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4C involves PCR amplification of DNA fragments cross-linked and ligated to a DNA restriction fragment of choice (here,HindIII fragments). Typically, this yields a pattern of PCR fragments specific for a given tissue and highly reproducible between independent PCR reactions. The amplified material, representing the fragment’s genomic environment, is labeled and hybridized to a tailored microarray that contains probes each located < 100 bp from a different HindIII restriction end in the genome.
(Simonis et al., 2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet.