Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. Export

@article{citeulike:5047773, abstract = {In species with large effective population sizes, highly expressed genes tend to be encoded by codons with highly abundant cognate tRNAs to maximize translation rate. However, there has been little evidence for a similar bias of synonymous codons in highly expressed human genes. Here, we ask instead whether there is evidence for the selection for codons associated with low abundance tRNAs. Rather than averaging the codon usage of complete genes, we scan the genes for windows with deviating codon usage. We show that there is a significant over representation of human genes that contain clusters of codons with low abundance cognate tRNAs. We name these regions, which on average have a 50\% reduction in the amount of cognate tRNA available compared to the remainder of the gene, RTS (rare tRNA score) clusters. We observed a significant reduction in the substitution rate between the human RTS clusters and their orthologous chimp sequence, when compared to non-RTS cluster sequences. Overall, the genes with an RTS cluster have higher tissue specificity than the non-RTS cluster genes. Furthermore, these genes are functionally enriched for transcription regulation. As genes that regulate transcription in lower eukaryotes are known to be involved in translation on demand, this suggests that the mechanism of translation level expression regulation also exists within the human genome.}, author = {Parmley, Joanna L. and Huynen, Martijn A.}, citeulike-article-id = {5047773}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1000548}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19578405}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19578405}, day = {3}, doi = {10.1371/journal.pgen.1000548}, issn = {1553-7404}, journal = {PLoS genetics}, keywords = {bias, evolution, human, proteins}, month = {July}, number = {7}, pages = {e1000548+}, posted-at = {2009-07-03 17:22:37}, priority = {2}, publisher = {Public Library of Science}, title = {Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation.}, url = {http://dx.doi.org/10.1371/journal.pgen.1000548}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:5047773 L3 - citeulike-article-id:5047773 N2 - In species with large effective population sizes, highly expressed genes tend to be encoded by codons with highly abundant cognate tRNAs to maximize translation rate. However, there has been little evidence for a similar bias of synonymous codons in highly expressed human genes. Here, we ask instead whether there is evidence for the selection for codons associated with low abundance tRNAs. Rather than averaging the codon usage of complete genes, we scan the genes for windows with deviating codon usage. We show that there is a significant over representation of human genes that contain clusters of codons with low abundance cognate tRNAs. We name these regions, which on average have a 50% reduction in the amount of cognate tRNA available compared to the remainder of the gene, RTS (rare tRNA score) clusters. We observed a significant reduction in the substitution rate between the human RTS clusters and their orthologous chimp sequence, when compared to non-RTS cluster sequences. Overall, the genes with an RTS cluster have higher tissue specificity than the non-RTS cluster genes. Furthermore, these genes are functionally enriched for transcription regulation. As genes that regulate transcription in lower eukaryotes are known to be involved in translation on demand, this suggests that the mechanism of translation level expression regulation also exists within the human genome. IS - 7 JF - PLoS genetics SN - 1553-7404 TI - Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PB - Public Library of Science VL - 5 SP - e1000548 KW - bias KW - evolution KW - human KW - proteins AU - Parmley, Joanna AU - Huynen, Martijn PY - 2009/07/03/ UR - http://dx.doi.org/10.1371/journal.pgen.1000548 ER -