@article {308992,
	title = {Exonic transcription factor binding directs codon choice and affects protein evolution.},
	journal = {Science},
	volume = {342},
	year = {2013},
	note = {http://www.sciencemag.org/content/342/6164/1367.full},
	month = {2013 Dec 13},
	pages = {1367-72},
	abstract = {<p>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.</p>},
	keywords = {Codon, Deoxyribonuclease I, DNA Footprinting, Evolution, Molecular, Exome, Exons, Genome, Human, Humans, Polymorphism, Single Nucleotide, Transcription Factors},
	issn = {1095-9203},
	doi = {10.1126/science.1243490},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24337295},
	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}
}
