title: Spec-seq: determining protein-DNA-binding specificity by sequencing.
abstract: 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.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Stormo
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zuo
authors.forename: Yiming Kenny
authors.initials: YK
authors.lastname: Chang
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D056968:Lac Repressors / Q000378:metabolism; D009875:Operator Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004268:DNA-Binding Proteins; D056968:Lac Repressors; D004247:DNA
keywords: protein–DNA interaction; specificity; transcription factors