Spec-seq: determining protein-DNA-binding specificity by sequencing

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 model...

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Bibliographic Details
Published in:Briefings in functional genomics 2015-01, Vol.14 (1), p.30-38
Main Authors: Stormo, Gary D, Zuo, Zheng, Chang, Yiming Kenny
Format: Article
Language:English
Subjects:
Animals
Base Sequence
DNA - metabolism
DNA-Binding Proteins - metabolism
Humans
Lac Repressors - metabolism
Operator Regions, Genetic - genetics
Protein Binding
Sequence Analysis, DNA - methods
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Summary: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.
ISSN:2041-2649
2041-2657
DOI:10.1093/bfgp/elu043