Chromatin immunoprecipitation and chromatin immunoprecipitation with massively parallel sequencing on mouse embryonic tissue.

Regulation of gene expression must be tightly controlled during embryonic development. A central mechanism to control gene expression is the binding of sequence-specific transcription factors to cis-regulatory elements in the genome. Chromatin immunoprecipitation (ChIP) is a widely used technique to analyze binding of transcription factors and histone modifications on chromatin; however, it is limited to looking at a small number of genes. ChIP with massively parallel sequencing (ChIP-seq) is a recently developed powerful tool to analyze genome-wide binding of transcription factors and histone modifications and provides a vast amount of information into the regulation of gene expression. This chapter describes how ChIP and ChIP-seq are performed on mouse embryonic tissue.