2015
DOI: 10.1186/s13059-015-0777-z
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Determining exon connectivity in complex mRNAs by nanopore sequencing

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 … Show more

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Cited by 144 publications
(123 citation statements)
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“…To illustrate, Bolisetty et al [8] used the MinION to determine RNA splice variants and to detect isoforms for four genes in Drosophila . Among these is Dscam1 , the most complex alternatively spliced gene known in nature, with 18,612 possible isoforms ranging in length from 1806 bp to 1860 bp [8].…”
Section: Benefits Of Minion Compared To Other Next Generation Sequencmentioning
confidence: 99%
See 1 more Smart Citation
“…To illustrate, Bolisetty et al [8] used the MinION to determine RNA splice variants and to detect isoforms for four genes in Drosophila . Among these is Dscam1 , the most complex alternatively spliced gene known in nature, with 18,612 possible isoforms ranging in length from 1806 bp to 1860 bp [8].…”
Section: Benefits Of Minion Compared To Other Next Generation Sequencmentioning
confidence: 99%
“…Among these is Dscam1 , the most complex alternatively spliced gene known in nature, with 18,612 possible isoforms ranging in length from 1806 bp to 1860 bp [8]. They detected over 7000 isoforms for Dscam1 with >90% alignment identity.…”
Section: Benefits Of Minion Compared To Other Next Generation Sequencmentioning
confidence: 99%
“…A good agreement between the abundance of targeted cDNA amplicons sequenced with the ONT MinION and the Illumina MiSeq platforms, has been observed in another study10. Given that the platform can be used for accurate quantification of isoform expression abundance it is very important to be able to use as many sequenced reads as possible with the caveat of being of a lower quality.…”
Section: Discussionmentioning
confidence: 62%
“…Many of the events are reminiscent of wellstudied examples of high-entropy AS in other systems, such as the myriad of splice variants generated by tandem arrays of alternative exons in the Drosophila DSCAM gene 32 . In this classic example, high-entropy AS events overlap tandemly repeated immunoglobulin-like domains that function as interaction surfaces in neural circuit assembly 33 .…”
Section: Discussionmentioning
confidence: 99%