%0 Journal Article %J Nat Rev Genet %D 2009 %T ChIP-seq: advantages and challenges of a maturing technology. %A Park, Peter J %K Animals %K Chromatin Immunoprecipitation %K Computational Biology %K DNA-Binding Proteins %K Epigenesis, Genetic %K Humans %K Nucleosomes %K Sequence Analysis, DNA %X

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

%B Nat Rev Genet %V 10 %P 669-80 %8 2009 Oct %G eng %N 10 %1 http://www.ncbi.nlm.nih.gov/pubmed/19736561?dopt=Abstract %R 10.1038/nrg2641