongside with their utility for transcriptome analysis, including the analysis of transcript isoforms. The prospects and limitations of the single molecule sequencing technology in application to quantitative transcriptome profiling are also discussed.

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Published
2018-12-20
Section
Reviews