ChIP-seq analysis of condensin complex in cultured Mammalian cells

Abstract

ChIP-seq, or chromatin immunoprecipitation combined with massively parallel DNA sequencing, is a powerful technique to investigate in vivo protein–DNA interactions on a genome-wide scale at high resolution. Here we describe a ChIP-seq protocol optimized for analysis of condensin I complex on human mitotic chromosomes. The protocol includes procedures of intensive cell fixation by two cross-linking reagents and thorough chromatin shearing by nuclease and sonication treatments, both of which contribute to improving the signal-to-noise ratio of condensin I ChIP-seq profiles. The optimized protocol may also be helpful to explore chromosomal binding sites of other “hard-to-see” proteins by ChIP-seq.