DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Abstract

microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has now been extended to support predictions for two widely studied species: Drosophila melanogaster and Caenorhabditis elegans. In the updated version, the Web server enables the association of miRNAs to diseases through bibliographic analysis and provides insights for the potential involvement of miRNAs in biological processes. The nomenclature used to describe mature miRNAs along different miRBase versions has been extensively analyzed, and the naming history of each miRNA has been extracted. This enables the identification of miRNA publications regardless of possible nomenclature changes. User interaction has been further refined allowing users to save results that they wish to analyze further. A connection to the UCSC genome browser is now provided, enabling users to easily preview predicted binding sites in comparison to a wide array of genomic tracks, such as single nucleotide polymorphisms. The Web server is publicly accessible in www.microrna.gr/microT-v4.

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…DIANA-MicroT tools are being developed in Artemis Hatzigeorgiou's laboratory for over a decade (Kiriakidou et al, 2004;Sethupathy et al, 2006;Megraw et al, 2007;Maragkakis et al, 2009;Alexiou et al, 2010;Maragkakis et al, 2011;Reczko et al, 2011;Vergoulis et al, 2012;Vlachos et al, 2012;Paraskevopoulou et al, 2013a;Paraskevopoulou et al, 2013b;Paraskevopoulou et al, 2016). MicroT is specifically trained on a positive and a negative set of miRNA binding sites located in 3'-UTR and CDS regions.…”

Large-scale screening identifies a novel microRNA, miR-15a-3p, which induces apoptosis in human cancer cell lines

“…The a result, four anti-apoptotic genes (bcl2l1, naip5, fgfr2, mybl2) were identified; these genes were also confirmed to be predicted targets of mmu-miR-15a-3p by using the miRanda and DIANA-microT target prediction engines. 29,30 The identified genes, their anti-apoptotic roles and possible mmu-miR-15a-3p-binding sites are summarized in Table 3. Since these genes have a known anti-apoptotic role in mammalian cells, [31][32][33][34][35][36] it is likely that the pro-apoptotic activity of mmu-miR-15a-3p is the result of inhibiting those genes, especially bcl2l1 (bcl-x L ), which is known to protect cells from apoptosis by being overexpressed particularly in stress-resistant cancer cell lines.…”

“…The effect of hsa-miR15a-3p on the viability of several human cell lines was evaluated by mining some of our existing data from previous screens conducted UGGccU (2-7) 2.61 ± 0.22 0.011 Mybl2 belongs to the family of transcription factors which are involved in regulation of cell survival by induction of bcl2 transcription with the seed sequences of this miRNA by using DIANA-microT targets prediction tool. 30 The multiplicity of binding sites for hsamiR-15a-3p in the 3'-UTR region of the human bcl-x L gene and the high degree of complementarity shown in Table 5 are indicative of the high affinity of this miRNA for targeting bcl-x L gene. 40 At the same time, the affinity of hsa-miR-15a-3p for human homologs of mybl2 and fgfr2 genes (naip5 is not conserved in human) was not predicted to be high (Table S1).…”

“…40 At the same time, the affinity of hsa-miR-15a-3p for human homologs of mybl2 and fgfr2 genes (naip5 is not conserved in human) was not predicted to be high (Table S1). 30 The mRNA expression levels of bcl-x L gene were compared in hsa-miR-15a-3p transfected, negative control transfected, mocked transfected and non-transfected HeLa and AsPc-1 cells (Fig. 4A and B).…”

miR-92b regulates Mef2 levels through a negative-feedback circuit during Drosophila muscle development

“…Using the online targeting prediction databases generated based on these methods, we searched the 3ЈUTR of the Drosophila Mef2 and found putative targeting sites for 35 microRNAs (Betel et al, 2010; 3545 RESEARCH ARTICLE miR-92b regulates Mef2 levels Lewis et al, 2005;Maragkakis et al, 2011;Ruby et al, 2007). Among these, 17 microRNAs have targeting sites that are conserved in 12 Drosophila species.…”