Prokaryotic transcripts constitute almost always uninterrupted intervals when mapped back to the genome. Split reads, i.e., RNA-seq reads consisting of parts that only map to discontiguous loci, are thus disregarded in most analysis pipelines. There are, however, some well-known exceptions, in particular, tRNA splicing and circularized small RNAs in Archaea as well as self-splicing introns.
Here, researchers at the University of Leipzig, Germany reanalyze a series of published RNA-seq data sets, screening them specifically for non-contiguously mapping reads. They recover most of the known cases together with several novel archaeal ncRNAs associated with circularized products. In Eubacteria, only a handful of interesting candidates were obtained beyond a few previously described group I and group II introns. Most of the atypically mapping reads do not appear to correspond to well-defined, specifically processed products. Whether this diffuse background is, at least in part, an incidental by-product of prokaryotic RNA processing or whether it consists entirely of technical artifacts of reverse transcription or amplification remains unknown.
- Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. (2013) Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol [Epub ahead of print]. [abstract]