Abstract
Developmental-stage-related patterns of gene expression correlate with codon usage and genomic GC content in stem cell hierarchies.
Highlights
The usage of synonymous codons shows considerable variation among mammalian genes
We investigated the variation of codon usage between 'highly expressed genes' and 'mid to lowly expressed genes', which were divided by quantiles of 0.67 (Q0.67) of the levels of gene expression in each cell type
We suggest that gene lengths do not substantially influence these observations because, in our datasets, the levels of gene expression were negatively correlated with the lengths of both transcripts and coding sequences (Additional data file 2), whereas the levels of gene expression were negatively correlated with GC3 in most cases (Table 2)
Summary
The usage of synonymous codons shows considerable variation among mammalian genes. How and why this usage is non-random are fundamental biological questions and remain controversial. In a number of rodent and human tissues, recent studies have indicated positive correlations between levels of gene expression, as estimated by SAGE and/or microarray analysis, and GC3 [16,17,18,19]. These results are in contradiction with observations made by analyzing expressed sequence tags (ESTs) [11,16]. Codon usage has been found to exhibit variations in human genes expressed in six tissues [30], the effect is very weak [31] and cannot be generalized to interpret the global variation (the preference of AT-ending or GC-ending codons) of synonymous codons in the thousands of mammalian genes
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