RNA-seq: from technology to biology

Abstract

Next-generation sequencing technologies are now being exploited not only to analyse static genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these powerful and rapidly evolving technologies have only been available for a couple of years, they are already making substantial contributions to our understanding of genome expression and regulation. Here, we briefly describe technical issues accompanying RNA-seq data generation and analysis, highlighting differences to array-based approaches. We then review recent biological insight gained from applying RNA-seq and related approaches to deeply sample transcriptomes in different cell types or physiological conditions. These approaches are providing fascinating information about transcriptional and post-transcriptional gene regulation, and they are also giving unique insight into the richness of transcript structures and processing on a global scale and at unprecedented resolution.

Fig. 1

Flowchart of a typical RNA-seq experiment

Fig. 2

Detection of post-transcriptional modifications and rearrangements by RNA-seq. a Reads spanning exon–exon junctions give positive evidence for splicing events (trans-reads in red). Comparing the number of trans-reads for a selected junction to the number of reads spanning its corresponding exon–intron junctions (blue) gives a measure of splicing efficiency. b Reads containing poly(A) tracts which are not encoded in the reference genome are diagnostic of polyadenylation events. c Reads containing sequence polymorphisms compared with the reference genome are potential polymorphisms or editing sites