Appendix 1

Chromatin immunoprecipitation (ChIP)

    ChIP is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells, thereby providing a snapshot of the native chromatin structure and factors bound to genes in different functional states.  ChIP involves treating cells or tissue briefly with formaldehyde to cross-link proteins to DNA.  An antibody against a protein suspected of binding a given cis-element is then used to immunoprecipitate chromatin fragments.  Polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element reveals whether a specific DNA sequence is recovered in an immune-specific manner and therefore whether the protein contacted the site in living cells.  Go to http://www.bio.brandeis.edu/haberlab/jehsite/chip.html for a schematic representation of the procedure.