Identification and Classification of Small Rnas in Transcriptome Sequence Data

Abstract

Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.

Animal snoRNAs and scaRNAs with exceptional structures

“…In addition, paralogous sequences are found in several species, often populating additional exons of LARP4. Short RNA fragments deriving from ggn68, as observed for many other snoRNAs, 31,32 have been reported a long low complexity region in the central part of the sequence. The total length of the gene is thus highly variable, ranging from 163 nt in Mus to 289 nt in Tursiops.…”

Dicer‐Processed Small RNAs: Rules and Exceptions

“…Short, microRNAlike RNAs are processed from a diverse set of usually well-structured non-coding RNAs that includes tRNAs (Lee et al, 2009;Cole et al, 2009;Haussecker et al, 2010;Findeiß et al, 2011;Sobala and Hutvagner, 2011), snoRNAs (Kawaji et al, 2008;Taft et al, 2009;Langenberger et al, 2010;Brameier et al, 2011), vault RNAs Persson et al, 2009), Y RNAs (Langenberger et al, 2010Meiri et al, 2010;Verhagen and Pruijn, 2011), and snRNAs (Langenberger et al, 2010). Not much is known about the maturation of most of these small RNAs.…”

MicroRNA or Not MicroRNA?

“…While microRNAs are matured to ∼ 20nt sequences that direct post-transcriptional gene silencing, snoRNAs canonically guide, in their complete form, the chemical modification of mostly rRNAs and snRNAs [1]. On the other hand, high-throughput sequencing studies revealed that snoRNAs are a prolific source of sequence fragments of microRNA size [2][3][4][5], termed sdRNAs. At least some of these snoRNA-derived small RNAs, similar to microRNAs, interact human Argonaut and affect gene expression [6].…”

“…Recently, efficient gene silencing has been demonstrated for 11 small RNAs derived from box C/D sno-miRNA [5]. Similar short RNAs, in a few cases with validated functions in gene silencing, are also produced from most other well-known structured RNAs including Y RNA [4,7], vault RNAs [8][9][10], snRNAs [4], and tRNAs [11][12][13][14]. Recent work [15], furthermore, cast doubt on the microRNA nature of several short RNA products that likely originate from the 3'-end of matured tRNAs since they include the post-transcriptionally append CCA tail.…”