ChIP-seq: a New Technique for Genome-wide Profiling of Protein-DNA Interaction

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a burgeoning technique which combines Chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to detect protein-DNA binding events, histone modifications, nucleosomes positioning and DNA methylation on a genome-wide scale. Motivated by the tremendous progress in next-generation sequencing (NGS) technology, ChIP-seq offers higher resolution, less noise, and broader coverage than conventional microarray based 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, we describe its latest advances, with an emphasis on issues related to data analysis and its application.