Transcriptome-wide discovery of circular RNAs in Archaea

RNase R is a unique Epicentre enzyme that is finding greater use in studying single-stranded RNAs, including circular RNAs that contain linear single protruding strands ("lariats"). These molecules have important biological functions, including roles in viral life cycles and tRNA maturation. However, discovery of circular RNAs has so far been mostly serendipitous, and methods to study these molecules are needed.

Danan et al. developed a directed method to pinpoint RNA-Seq reads that have a permuted mapping to the genome, a characteristic of circular RNA. They developed a workflow to enrich for circular transcripts and overcome possible artifacts, by pretreating the RNA sample using RNase R. The isolated circular RNA was used in the development of a new sequencing method, "circRNA-Seq", which uses enriched circular RNAs and allows quantification of relative abundance/prevalence of these RNAs in the cell in an unbiased way. The authors applied the technique to the archaeon Sulfolobus solfataricus P2. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but also many noncoding RNAs and circular RNAs of unknown function. Many of the identified circles were conserved in S. acidocaldarius, further supporting their functional significance. The data suggest that circular RNAs, especially circular noncoding RNAs, are more common in archaea than previously recognized. The circRNA-seq method will enable the study of these novel RNAs in any organism and will help to determine their relative importance in the biology of the cell.

Danan, M. et al. (2011). Transcriptome-wide discovery of circular RNAs in Archaea Nucleic Acids Research DOI: 10.1093/nar/gkr1009