Practice question

Chromatin immunoprecipitation investigates in vivo association of proteins with genomic DNA. Living cells are treated with formaldehyde, which cross-links proteins to DNA and proteins to proteins preserving physiological interactions. Chromatin is sheared by sonication or enzymatic digestion into 200-500 base fragments. An antibody specific to transcription factor, histone modification, or cofactor immunoprecipitates cross-linked chromatin, enriching bound DNA fragments. After reversal of cross-links and protease digestion, recovered DNA is analyzed. Thus final immunoprecipitate comprises protein-DNA complex, not naked DNA or RNA alone, reflecting chromatin context and occupancy.