Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

The mammalian transcriptome contains many non-protein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

Introduction

Recent transcriptome analyses have shown that most of the metazoan genome is transcribed 1, 2. Using cDNA cloning 3, 4, 5, 6, 7, 8, 9 and genome tiling arrays 10, 11, 12, 13, 14, 15, 16, researchers have detected surprisingly large numbers of candidate non protein-coding RNAs (ncRNAs), many of which appear to be localized to the nucleus and/or lack polyadenylation [15]. The function – if any – of these transcripts remains a matter of debate 17, 18, the resolution of which will have important implications for our understanding of genome biology.

Wang and colleagues recently reported that non-protein-coding transcripts identified in mouse cDNA collections are poorly conserved and therefore argued that they are likely to be non-functional [19]. By contrast, many members of known functional classes of ncRNAs – including microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) – are well-conserved across a diverse range of species 4, 5, 6, 7. Candidate ncRNAs however average ∼2 kb in length 9, 20 and hence are different from miRNAs and snoRNAs (which are typically 21–25 nt and 60–300 nt, respectively), and it might be more meaningful to compare their evolution with longer ncRNAs whose functions have been validated. Well-studied large ncRNAs such as Xist and Air are poorly conserved, although there are small segments of their sequences that are highly conserved 21, 22, 23, 24, 25. Therefore, the possibility arises that different types of ncRNAs can exhibit different patterns of sequence conservation. Here we provide evidence that supports this hypothesis and discuss the possible interpretations and implications of our results.