Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

Hagen Tilgner, Fereshteh Jahanbani, Tim Blauwkamp, Ali Moshrefi, Erich Jaeger, Feng Chen, Itamar Harel, Carlos D. Bustamante, Morten Rasmussen, Michael P. Snyder*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

140 Scopus citations

Abstract

Alternative splicing shapes mammalian transcriptomes, with many RNA molecules undergoing multiple distant alternative splicing events. Comprehensive transcriptome analysis, including analysis of exon co-association in the same molecule, requires deep, long-read sequencing. Here we introduce an RNA sequencing method, synthetic long-read RNA sequencing (SLR-RNA-seq), in which small pools (≤ 1,000 molecules/pool, ≤ 1 molecule/gene for most genes) of full-length cDNAs are amplified, fragmented and short-read-sequenced. We demonstrate that these RNA sequences reconstructed from the short reads from each of the pools are mostly close to full length and contain few insertion and deletion errors. We report many previously undescribed isoforms (human brain: ∼ 13,800 affected genes, 14.5% of molecules; mouse brain ∼ 8,600 genes, 18% of molecules) and up to 165 human distant molecularly associated exon pairs (dMAPs) and distant molecularly and mutually exclusive pairs (dMEPs). Of 16 associated pairs detected in the mouse brain, 9 are conserved in human. Our results indicate conserved mechanisms that can produce distant but phased features on transcript and proteome isoforms.

Original languageAmerican English
Pages (from-to)736-742
Number of pages7
JournalNature Biotechnology
Volume33
Issue number7
DOIs
StatePublished - 13 Jul 2015
Externally publishedYes

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© 2015 Nature America, Inc. All rights reserved.

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