Comparing normal human embryonic stem cells (hESCs) to those that have acquired cellular properties of neoplasm provides a unique opportunity to study the distinguishing molecular features of human cellular transformation. As global alterations in the epigenetic landscape are a common feature of cancer, we sought to investigate the loci-specific and global differences between normal and transformed hESCs using ChIP-PCR and ChIP-microarray (also known as ChIP-chip). Here, specific emphasis was placed on optimizing ChIP for low cell numbers (termed micro-ChIP; μChIP) towards applications where the target population is rare, such as the case for somatic human tumors containing a low frequency of cancer stem cell populations and for single-colony analysis of embryonic and induced pluripotent stem cells emerging from initial derivation. Using these methods, we suggest that μChIP-PCR and microarray analysis is thus a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer, and regenerative medicine where target populations regulating the biological process can only be isolated in small numbers.
