ChIP–seq: advantages and challenges of a maturing technology

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP–seq) can be used to map DNA-binding proteins and histone modifications in a genome-wide manner at base-pair resolution. ChIP–seq offers superior data quality to chromatin immunoprecipitation followed by microarray (ChIP–chip), and its advantages include higher resolution, less noise, higher genome coverage and wider dynamic range. To eliminate bias in fragmentation and sequencing, a control sample (generally input DNA) should also be sequenced. Other issues to consider in experimental design include the quality of the antibodies and the depth of sequencing. Genome alignment and the identification of enriched regions present challenges for data analysis, and there are several strategies available. Owing to increased genome coverage, a substantial fraction of the repetitive regions in the genome can now be examined. Increased sensitivity and specificity in the mapping of transcription factor binding sites has facilitated motif discovery and target identification. Detailed profiling of histone modifications and nucleosome positions enables greater understanding of epigenetic mechanisms in development and differentiation. As the cost of sequencing continues to decrease, ChIP–seq will be the method of choice over array-based approaches in nearly all cases.