Journal
SCIENCE
Volume 324, Issue 5935, Pages 1720-1723Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.1162327
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Funding
- Canadian Institutes of Health Research [MOP-77721]
- Genome Canada through the Ontario Genomics Institute
- Ontario Research Fund
- Canadian Institute for Advanced Research
- NSF
- Canadian Foundation for Innovation
- NIH/National Human Genome Research Institute [R01 HG003985]
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Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.
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