Non-coding RNAs have broadly been divided into small (<200 nt) and long (>200 nt) transcripts. However, eukaryote transcriptomes are also composed of several classes of transcripts whose size range spans the border between small and long RNA. Transcripts in this size range (70–500 nt) are referred as ‘intermediate-size ncRNAs’ (is-ncRNAs), the functional properties of which are just beginning to be touched upon.

Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to is-ncRNAs of mostly unknown function.

Professor Runsheng Chen’s group at the Institute of Biophysics, Chinese Academy of Sciences carried out a tiling array analysis which identified approximately 1200 novel intermediate-size transcripts in a mixed stage culture of C. elegans. Recently, they further identified 5866 novel intermediate-size transcripts through the C. elegans life cycle. The novel loci have been shown distributed across intronic and intergenic space, with some enrichment toward protein-coding gene termini. They found the majority of the putative is-ncRNAs show either stage-specific expression, or distinct developmental variation in their expression levels, such as involvement of is-ncRNAs in sex-specific functions. In addition, they also observed that half of the novel loci are conserved in other nematodes, and numerous loci show significant conservational correlations to nearby coding genes. Their data imply a nematode is-ncRNA tool kit of considerable size and variety.

This work exhibits more complex expression patterns of is-ncRNA across stages of C. elegans, which have features different from that of known is-ncRNAs types and coding genes, suggesting the existence of novel functional types of intermediate-size RNAs. It is published in the latest issue of the Journal of NUCLEIC ACIDS RESEARCH (2011,39(12):5203-5214).