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Background: MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean. Results: Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed. Conclusions: The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae. [ABSTRACT FROM AUTHOR]

Abstract: MicroRNAs (miRNAs) have recently received much interest for their role in post-transcriptional regulation. However, the study of miRNA transcription lags behind that of gene cloning and functional analysis. The MiR-281 in Drosophila melanogaster is located in the first intron of isoform RA of the ornithine decarboxylase antizyme (ODA) gene. ODA has three isoforms because of alternative transcription start sites (TSSs). Expression profile analysis indicated that miR-281 is not co-expressed with any ODA isoform. We amplified the primary transcripts of miR-281 using the RACE technique. The pri-miRNA is 2149bp with a poly (A) tail and a canonical polyadenylation signal (AATAAA). Chromatin immunoprecipitation analysis confirmed the binding of hypophosphorylated Pol-II and the transcription factor Myc at the core miR-281 promoter region. The abundance of miR-281 does not correlate, either positively or negatively, with the expression of any ODA isoform, indicating that ODA has little influence on the transcription of miR-281. [Copyright &y& Elsevier]