Abstract
BackgroundPlant microRNA (miRNA) has an important role in controlling gene regulation in various biological processes such as cell development, signal transduction, and environmental responses. While information on plant miRNAs and their targets is widely available, accessible online plant miRNA resources are limited; most of them are intended for economically important crops or plant model organisms. With abundant sequence data of numerous plants in public databases such as NCBI and PlantGDB, the identification of their miRNAs and targets would benefit researchers as a central resource for the comparative studies of plant miRNAs.ResultsMicroPC (μPC) is an online plant miRNA resource resulted from large-scale Expressed Sequence Tag (EST) analysis. It consists of 4,006 potential miRNA candidates in 128 families of 125 plant species and 2,995 proteins (4,953 EST sequences) potentially targeted by 78 families of miRNA candidates. In addition, it is incorporated with 1,727 previously reported plant mature miRNA sequences from miRBase. The μPC enables users to compare stored mature or precursor miRNAs and user-supplied sequences among plant species. The search utility allows users to investigate the predicted miRNAs and miRNA targets in detail via various search options such as miRNA family and plant species. To enhance the database usage, the prediction utility provides interactive steps for determining a miRNA or miRNA targets from an input nucleotide sequence and links the prediction results to their homologs in the μPC.ConclusionThe μPC constitutes the first online resource that enables users to comprehensively compare and predict plant miRNAs and their targets. It imparts a basis for further research on revealing miRNA conservation, function, and evolution across plant species and classification. The μPC is available at http://www.biotec.or.th/isl/micropc.
Highlights
Plant microRNA has an important role in controlling gene regulation in various biological processes such as cell development, signal transduction, and environmental responses
[5,6,7,8,9,10,11,12] and experimental [13,14,15,16] approaches, existing public resources focusing on plant miRNAs and their targets are limited to economically important crops or specially implemented for plant model organisms such as Arabidopsis, rice, and maize
SFeigarucrher3esults of a miRNA and miRNA targets Search results of a miRNA and miRNA targets. (A) an Expressed Sequence Tag (EST) sequence of Brassica napus and its secondary structure predicted as a miRNA 156 gene, (B) targeted EST sequences from all plants searched by UniProt accession number [SwissProt:P93015] (SPL3 protein in Arabidopsis), the red box suggests that targeted EST sequences in Raphanus raphanistrum could be the targets of miRNA 414 besides miRNA 156
Summary
Plant microRNA (miRNA) has an important role in controlling gene regulation in various biological processes such as cell development, signal transduction, and environmental responses. With abundant sequence data of numerous plants in public databases such as NCBI and PlantGDB, the identification of their miRNAs and targets would benefit researchers as a central resource for the comparative studies of plant miRNAs. MicroRNA (miRNA) is a class of non-coding small RNAs with a single strand molecule of 18–22 nucleotides. MicroRNA (miRNA) is a class of non-coding small RNAs with a single strand molecule of 18–22 nucleotides It plays a pivotal role in gene regulation in various species by targeting mRNAs at the post-transcriptional levels [1]. Plant MPSS (Massively Parallel Signature Sequencing) databases [18] of Arabidopsis, rice, grape, and rice blast fungus (Magnaporthe grisea) were developed to provide an online resource for mRNA and small RNA analyses. CSRDB (Cereal Small RNA Database) [21] consists of maize and rice small RNA sequences generated by high-throughput pyrosequencing with the provided maps to the available rice and maize genomes
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