A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

 

Tomas Babak^1,2, Benjamin J Blencowe^1,2, and Timothy R Hughes^1,2

¹Banting and Best Department of Medical Research, 112 College St., Toronto, ON M5G 1L6 Canada

²Department of Medical Genetics and Microbiology, 10 King’s College Circle, Toronto, ON M1R 4F9 Canada

 

Correspondence: Timothy R Hughes. E-mail: t.hughes@utoronto.ca

 

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Abstract

 

Background.  Systematic identification and functional characterization of novel types of noncoding (nc)RNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs typically do not possess sequence features such as splicing signals, translation signals, or significant reading frames.  Recent analyses have reported that a surprisingly larger proportion of mammalian genomes is transcribed than was previously anticipated.  However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known.

 

Results.  To systematically search for functional ncRNAs, we designed microarrays to detect 3,478 intergenic and intronic sequences that are conserved between the human, mouse, and rat genomes, and that score highly by other criteria that characterize ncRNAs.  We probed these arrays with total RNA isolated from 16 wild-type mouse tissues.  Among 55 candidates tested by northern blotting, eight were confirmed as small, highly- and ubiquitously-expressed RNAs in mouse, five were detected in rat tissues, but none were detected at appreciable levels in human tissues or cultured cells.

 

Conclusions.  Since the sequence and expression of most known coding transcripts and functional ncRNAs is conserved between human and mouse, the lack of expression in human cells and tissues of the novel mouse and rat ncRNAs that we identified suggests that they are not functional or possibly have rodent-specific functions.  Our results also confirm that relatively little of the intergenic sequence conserved between human, mouse and rat is transcribed at high levels in mammalian tissues, further suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements.