DIP-chip: Rapid and accurate determination of DNA-binding specificity
Abstract
We have developed a new method for determining the DNA-binding specificity of proteins. In DIP-chip (DNA immunoprecipitation with microarray detection), protein·DNA complexes are isolated from an in vitro mixture of purified protein and naked genomic DNA. Whole-genome DNA microarrays are used to identify the protein-bound DNA fragments, and the sequence of the identified fragments is used to derive binding-site descriptions. Using objective criteria for assessing the accuracy of DNA-binding motifs, and using yeast Leu3p as a model, we demonstrate that motifs determined by DIP-chip are as effective at predicting the location of bound proteins in vivo as are motifs determined by conventional low-throughput in vitro methods.
Footnotes
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[Raw data, array images, and compiled tabular data are publicly available as Supplemental material online at www.genome.org and from the UNC Microarray database at https://genome.unc.edu.]
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Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.3256505. Article published online before print in February 2005.
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↵3 Corresponding author. E-mail nclarke{at}jhmi.edu; fax (410) 614-0338.
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- Accepted December 15, 2004.
- Received September 13, 2004.
- Cold Spring Harbor Laboratory Press
