Beyond microRNAs: treasures in short-read sequencing data

Current methods for high throughput sequencing offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. Primarily focussed at quantifying microRNA expression, extensive datasets of small RNAs with a length of less than 30nt are being produced. These data sets turn out to be a rich treasure trove of information on novel RNA classes as well as details of RNA processing.

The well-known classes of structured ncRNAs, including snoRNAs, snRNAs, and tRNAs, undergo maturation processes that lead to the production of shorter RNAs that are similar to mature microRNAs. The corresponding read patterns are largely determined by the parental structure. They can be employed, therefore, for the detection of new housekeeping ncRNAs from short-read libraries. In addition these data sets also contain novel classes of short RNAs such as microRNA-offset RNAs (moRNAs). Surprisingly, microRNA precursors that also produce moRNAs are typically evolutionarily old.

Many aspects of the RNA maturation, furthermore, leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. In particular, chemical modifications leave their signatures in forms of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes. Starting from the recovery of many well-known modified sites in tRNAs we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which, surprisingly, can be found in a diverse collection of transcripts, including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.