Recent probes of the dynamic nature of chromatin have revealed that this structure is more than a simple genomic packaging tool. Indeed, chromatin remodeling plays a role in regulating processes such as transcription, replication, repair, and epigenetic silencing. Understanding how chromatin's structure responds to histone modifications and how transcription factors bind to DNA in chromatin in vivo can reveal much about transcriptional regulation.

Studying protein-DNA interactions in a native chromatin setting has historically been a challenge, as these interactions are transient, owing to chromatin's constantly changing structure. Early efforts employed fractionation of transcriptionally active from inactive chromatin, but these methods often failed to preserve interactions in their physiological state.1 Chromatin immunoprecipitation (ChIP) addresses this problem.

In ChIP, protein-DNA interactions in living cells are frozen in situ via covalent cross-linking with formaldehyde. Cells are sonicated to shear the DNA into fragments, and the complexes are precipitated using antibodies directed against...

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