ChIP-seq: advantages and challenges of a maturing technology.
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.
Park
Peter J
PJ
Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA. peter_park@harvard.edu
D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000235:genetics*; D044127:Epigenesis, Genetic; D006801:Humans; D009707:Nucleosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004268:DNA-Binding Proteins; D009707:Nucleosomes