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Nat Rev Genet. 2012 Dec;13(12):840-52. doi: 10.1038/nrg3306. Epub 2012 Oct 23.

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

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Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, CB#7264, Chapel Hill, North Carolina 27599, USA.


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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