Abstract
BackgroundSmall RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of gene regulation in plants and animals. Thus far, conventional sequencing of small RNA libraries from rice led to the identification of most of the conserved miRNAs. Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism.ResultsIn order to identify new miRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. A total of 58,781, 43,003 and 80,990 unique genome-matching small RNAs were obtained from the control, drought and salt stress libraries, respectively. Sequence analysis confirmed the expression of most of the conserved miRNAs in rice. Importantly, 23 new miRNAs mostly each derived from a unique locus in rice genome were identified. Six of the new miRNAs are conserved in other monocots. Additionally, we identified 40 candidate miRNAs. Allowing not more than 3 mis-matches between a miRNA and its target mRNA, we predicted 20 targets for 9 of the new miRNAs.ConclusionDeep sequencing proved to be an effective strategy that allowed the discovery of 23 low-abundance new miRNAs and 40 candidate miRNAs in rice.
Highlights
Small RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of gene regulation in plants and animals
Transcriptional or post-transcriptional gene silencing is directed by genome-encoded 21–24-nt small RNAs. These small RNAs can be divided into two major classes: microRNAs and short-interfering RNAs. miRNAs function in post-transcriptional gene silencing by guiding mRNA degradation or translational repression [1,2,3,4]
Results miRNA expression profiling in rice seedlings In the present study, we carried out high-throughput sequencing of small RNA libraries in order to identify lowabundance candidate new miRNAs and potential stressresponsive miRNAs in rice
Summary
Small RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of gene regulation in plants and animals. MiRNAs function in post-transcriptional gene silencing by guiding mRNA degradation or translational repression [1,2,3,4]. The 21-nt size class siRNAs represented by trans-acting siRNAs (tasiRNAs) and others guide the cleavage of the target mRNAs at the post-transcriptional level, whereas 24-nt size class siRNAs are implicated in DNA and histone modifications leading to transcriptional gene silencing [5,6]. Mature miRNAs are single-stranded ~21 nt small RNAs which are generated from a single-stranded primary transcript (pri-miRNA) forming an imperfect hairpin-like structure, by a series of enzymatic activities of double-stranded RNA recognizing RNase III enzymes (Drosha and DCR1 in animals and DCL1 in plants). Guided by miRNAs, the RISC recognizes the complementary sites on the target mRNAs to cause transcript cleavage [1,3,17] or translational arrest [2,4]
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