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. Author manuscript; available in PMC: 2010 May 5.
Published in final edited form as: Nature. 2009 Nov 5;462(7269):58–64. doi: 10.1038/nature08497

Figure 1. ChIA-PET method with validations.

Figure 1

(a) ChIA-PET schematic. DNA fragments in sonicated, ChIP-enriched chromatin complexes were processed by linker ligation, proximity ligation, PET extraction, sequencing, and mapping to reveal interacting loci. (b) ChIA-PET browser tracks: 1, H3K4me3 ChIP-Seq; 2, RNAPII ChIP-Seq; 3, ERα (orange) and FoxA1 ChIP-chip (green)9; 4, ERα ChIA-PET density ; 5, Inter-ligation PETs. Inset: 3C validation of interacting ERαBS (purple) and controls (blue) under ethanol (ET) and oestrogen-induction (E2). (c) 4C validation, showing 4C bait region (blue) and interaction targets (purple bars). (d) FISH validation, showing increased P2/P1 interactions under E2-induction with background normalization (P3/P2). FISH probe genomic locations (P1/P2/P3) are indicated.