Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in the results and the requirement for significant computational resources. Here we present a fast and practical algorithm for shRNA design based on the thermodynamic parameters.
RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, folding pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the folding process of RNA sequences. We describe the web server RNALOSS, which provides information about the distribution of locally optimal secondary structures, that possibly form kinetic traps in the folding process.
Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs.
MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing.
Traditional forward genetic screens are limited in the identification of homologous genes with overlapping functions. Here, we report the analyses and assembly of genome-wide protein family definitions that comprise the largest estimate for the potentially redundant gene space in Arabidopsis thaliana. On this basis, a computational design of genome-wide family-specific artificial microRNAs (amiRNAs) was performed using high-performance computing resources. The amiRNA designs are searchable online (http://phantomdb.ucsd.edu).
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations.
MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose.
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking.
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants.
Since the initial annotation of microRNAs (miRNAs) in 2001, many studies have sought to identify additional miRNAs experimentally or computationally in various species. MiRNAs act with the Argonaut family of proteins to regulate target messenger RNAs (mRNAs) post-transcriptionally. Currently, researches mainly focus on single miRNA function study.
Our database aim to make it easy for researchers to find the right tools or data source for their own specific study in miRNA field. Now we have collect >1000 tools. This database will update when every new 100 tools add in. Last update time 22nd April, 2018 (v1.2).
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