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KMID : 0811720040080000184
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Korean Journal of Physiology & Pharmacology
2004 Volume.8 No. 0 p.184 ~ p.0
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A Bioinformatics Approach for the Prediction of RNAi Functions in Controlling Gene Expressions
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Joo Hyun
Kim Tae-Ho
Kim Na-Ri
Youm Jae-Boum
Kim Eui-Yong
Han Jin
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Abstract
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A parallel computing system named "PRUSTER" was designed for high performance distributed memory computations to solve complex biological problems. The machine was applied for implementing a LINUX-based high performance ClustalW-MPI which aligns huge sequences of C. elegans EST and RNAi genes. Our pair-align result indicated that the sequence homology of RNAi does not provide EST-like information: only few pairs (0.15%) among 1.37×109 pairs of C. elegans ESTs and RNAi gene sequences have the potential to be subject to direct gene transcript binding. At this point, we postulate that some critical considerations for understanding RNAi’s mechanism should be addressed. Basically PTGS (post-translational gene silencing) and TGS (translational gene silencing) manners in RNAi were believed to be dependant on the sequence homology between their mRNA and siRNAs or miRNAs, and RISC might be important for this recognition. However, our results exclude those interpretations: there were no other EST matches found with RNAi’s, although some of which may represent RNAi homology. This discrepancy makes difficult to understand RNAi mechanism. To address this we suggest other possible regulating mechanisms which are based on that siRNAs and miRNAs bind to unknown regulating region or specific structures of siRNAs and miRNAs regulate their bindings more effectively.
Source: Korean Journal of Physiology & Pharmacology.2004 Oct;8(Suppl I):S137-S137
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KEYWORD
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EST, RNAi, Bioinformatics, C. elegans, ClustalW-MPI
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