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Articles by I Lee
Total Records ( 3 ) for I Lee
  I Lee , S. S Ajay , J. I Yook , H. S Kim , S. H Hong , N. H Kim , S. M Dhanasekaran , A. M Chinnaiyan and B. D. Athey

MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5'-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5'-UTR motifs, implying both miRNA and 5'-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3'-end interaction sites in the 5'-UTRs turn out to simultaneously contain 5'-end interaction sites in the 3'-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5'-UTR and keep it from reaching the start-codon, preventing 60S association.

  I Lee , B Lehner , T Vavouri , J Shin , A. G Fraser and E. M. Marcotte

Most phenotypes are genetically complex, with contributions from mutations in many different genes. Mutations in more than one gene can combine synergistically to cause phenotypic change, and systematic studies in model organisms show that these genetic interactions are pervasive. However, in human association studies such nonadditive genetic interactions are very difficult to identify because of a lack of statistical power—simply put, the number of potential interactions is too vast. One approach to resolve this is to predict candidate modifier interactions between loci, and then to specifically test these for associations with the phenotype. Here, we describe a general method for predicting genetic interactions based on the use of integrated functional gene networks. We show that in both Saccharomyces cerevisiae and Caenorhabditis elegans a single high-coverage, high-quality functional network can successfully predict genetic modifiers for the majority of genes. For C. elegans we also describe the construction of a new, improved, and expanded functional network, WormNet 2. Using this network we demonstrate how it is possible to rapidly expand the number of modifier loci known for a gene, predicting and validating new genetic interactions for each of three signal transduction genes. We propose that this approach, termed network-guided modifier screening, provides a general strategy for predicting genetic interactions. This work thus suggests that a high-quality integrated human gene network will provide a powerful resource for modifier locus discovery in many different diseases.

  I Lee and F. Solivan

Objects are often remembered with their locations, which is an important aspect of event memory. Despite the well-known involvement of the hippocampus in event memory, detailed intrahippocampal mechanisms are poorly understood. In particular, no experimental evidence has been provided in support of the role of the dentate gyrus (DG) in disambiguating such events, even though computational models suggest otherwise. In the current study, rats encountered multiple objects in different locations and were required to discriminate the object-place paired associates for reward. Specifically, two different objects appeared in one of two locations (arms in a radial maze) that were relatively close to each other. Different objects were rewarded depending on the arm in which the objects appeared. The rats with colchicine-based, dorsal DG (dDG) lesions showed severe and sustained impairment in disambiguating the objects compared with controls (Experiment 1). The dDG-lesioned rats were normal, however, in discriminating four different objects presented (Experiment 2) in the same locations as in Experiment 1. Finally, when the two different objects used in Experiment 1 were presented at two remote locations (Experiment 3) involving less overlap between arm-associated contextual cues, the dDG-lesioned animals showed initial deficits in discriminating the objects, but gradually relearned the task, in contrast to the sustained deficits observed in Experiment 1. These results collectively suggest that the DG is necessary when the similarity is maximal between object-place paired associates due to overlapping object and/or spatial information, whereas its role becomes minimal as the overlap in either object or spatial information decreases.

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