cruncs

Transcript

1. Detecting anomalous conservation in non- coding essential mRNA components Investigating the role and origin of coding regions under non coding selection in mRNA
2. Some background info…
3. The central dogma • mRNA is basically a medium of data exchange • There exists redundancy in the code • Almost always, the third base pair is interchangeable
4. What does interchangeable mean? • The interchangeability of the third base pair means it is non-essential to the viability of the protein • So why are they conserved?
5. Possible ideas • mRNA localization • Post-transcription regulation Both roles require the binding of proteins to mRNA, most likely an interaction with the higher order structures of mRNA
6. What are we interested in? • Codons with the third base pair being perfectly conserved • If there is no change despite no role in coding, then there must be non-coding selection happening
7. The Process • BLASTing a sequence to find its orthologs • Capture sequences from unrelated species • Find their coding regions and reading frames • Find anomalous regions of conservation
8. What is anomalous? • We look at the entropy of the found base pairs • If we randomize the codons used, if we get a higher entropy than what is found, then we can say that the apparent conservation is surprising. = − 2 ⁡ (()) =,,,
10. Our Assumptions • We are assuming the species are so far apart, that the variable base pair has mutated randomly • We are assuming codons are used based on a set of pre-determined probabilities
11. Things to watch out for… • There are some obvious and non- interesting reasons why a particular base pair might be conserved unexpectedly: • Intron/exon excision site • Codon usage bias • Lack of evolutionary history for mutations
12. Our findings…
13. NM_005445 SMC3 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 GGA GGC GGT GGG
14. How likely is this? • Using randomized trials, we randomly scrambled the genes according to each species’ codon preference, and compared the entropy to the observed entropy. • The estimated p-value is <1e-7 • There are 57740 codons in the entire data set. • We expect at most 1 of these to exist. • We find 29 of such codons
15. Expanding the scope • We ran this data analysis over 71 genes that we previously classified as “CRUNCS” genes, and 177 genes that are categorized as “CEGMA” – Core Eukaryotic Genes • In the CEGMA set, we find 38 of such codons out of 109817 in total. • CRUNCS more enriched in these “perfect codons”?
16. The next steps • Determining the function of these codons • Even bigger scope – the entire genome?