Transcript Identification of RNAi-Related Genes in Archaea

Identification of RNAi-Related
Genes in Archaea
David M. Ng
BME 230
16 March 2005
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RNA Interference
• Gene expression regulation mechanism
• Known in eukaryotes
• dsRNA suppresses the expression of the
matching gene
• Applications in medicine, lab techniques
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Why Archaea?
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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
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Approach
• Identify RNAi-related genes
• Select target protein sequences
• Search for target sequences in Archaeal
genomes
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RNAi Genes and Protein
Sequences
• Genes: Argonaute, Dicer, and Drosha
• Protein sequences
– Argonaute: P. furiosus, fly
– Dicer: human, mouse
– Drosha: human
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Search Tools
• SAM
– Based on two-track HMMs
– Iterative search
• SAM-T02
– Easy to use
• SAM-T04
– More sensitive than SAM-T02
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Results
• SAM-T02
– 2 hits for Argonaute from P. furiosus
• SAM-T04
– 21 hits in Archaea
– From all proteins except Argonaute from fly
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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
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Future Work
• Complete analyzing current data
• Search for matching protein structures
– This project looked for similar sequences
– But we are interested in similar function
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