%0 Journal Article %1 stergachis2013exonic %A Stergachis, Andrew B. %A Haugen, Eric %A Shafer, Anthony %A Fu, Wenqing %A Vernot, Benjamin %A Reynolds, Alex %A Raubitschek, Anthony %A Ziegler, Steven %A LeProust, Emily M. %A Akey, Joshua M. %A Stamatoyannopoulos, John A. %D 2013 %J Science %K codon_bias regulatory_elements %N 6164 %P 1367-1372 %R 10.1126/science.1243490 %T Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution %U http://www.sciencemag.org/content/342/6164/1367.abstract %V 342 %X Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.

@article{stergachis2013exonic, abstract = {Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.}, added-at = {2013-12-28T18:09:09.000+0100}, author = {Stergachis, Andrew B. and Haugen, Eric and Shafer, Anthony and Fu, Wenqing and Vernot, Benjamin and Reynolds, Alex and Raubitschek, Anthony and Ziegler, Steven and LeProust, Emily M. and Akey, Joshua M. and Stamatoyannopoulos, John A.}, biburl = {https://www.bibsonomy.org/bibtex/233c29d710e4582397b94049ddb0242fe/peter.ralph}, doi = {10.1126/science.1243490}, eprint = {http://www.sciencemag.org/content/342/6164/1367.full.pdf}, interhash = {fe053458491330eb5c66c0ee33896044}, intrahash = {33c29d710e4582397b94049ddb0242fe}, journal = {Science}, keywords = {codon_bias regulatory_elements}, number = 6164, pages = {1367-1372}, timestamp = {2014-01-07T22:02:31.000+0100}, title = {Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution}, url = {http://www.sciencemag.org/content/342/6164/1367.abstract}, volume = 342, year = 2013 }