How does chromatin immunoprecipitation (ChIP) work?

ChIP identifies DNA sequences associated with specific proteins in vivo. The procedure involves: cross-linking proteins to DNA using formaldehyde, cell lysis and chromatin shearing (sonication or enzymatic), immunoprecipitation with antibody against target protein, reversing cross-links and purifying DNA, and analyzing precipitated DNA. Detection methods include ChIP-qPCR for specific loci, ChIP-chip (microarray), or ChIP-seq (next-generation sequencing) for genome-wide analysis. ChIP is essential for studying transcription factor binding, histone modifications, and chromatin-associated proteins. Controls include input DNA and IgG negative controls.