MiRonTop: mining microRNAs targets across large scale gene expression studies
58
Citation
13
Reference
10
Related Paper
Citation Trend
Abstract:
Abstract Summary: Current challenges in microRNA (miRNA) research are to improve the identification of in vivo mRNA targets and clarify the complex interplay existing between a specific miRNA and multiple biological networks. MiRonTop is an online java web tool that integrates DNA microarrays or high-throughput sequencing data to identify the potential implication of miRNAs on a specific biological system. It allows a rapid characterization of the most pertinent mRNA targets according to several existing miRNA target prediction approaches. It also provides useful representations of the enrichment scores according to the position of the target site along the 3′-UTR, where the contribution of the sites located in the vicinity of the stop codon and of the polyA tail can be clearly highlighted. It provides different graphs of miRNA enrichment associated with up- or down-regulated transcripts and different summary tables about selections of mRNA targets and their functional annotations by Gene Ontology. Availability: http://www.microarray.fr:8080/miRonTop/index Contact: barbry@ipmc.cnrs.frKeywords:
Identification
The growth-related protein p23 of the Ehrlich ascites tumor (EAT) is preferentially expressed in the exponentially growing tumor; its synthesis is translationally controlled. p23 mRNA is efficiently translated in the wheat germ cell-free lysate. In contrast, p23 mRNA present in poly(A)+RNA isolated from EAT is not translated in cell-free systems of EAT and reticulocytes. Moreover, translation of a p23 transcript is inhibited in the presence of total poly(A)+RNA. This inhibition is abolished by the removal of the 5'-UTR of the p23 transcript. Solution hybridization/RNase protection experiments point to the presence of a nucleotide sequence complementary to the 5'-UTR of p23 mRNA which might be involved in p23 mRNA inhibition.
Ehrlich ascites
Cite
Citations (16)
Translational regulation
Translational efficiency
Cite
Citations (5)
Cite
Citations (20)
Abstract When S. cerevisiae are grown with glucose, SDH2 mRNA encoding the iron protein of the succinate dehydrogenase complex is unstable and present at low level. In yeast grown without glucose, SDH2 mRNA is stable and its level rises. Addition of glucose to a glucose‐limited culture causes the SDH2 mRNA level to fall rapidly with a half‐life of ∼5–7 min. Previously the 5′UTR of the mRNA of SDH2 was shown to be necessary and sufficient to destabilize it in glucose (Lombardo et al ., 1992 ). We now show that the SDH1 and SUC2 5′UTRs are capable of conferring glucose‐sensitive mRNA instability. We also examine how changes in the SDH2 5′UTR affect glucose‐triggered degradation. Finally, we show that changes in mRNA stability are correlated with changes in translational efficiency for these transcripts. Copyright © 2002 John Wiley & Sons, Ltd.
Cite
Citations (26)
Transforming growth factor-beta 1 (TGF-beta 1) is encoded predominantly by a 2.4-kb mRNA in most tissues. However, an additional transcript of 1.9 kb can be detected in rat heart after experimental myocardial infarction caused by ligation of the left coronary artery. This transcript level is significantly higher in infarcted heart tissue than in normal heart tissue, suggesting an important role for this mRNA species in response to injury. Structural characterization of the 1.9-kb mRNA showed that it included the entire coding sequence present in the 2.4-kb TGF-beta 1 mRNA, but also contained an additional nonhomologous 3'-untranslated region (UTR). The junction between the shared and unique 3' sequence in the 1.9-kb mRNA occurred only two nucleotides before the proposed polyadenylation site of the rat TGF-beta 1 2.4-kb mRNA. The unique 3'-UTR and the deduced shortened 5'-UTR in the novel 1.9-kb TGF-beta 1 mRNA suggest different transcriptional and translational regulatory mechanisms under conditions of tissue injury.
Coding region
Cite
Citations (53)
Cite
Citations (28)
AU-rich element
Cite
Citations (4)
AU-rich element
Cite
Citations (20)
Cite
Citations (22)
Nerve growth factor (NGF) mRNA is rapidly degraded in many non-neuronal cell types with a half-life of between 30 and 60 min. Similar to other short-lived mRNAs the 3'-untranslated region (3'-UTR) of the NGF mRNA contains a short AU nucleotide-rich sequence. To implicate this region as a cis-acting determinant of NGF mRNA instability, expression vectors containing NGF cDNA with and without the 3'-UTR, and vectors containing only the 3'-UTR were constructed and used in cell transfection experiments. Transfection of HEK293 or NIH3T3 cells with these expression vectors followed by measurement of NGF mRNA half-life indicated that NGF mRNA without the AU-rich 3'-UTR was approximately 3-fold more stable than NGF mRNA containing the 3'-UTR. Similar results were seen in a polysome-based cell-free RNA decay assay using NGF mRNA with and without the 3'-UTR prepared from transfected cells. Addition of a short RNA containing the AU-rich 3'-UTR to the cell-free RNA decay system prolonged the half-life of the full-length NGF mRNA, suggesting competition between these two RNA species for polysome-associated factors which degrade the NGF mRNA. Moreover, transfection of HEK293 or astroglial cells with vectors designed to express only the AU-rich region of the 3'-UTR resulted in enhanced expression of NGF mRNA. The results indicate that the 3'-UTR of the NGF mRNA contains a cis-acting instability determinant which, perhaps by interacting with trans-acting RNA-binding proteins, controls the rate of NGF mRNA turnover.
Polysome
HEK 293 cells
P-bodies
AU-rich element
Cite
Citations (20)