2. Codon Bias and its Relationship to Gene Expression Presented through a virtual grant by the Virtual Student Union.

3. What is Codon Bias? b Codon bias is the probability that a given codon will be used to code for an amino acid over a different codon which codes for the same amino acid.

4. How May Codon Bias Relate to Gene Expression? b Genes that are always expressed at a high rate should have a different codon bias than those genes that are always expressed at a low rate. b Genes whose expression varies from low expression to high expression as a given environmental condition changes may have a codon bias similar to the highly expressed genes.

5. How May Codon Bias Relate to Gene Expression? (cont’d) b If a gene is expressed at a low level for all known conditions, but shares a codon bias similarity with the highly or variably expressed genes, it is possible that the gene is expressed at a high rate under some as yet unknown environmental condition.

6. How Does One Verify This Hypothesis? b Must use a genome in which the sequence of every ORF is known. b Must use a genome in which the transcriptional rate is known for every ORF as a standard condition varies.

7. Specifically, How was this Done? b Specifically, the S. cerevisiae geneome was used, because every ORF is sequenced. b The Yeast Expression Database contains the rate of transcription for each ORF in the S. cerevisiae genome. b The Yeast Expression Database also measures the change in transcription rate as the yeast move from a high glucose to low glucose concentration.

8. What was Done with the Data? b First, the every ORF in the Metabolic Database was ranked from highest to lowest expressed genes. b Next, the ORFs in the Database were ranked using the genes that had the greatest difference in expression between high and low glucose concentration. b The codon frequencies from the 5 highest, 5 lowest and 3 most varied sequences were then analyzed further.

9. Codon Frequency Results b Glu and Val codon expression is similar in high and variably expressed genes. b Glu and Val codon expression appears different in the typical low expressed gene. b Chi squared analysis suggests that these variances are due to more than random probability.

10. b Increase the sample size to include the entire genome What are Our Future Goals? b Look for genes with low expression whose codon bias more closely resembles the highly expressed or variably expressed genes.

11. Future goals (cont’d) b A scoring system must be created to classify gene expression. b Must search genome using many different environmental condtions. b The technique can be applied to other genomes.