Despite recent technological advances such as RNA-Seq, we have still not yet reached the limits of the transcriptome nor realized its full scale and complexity, fueling ongoing debate as to the extent to which the genome is transcribed and the biological relevance of transcripts that are expressed at low levels.
Now, a group led by researchers at the University of Queensland has developed a new method that combines RNA capture with RNA-Seq to reveal the deep complexity of the human transcriptome. RNA CaptureSeq involves the construction of tiling arrays across genomic regions of interest, against which cDNAs are hybridized, eluted and sequenced. Although this ability to isolate and target RNA has been used in genetic analysis for some time, here the researchers combine this ability with deep-sequencing technology to provide saturating coverage and permit the robust assembly of rare and unannotated transcripts.
The data also show that intermittent sequenced reads observed in conventional RNA sequencing data sets, previously dismissed as noise, are in fact indicative of unassembled rare transcripts. Collectively, these results reveal the range, depth and complexity of a human transcriptome that is far from fully characterized.
- Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. (2011) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotech [Epub ahead of print]. [abstract]