Download Codon Bias and its Relationship to Gene Expression

Codon Bias and its
Relationship to Gene
Expression
Presented through a virtual grant by
the Virtual Student Union.
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.
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)
 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?
 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.
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.
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.
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?

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.
Future goals (cont’d)

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.
