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Identification of RNAi-Related Genes in Archaea

Identification of RNAi-Related Genes in Archaea. David M. Ng BME 230. RNA Interference. Gene expression regulation mechanism Known in eukaryotes dsRNA suppresses the expression of the matching gene Applications in medicine, lab techniques. Why Archaea?. RNAi not known in Archaea

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Identification of RNAi-Related Genes in Archaea

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  1. Identification of RNAi-Related Genes in Archaea David M. Ng BME 230 16 March 2005

  2. RNA Interference • Gene expression regulation mechanism • Known in eukaryotes • dsRNA suppresses the expression of the matching gene • Applications in medicine, lab techniques 16 March 2005

  3. Why Archaea? • RNAi not known in Archaea • More likely in Archaea than Bacteria • Provide information on evolution • An RNAi-related gene is known to be present in P. furiosus 16 March 2005

  4. Approach • Identify RNAi-related genes • Select target protein sequences • Search for target sequences in Archaeal genomes 16 March 2005

  5. RNAi Genes and Protein Sequences • Genes: Argonaute, Dicer, and Drosha • Protein sequences • Argonaute: P. furiosus, fly • Dicer: human, mouse • Drosha: human 16 March 2005

  6. Search Tools • SAM • Based on two-track HMMs • Iterative search • SAM-T02 • Easy to use • SAM-T04 • More sensitive than SAM-T02 16 March 2005

  7. Results • SAM-T02 • 2 hits for Argonaute from P. furiosus • SAM-T04 • 21 hits in Archaea • From all proteins except Argonaute from fly 16 March 2005

  8. Results • Examined hit to Sulfolobus tokodaii in detail • Compared multiple alignment of a “hypothetical protein” to HMM sequence logo • Found many matches, especially to highly conserved residues • Good candidate 16 March 2005

  9. Future Work • Complete analyzing current data • Search for matching protein structures • This project looked for similar sequences • But we are interested in similar function 16 March 2005

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