4.7 Review

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

Journal

NATURE REVIEWS GENETICS
Volume 13, Issue 12, Pages 840-852

Publisher

NATURE PUBLISHING GROUP
DOI: 10.1038/nrg3306

Keywords

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Funding

  1. US National Institutes of Health [U54-HG004563, R21-DA027040, U01 CA157703]
  2. Department of Defense [W81XWH-10-1-0772]
  3. University Cancer Research Fund from the University of North Carolina at Chapel Hill

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Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches-for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins-provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.

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