Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 107, Issue 10, Pages 4544-4549Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0914023107
Keywords
chemical genomics; Cognate Site Identification; DNA binders; genomescapes; Energy Landscapes
Categories
Funding
- National Institutes of Health [GM069420, HL67050]
- March of Dimes
- U.S. Department of Agriculture, Innovation and Economic Development Research Program
- Vilas Associate and Shaw scholar awards
- American Heart Association [0615615Z]
- National Institutes of Health/National Library of Medicine [T15LM007359]
- Natural Sciences and Engineering Research Council
- Khorana program
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Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that hinders the ability to decipher gene regulatory networks or engineer molecules that act on genomes. Here we compare the DNA sequence specificities for different classes of proteins and engineered DNA binding molecules across the entire sequence space. These high-content data are visualized and interpreted using an interactive specificity landscape which simultaneously displays the affinity and specificity of a million-plus DNA sequences. Contrary to expectation, specificity landscapes reveal that synthetic DNA ligands match, and often surpass, the specificities of eukaryotic DNA binding proteins. The landscapes also identify differential specificity constraints imposed by diverse structural folds of natural and synthetic DNA binders. Importantly, the sequence context of a binding site significantly influences binding energetics, and utilizing the full contextual information permits greater accuracy in annotating regulatory elements within a given genome. Assigning such context-dependent binding values to every DNA sequence across the genome yields predictive genome-wide binding landscapes (genomescapes). A genomescape of a synthetic DNA binding molecule provided insight into its differential regulatory activity in cultured cells. The approach we describe will accelerate the creation of precision-tailored DNA therapeutics and uncover principles that govern sequence-specificity of DNA binding molecules.
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