Practice question

Chromatin Immunoprecipitation followed by quantitative PCR provides locus-specific validation of protein occupancy. After formaldehyde crosslinking, chromatin shearing and immunoprecipitation using antibody against transcription factor or histone modification, recovered DNA is analyzed with primers flanking candidate promoter or enhancer. Amount of enrichment relative to input or IgG control reflects strength of in vivo binding at that region. This focused approach complements genome-wide ChIP sequencing. It does not detect point mutations, gene fusions or replication fork structures; its purpose is quantification of specific protein-DNA interactions.