Abstract
BackgroundMicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism.DescriptionThe mirEX 2.0 web portal (http://www.combio.pl/mirex) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page.ConclusionsThe mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0533-2) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses
SERRATE interacts with the Cap-Binding Complex (CBC), which is a heterodimer of CAP BINDING PROTEIN 20 (CBP20) and CAP BINDING PROTEIN 80 (CBP80) [5]
In the cytoplasm the miRNA guide strand is selectively loaded into ARGONAUTE1 (AGO1) to form the RNA-Induced Silencing Complex (RISC) responsible
Summary
The mirEX 2.0 web-based portal is a one-stop solution for the exploration of plant microRNA expression data covering mutants and three plant species representing scientifically (Arabidopsis thaliana), economically (Hordeum vulgare), and evolutionarily (Pellia endiviifolia) attractive research models. The developed technology allows for unlimited further expansion of the data content and provides an environment for the design of novel tools following the needs of the plant community involved in the exploration of microRNA biology. DB carried out experiments on novel arabidopsis pri-miRNAs. AL participated in the analysis of pri-miRNA expression levels in microRNA biogenesis mutants. ZSK designed and coordinated the whole experimental part of this work and participated in the writing of this manuscript. AJ participated in the design and coordination of the experimental part of this work and discussed the manuscript. WMK designed the database, coordinated the whole informatics part of the project and wrote the manuscript.
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