Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
Despite increasing interest in the noncoding fraction of transcriptomes, the number, species-conservation and functions, if any, of many non-protein-coding transcripts remain to be discovered. Two extensive long intergenic noncoding RNA (ncRNA) transcript catalogues are now available for mouse: over 3000 macroRNAs identified by cDNA sequencing, and 1600 long intergenic noncoding RNA (lincRNA) intervals that are predicted from chromatin-state maps.
Previously we showed that macroRNAs tend to be more highly conserved than putatively neutral sequence, although only 5% of bases are predicted as constrained. By contrast, over a thousand lincRNAs were reported as being highly conserved.
This apparent difference may account for the surprisingly small fraction (11%) of transcripts that are represented in both catalogues. Here we sought to resolve the reported discrepancy between the evolutionary rates for these two sets.
Results: Our analyses reveal lincRNA and macroRNA exon sequences to be subject to the same relatively low degree of sequence constraint.
Nonetheless, our observations are consistent with the functionality of a fraction of ncRNA in these sets, with up to a quarter of ncRNA exons having evolved significantly slower than neighbouring neutral sequence. The more tissue-specific macroRNAs are enriched in predicted RNA secondary structures and thus may often act in trans, whereas the more highly- and broadly-expressed lincRNAs appear more likely to act in the cis-regulation of adjacent transcription factor genes.
Conclusions: Taken together, our results indicate that each of the two ncRNA catalogues unevenly and lightly samples the true, much larger, ncRNA repertoire of the mouse.
Author: Ana MarquesChris Ponting
Credits/Source: Genome Biology 2009, 10:R124
Published on: 2009-11-06
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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