PT  - JOURNAL ARTICLE
AU  - Robin Andersson
AU  - Peter Refsing Andersen
AU  - Eivind Valen
AU  - Leighton J. Core
AU  - Jette Bornholdt
AU  - Mette Boyd
AU  - Torben Heick Jensen
AU  - Albin Sandelin
TI  - Nuclear stability and transcriptional directionality separate functionally distinct RNA species
AID  - 10.1101/005447
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 005447
4099  - http://biorxiv.org/content/early/2014/08/29/005447.short
4100  - http://biorxiv.org/content/early/2014/08/29/005447.full
AB  - Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. While recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.