mrSNP is a highly adaptable and performing web based tool for predicting the effect a 3′UTR SNP will have on miRNA binding. This tool has advantages over existing algorithms because it can assess the effect of novel SNPs on miRNA binding without requiring significant hands on time.
Project home page: http://mrsnp.osu.edu
License: Free for commercial and academic use
Background
MicroRNAs (miRNAs) bind to sites in the 3′untranslated regions (3′UTR) of a targeted messenger RNA (mRNA). Binding leads to degradation of the transcript or blocked translation resulting in decreased expression of the targeted gene. Single nucleotide polymorphisms (SNPs) have been found in 3′UTRs that disrupt normal miRNA binding or introduce new binding sites and some of these have been associated with disease pathogenesis. This raises the importance of detecting miRNA targets and [click to continue…]
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The organizers are happy to announce the upcoming “NGS and non-coding RNA data analysis” workshop II (2014) 15-16 May, Plovdiv, Bulgaria
The SeqAhead COST action BM1006 is organizing a 2 day workshop with presentations on non-coding RNA (ncRNA) research, bioinformatics, data analysis and stimulating discussions between biologists and bioinformaticians. The registration for this COST WS is now open.
The Workshop will concentrate on current topics in NGS and non-coding RNAs, with special emphasis on data analysis. The ultimate goal of the workshop is to bring software developers, bioinformaticians and experimental scientists together, bridging the gap between users’ needs and developers’ goals.
Workshop Target:
-biologists with research in ncRNA (ncRNA, small RNAs, miRNAs) applying or planning to apply Next Generation Sequencing technologies
-bioinformaticians involved in data analysis or developing algorithms for data analysis of ncRNA data.
The workshop is open for everybody in the ncRNA and NGS field. The workshop is free of charge and participants have to pay their own hotel and travel. COST will offer travel reimbursement to some selected researchers and you will need to provide a poster abstract.
For more detailed information visit the WS homepage:
For more specific information please contact Dr. Vesselin Baev {vebaev@plantgene.eu}
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Researchers at the University of Oxford and the Scripps Research Institute recently published an article evaluating the use of several different RT-qPCR normalization strategies when profiling miRNA gene expression in mouse serum. In their research article entitled “Assessment of RT-qPCR Normalization Strategies for Accurate Quantification of Extracellular microRNAs in Murine Serum,” Roberts et. al. compare three miRNA expression normalization strategies: 1.) normalization of miRNA expression to the average Cq (Ct) of all measured miRNA genes, 2.) Normalization of gene expression to individual miRNAs such as miR-16, miR-223, or miR-31 (all miRNA genes previously identified as normalization controls in the literature), and 3.) Normalization to a ‘spike-in’ external control miRNA gene expressed in C. elegans (cel-miR-39).
Normalization strategies have been an increasingly important topic in miRNA expression studies. This is especially true when profiling miRNA expression in serum or tissues and when quantifying miRNA genes which can have considerable variability in their endogenous expression. The authors identified a panel of 124 serum miRNA genes present in all their samples between normal, dystrophic, and dystrophic-treated mice. Their results suggest that [click to continue…]
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The goal of pharmacogenetics is to better understand human response to both environmental toxins and drug treatment. Recently, several laboratories have investigated the hypothesis that microRNA regulation of drug metabolizing enzymes may influence their expression and ultimately effect enzymatic activity and patient drug toxicities. Researchers at the Pennsylvania State Hershey College of Medicine and Washington State University, Spokane, identified miR-491-3p as a microRNA regulator of UDP-Glucuronosyltransferase (UGT) gene family members. In their article ‘Regulation of the UDP-Glucuronosyltransferase 1A1 Expression and Activity by MicroRNA 491-3p’, miR-491-3p is identified to target and bind with the common 3’ UTR of several UGT1A sub family gene members. Endogenous miR-491-3p expression in vitro had a significant impact on the gene expression of UGT1A1, UGT1A3, and UGT1A6 genes. miR-491-3p expression also effected UGT1A1 protein expression and metabolic activity against the substrate raloxifene, a chemotherapeutic drug used in the prevention and treatment of breast cancer.
Interestingly, Dluzen et. al. also observed inter-individual variable expression of miR-491-3p in human liver. Nearly one-third of the 39 liver samples analyzed lacked [click to continue…]
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