Mining diverse small RNA species in the deep transcriptome

Abstract

Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance.

Keywords: RNA sequencing; data analysis; high-throughput sequencing; long-noncoding RNA; microRNA; small RNA; transcriptome.

Figure 1

Schematic illustrating the diversity of long and small RNAs. The gold edge represents small RNAs (sRNA) derived from long parent RNA; sRNAs are RNAs ≤200 nt in length whereas long RNA are significantly bigger. (Long RNAs) hTR, human telomerase RNA; lincRNA, large intergenic non-coding RNA; LINE, long interspersed element; lncRNA, long non-coding RNA; LTR, long terminal repeat; mRNA; PASR, promoter-associated long RNA; RMPR, RNA component of mitochondrial RNA processing endoribonuclease RPPH1, ribonuclease P RNA component H1; rRNA, ribosomal RNA; SINE, short interspersed element; TASR, termini-associated sRNA; TERRA, telomeric repeat-containing RNA; T-UCR, transcribed ultraconserved region. (Small RNAs) casiRNA, cis-acting siRNA; crasiRNA, centromere repeat-associated sRNA; diRNA, double-strand break-induced sRNA; endo-siRNA, endogenous small interfering RNA; exo-siRNA, exogeneous small interfering RNA; hc-siRNA, heterochromatic small interfering RNA; miRNA, microRNA; natsiRNA, natural antisense siRNA; piRNA, Piwi-interacting RNA; qiRNA, QDE-2-interacting sRNA; rasiRNA, repeat-associated siRNA; ScaRNA, small Cajal-body RNA; sbRNA, stem-bulge RNA; sdRNA, snoRNA-derived small RNA; SNAR, small NF90-associated RNA; snoRNA, small nucleolar RNA; snRNA, small nuclear RNA; srRNA, sRNAs-derived from rRNA; svRNA, small vault RNA; tasiRNA, trans-acting siRNA; tDR, tRNA-derived sRNA; tel-sRNA, telomere-specific sRNA; tiRNA, transcription initiation sRNA; tRH, tRNA-derived halves; tRF, tRNA-derived fragments; TSS-miRNA, transcriptional start-site-microRNA; usRNA, unusually small RNA; vtRNA, vault RNA; Y, Y RNA.