Journal
BRIEFINGS IN FUNCTIONAL GENOMICS
Volume 14, Issue 1, Pages 30-38Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bfgp/elu043
Keywords
protein-DNA interaction; specificity; transcription factors
Funding
- National Institutes of Health [HG000249, HG005970]
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The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, such as position weight matrices, can be assessed for their accuracy and more complex models developed if useful. Those may provide more accurate predictions of in vivo binding sites and can help us to understand the details of recognition. As an example, we demonstrate new information gained about the binding of lac repressor. One can apply the same method to combinations of factors that bind simultaneously to a single DNA and determine both the specificity of the individual factors and the cooperativity between them.
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