1. 16 March 20051 Identification of RNAi-Related Genes in Archaea David M. Ng BME 230

2. 16 March 20052 RNA Interference Gene expression regulation mechanism Known in eukaryotes dsRNA suppresses the expression of the matching gene Applications in medicine, lab techniques

3. 16 March 20053 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

4. 16 March 20054 Approach Identify RNAi-related genes Select target protein sequences Search for target sequences in Archaeal genomes

5. 16 March 20055 RNAi Genes and Protein Sequences Genes: Argonaute, Dicer, and Drosha Protein sequences –Argonaute: P. furiosus, fly –Dicer: human, mouse –Drosha: human

6. 16 March 20056 Search Tools SAM –Based on two-track HMMs –Iterative search SAM-T02 –Easy to use SAM-T04 –More sensitive than SAM-T02

7. 16 March 20057 Results SAM-T02 –2 hits for Argonaute from P. furiosus SAM-T04 –21 hits in Archaea –From all proteins except Argonaute from fly

8. 16 March 20058 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

9. 16 March 20059 Future Work Complete analyzing current data Search for matching protein structures –This project looked for similar sequences –But we are interested in similar function