Specific gene transcription is a key biological process that underlies cell fate 
decision during embryonic development. The biological process is mediated by 
transcription factors which bind genomic regulatory regions including enhancers 
and promoters of cardiac constitutive genes. DNA is wrapped around histones that 
are subjected to chemical modifications. Modifications of histones further lead 
to repressed, activated or poised gene transcription, thus bringing another 
level of fine tuning regulation of gene transcription. Embryonic Stem cells (ES 
cells) recapitulate within embryoid bodies (i.e., cell aggregates) or in 2D 
culture the early steps of cardiac development. They provide in principle enough 
material for chromatin immunoprecipitation (ChIP), a technology broadly used to 
identify gene regulatory regions. Furthermore, human ES cells represent a human 
cell model of cardiogenesis. At later stages of development, mouse embryonic 
tissues allow for investigating specific epigenetic landscapes required for 
determination of cell identity. Herein, we describe protocols of ChIP, 
sequential ChIP followed by PCR or ChIP-sequencing using ES cells, embryoid 
bodies and cardiac specific embryonic regions. These protocols allow to 
investigating the epigenetic regulation of cardiac gene transcription.