Dataset Information

Getting the Entire Message: Progress in Isoform Sequencing.

ABSTRACT: The advent of second-generation sequencing and its application to RNA sequencing have revolutionized the field of genomics by allowing quantification of gene expression, as well as the definition of transcription start/end sites, exons, splice sites and RNA editing sites. However, due to the sequencing of fragments of cDNAs, these methods have not given a reliable picture of complete RNA isoforms. Third-generation sequencing has filled this gap and allows end-to-end sequencing of entire RNA/cDNA molecules. This approach to transcriptomics has been a "niche" technology for a couple of years but now is becoming mainstream with many different applications. Here, we review the background and progress made to date in this rapidly growing field. We start by reviewing the progressive realization that alternative splicing is omnipresent. We then focus on long-noncoding RNA isoforms and the distinct combination patterns of exons in noncoding and coding genes. We consider the implications of the recent technologies of direct RNA sequencing and single-cell isoform RNA sequencing. Finally, we discuss the parameters that define the success of long-read RNA sequencing experiments and strategies commonly used to make the most of such data.

SUBMITTER: Hardwick SA

PROVIDER: S-EPMC6706457 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Getting the Entire Message: Progress in Isoform Sequencing.

Hardwick Simon A SA Joglekar Anoushka A Flicek Paul P Frankish Adam A Tilgner Hagen U HU

Frontiers in genetics 20190816

The advent of second-generation sequencing and its application to RNA sequencing have revolutionized the field of genomics by allowing quantification of gene expression, as well as the definition of transcription start/end sites, exons, splice sites and RNA editing sites. However, due to the sequencing of fragments of cDNAs, these methods have not given a reliable picture of complete RNA isoforms. Third-generation sequencing has filled this gap and allows end-to-end sequencing of entire RNA/cDNA ...[more]

PMID: 31475029

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Dataset Information

Getting the Entire Message: Progress in Isoform Sequencing.

Publications

Getting the Entire Message: Progress in Isoform Sequencing.

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