16 March Identification of RNAi-Related Genes in Archaea David M. Ng BME 230
16 March RNA Interference Gene expression regulation mechanism Known in eukaryotes dsRNA suppresses the expression of the matching gene Applications in medicine, lab techniques
16 March 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 Approach Identify RNAi-related genes Select target protein sequences Search for target sequences in Archaeal genomes
16 March RNAi Genes and Protein Sequences Genes: Argonaute, Dicer, and Drosha Protein sequences –Argonaute: P. furiosus, fly –Dicer: human, mouse –Drosha: human
16 March Search Tools SAM –Based on two-track HMMs –Iterative search SAM-T02 –Easy to use SAM-T04 –More sensitive than SAM-T02
16 March 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 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 Future Work Complete analyzing current data Search for matching protein structures –This project looked for similar sequences –But we are interested in similar function