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Codon Bias and its Relationship to Gene Expression. Presented through a virtual grant by the Virtual Student Union. Eric aka "Virtual Student". What is Codon Bias?.

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Codon Bias and its Relationship to Gene Expression

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Codon bias and its relationship to gene expression l.jpg

Codon Bias and its Relationship to Gene Expression

Presented through a virtual grant by the Virtual Student Union.

Eric aka "Virtual Student"


What is codon bias l.jpg

What is Codon Bias?

  • 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.

Ex = GGT vs. GGG for Gly.


How may codon bias relate to gene expression l.jpg

How May Codon Bias Relate to Gene Expression?

  • 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.

  • 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.


How may codon bias relate to gene expression cont d l.jpg

How May Codon Bias Relate to Gene Expression? (cont’d)

  • 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.


How does one verify this hypothesis l.jpg

How Does One Verify This Hypothesis?

  • Must use a genome in which the sequence of every ORF is known.

  • Must use a genome in which the transcriptional rate is known for every ORF as a standard condition varies.

Gene Chips make this possible!!


Specifically how was this done l.jpg

Specifically, How was this Done?

  • Specifically, the S. cerevisiae geneome was used, because every ORF is sequenced.

  • The Yeast Expression Database contains the rate of transcription for each ORF in the S. cerevisiae genome.

  • The Yeast Expression Database also measures the change in transcription rate as the yeast move from a high glucose to low glucose concentration.


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What was Done with the Data?

  • First, the every ORF in the Metabolic Database was ranked from highest to lowest expressed genes.

  • Next, the ORFs in the Database were ranked using the genes that had the greatest difference in expression between high and low glucose concentration.

  • The codon frequencies from the 5 highest, 5 lowest and 3 most varied sequences were then analyzed further.


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Codon Frequency Results

  • Glu and Val codon expression is similar in high and variably expressed genes.

  • Glu and Val codon expression appears different in the typical low expressed gene.

  • Chi squared analysis suggests that these variances are due to more than random probability.


What are our future goals l.jpg

Increase the sample size to include the entire genome

Look for genes with low expression whose codon bias more closely resembles the highly expressed or variably expressed genes.

What are Our Future Goals?

=approx. 6000 genes


Future goals cont d l.jpg

A scoring system must be created to classify gene expression.

Must search genome using many different environmental condtions.

The technique can be applied to other genomes.

Future goals (cont’d)

High?

Low?

Variable?


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