Study The Role Of Codon Bias In Regulating Gene Expression Pre-Translationally

Codon usage bias exists in almost every eukaryote and prokaryote.Different codons encoding the same amino acid are known as synonymous codons,and the phenomenon that synonymous codons are used with different frequencies in different genomes is called codon usage bias.Studies have shown that codon usage bias is closely associated with protein translation.For example,codon usage bias could affect translation efficiency,protein conformation and function.Recently it has been reported that codon usage bias has an important role in regulating gene transcription as well.For example,in Neurospora crassa,histone modification is one of the mechanisms used by codon bias to regulate gene transcription.However,whether the similar mechanism exisits in other genomes,and its detailed regulatory mechanism towards gene transcription is not clearly understood yet.Therefore,here we are going to explore the detailed role of codon bias in regulating gene expression pre-translationallyFirst of all,we took the ?-amylase coding gene?amyA?as an example,and examined the role of codon usage bias in regulating gene expression in the typical prokaryote Escherichia coli.We confirmed the higher translation efficiency on codon optimized amyA RNAs,and found that RNA level itself was also affected by codon optimization.The decreased RNA level was at least partially contributed by altered mRNA stability at the post-transcriptional level.Codon optimization also increased the number of putative cytosine methylation sites largely,and we confirmed that these sites are indeed methylated in cells.By knocking out DNA methyltransferase?Dcm?,both amyA mRNA levels?with and without codon optimization?decreased,while the codon optimized one dropped with a larger extent.Threrfore cytosine methylation may be a mechanism adopted by codon bias to regulate gene RNA levels.More studies are required to verify its global effect and the detailed mechanism on transcription.Secondly,the endogenous gene PAS_chr2-2₀376 was studied in Pichia pastoris to investigate the possible role of codon bias in regulating histone modifications and gene transcriptional activity.We performed ChIP-qPCR and ChIP-seq with antibodies against Pol II CTD,H3K36me3 and H3K9ac,and examined the 0376 locus.As a result,the codon optimized sequence has a stronger Pol ? enrichment at the upstream GAP promoter?representing high transcriptional activity?,as well as a higher H3K36me3 level.Therefore,the sequence change by codon optimization may be related to elevated H3K36me3 level and increased transcriptional activity.Besides,between original and codon optimized sequences,the difference in H3K9ac level varies from 5' to 3' ORF,and H3K36me3 level is almost same.Based on our results,the codons in ORF region may affect the histome modification profile and transcription start activity of nearby sequences?especially promoters?through a certain mechanism.