Abstract
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5′ Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.
Highlights
Introduction iationsHigh-throughput sequencing (HTS) technologies revolutionized molecular biology and genetics by allowing the sequencing of entire genomes and transcriptomes [1,2,3,4,5,6]
Profile (8–30 nt) of six different species (H. sapiens, M. musculus, D. melanogaster, A. thaliana, S. pombe, S. cerevisiae) from 11 samples, and revealed the existence of very small RNAs of discrete sizes, with a large part coming from ribosomal RNAs (rRNAs) (Lambert et al, manuscript submitted)
The 50 end of C-doRNA is identical to that of the mature 5.8S rRNA sequence, suggesting that both doRNAs may be produced by the same ribonuclease or may derive from the mature form of 5.8S rRNA
Summary
We have used sRNA-seq analysis, and we investigated the sRNA profile (8–30 nt) of six different species (H. sapiens, M. musculus, D. melanogaster, A. thaliana, S. pombe, S. cerevisiae) from 11 samples, and revealed the existence of very small RNAs of discrete sizes, with a large part coming from rRNA (Lambert et al, manuscript submitted). Together, in these RNA-seq data (Figure 1A), a relatively high abundance of 12-nt and 13-nt RNAs was observed in human, mouse, Drosophila and S. pombe samples, but not in A. thaliana and S. cerevisiae.
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