Tamas Dalmay

..abstract:..

..For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races...

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..This paper reviews our current knowledge about microRNAs focusing on their involvement in cancer and their potential as diagnostics and therapeutics...

..The present paper reviews the different approaches to predict and experimentally identify genes targeted by miRNAs...

..The present study reviews the current state of tomato short RNAs research and suggests future directions...

..Initially, short RNAs were believed to primarily regulate the normal development of plants and animals, but recent advances implicate short RNAs in environmental adaptation...

..In addition, we found that a commercially available scrambled siRNA, which is regularly used as a negative control, regulate the accumulation of many genes...

..Our results also highlight potential problems for expression profiling-based microRNA target identification/validation...

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..This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation...

..Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit...

..By searching for targets of a complete 'sRNAome' we can facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks...

..One of the six new miRNAs is highly enriched in somite tissue suggesting that deep sequencing of other specific tissues has the potential to identify novel tissue specific miRNAs...

..Taken together our results demonstrate differential requirements of distinct MRFs for the induction of microRNA gene expression during skeletal myogenesis...

..Thus, miR395 is an integral part of the regulatory network of sulfate assimilation...

..This indicates that the concerted downregulation of multiple microRNA targets is not only crucial to the skeletal muscle differentiation program but also serves to prevent alternative cell fate choices...

..Herein, we present the UEA sRNA workbench, a suite of tools that is a successor to the web-based UEA sRNA Toolkit, but in downloadable format and with several enhanced and additional features...

..High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula)...

..In this review we present an overview of RNA silencing pathways in plants and the current challenges in analysing sRNA data, with a special focus on computational approaches...

..These results illustrate that negative temporal correlation between the expression level of a miRNA and its target gene in a complex tissue cannot be a requirement for target gene validation...

..Thus, miR395 is an integral part of the regulatory circuit controlling plant sulfate assimilation with a complex mechanism of action...

..In this chapter we will review RNA silencing, the different types of sRNAs that mediate it and the computational methods that have been developed to use high-throughput technologies in the study of sRNAs and their targets...

..This chapter describes optimised RNA extraction methods, which give good yields of short RNAs, and separation, transfer and hybridisation protocols to study the accumulation of short RNAs...

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..To use an in vitro model of chondrogenesis to identify microRNAs (miRNAs) with a functional role in cartilage homeostasis...

..Our results expand the range of esRNAs in eukaryotes and reveal a new role for esRNAs in fungi...

..Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci. AVAILABILITY: The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk...

..Our findings establish a valid strategy for the discovery of microRNA targets regulated only at protein level, and we propose that additional targets could be identified by re-analysis of existing microarray datasets...

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..As the sequence of SDE5 has sequence features shared by TAP, a human mRNA export factor, we propose that its role could be in the transport of RNA molecules that are converted into a double-stranded form by RDR6...

..This enabled several research groups to analyze the expression patterns of miRNAs in both plant and animal tissues. This review focuses on the results of recent publications on the detection of miRNAs by ISH...

..Taken together, these findings suggest that miR449 has a specific role in the development and functioning of choroid plexuses...

..Thus far, miRNAs have not been studied extensively in chicken embryos, and our results show that this system can complement other model organisms to investigate the regulation of many other miRNAs...

..The sequence profiles and Terminator digests suggest that CymRSV siRNAs are produced from the structured positive strand rather than from perfect double stranded RNA or by RNA dependent RNA polymerase...

..Therefore we conclude that Y RNA fragments do not enter the microRNA pathway...

..Interestingly, none of these were predicted by the published target prediction methods we used. One of the potential target mRNAs, Cxcl12, was experimentally validated by Northern blot analysis and a luciferase reporter assay...

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..5 embryos. A potential target of miR-140, histone deacetylase 4, was validated experimentally and the possible role of miR-140 in long bone development is discussed...

..Tests on sRNA datasets from model animals demonstrate that the tool is effective at predicting genuine miRNA duplexes, and, for some sets, achieves a high degree of precision when considering only the mature sequence...

..Interestingly, mir-451 was not detectable in a series of immortalised cell lines representing progenitor stages of all major blood lineages, suggesting that mir-451 may play a role in the differentiation of erythroid cells...

..In addition, the expression of miR-500 in limb buds showed very strong asymmetry in favour of the left hand side...

..Furthermore, dicot micro-(mi)RNAs displayed higher GC% than their DCL1 substrate RNAs, implicating that the GC bias may be ancient, therefore may be important for the RNAi technology...

..Concatamers containing as many as 15 small RNA inserts can be produced. This protocol has successfully been applied to leaf materials of monocots and dicots infected with poty-, carmo-, and sobemo-viruses...

..This supports the notion that GC preference is an ancient feature for plant DCLs, and suggests that monocot miRNA genes might have evolved to a high GC% resulting in GC bias being not detectable during mature miRNA production...

..Using the CDT-1 gene from the desiccation tolerant plant Craterostigma plantagineum as an example, it is discussed that generation of novel small RNAs could be an evolutionary pathway in plants to adapt to extreme environments...

..6%) from the +ss RNA. However, for TuMV infections, siRNAs were derived from both strands (+/-, 58.1-41.9%), indicating the presence of alternative siRNA production mechanisms...