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Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8.

ChIP-seq: advantages and challenges of a maturing technology.

Author information

  • Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA. peter_park@harvard.edu

Abstract

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.

PMID:
19736561
[PubMed - indexed for MEDLINE]
PMCID:
PMC3191340
Free PMC Article

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