In the past few years, ncRNAs have progressed from interesting anomalies to what some researchers think constitute the majority of the mammalian transcriptome. However, as reviewed by John Mattick and coworkers at the University of Queensland and the Ludwig Institute for Cancer Research (both in Australia), it’s increasingly difficult to distinguish coding from noncoding RNAs on the basis of sequence alone. Furthermore, the finding that some transcripts can function as both ncRNAs and protein-coding mRNAs suggests a false dichotomy between the two classes.
Several criteria have been proposed to discriminate between ncRNAs and mRNAs, including open reading frame (ORF) length, ORF conservation with known proteins or domains, and RNA secondary structure. Although some strategies, particularly those that combine several complementary approaches, have proven successful in certain contexts, all have limitations, and the functions of many novel transcripts remain ambiguous.
Because several bifunctional RNA transcripts that both encode proteins and function independently as ncRNAs have been reported, Mattick and colleagues suggest that RNA is a multi-tasking molecule that resists simple categorization into “protein-coding” and “noncoding” roles. Therefore, the characterization of RNA transcripts should be approached with an open mind to the full spectrum of RNA functionalities. Read all about it at PLoS Computational Biology, December 2008.