ChIA-PET proximity ligation generates two types of ligation products: self-ligation of the same DNA fragments and inter-ligation between different DNA fragments. PET sequences derived from self-ligation products are mapped in the reference genome within a 3 Kb span, demarcating ChIP DNA fragments, similar to the standard ChIP-sequencing method3 (link),8 (link). Tethered DNA fragments in individual chromatin complexes can also ligate with each other, and the mapping results of such inter-ligation PET sequences would reveal if they are intrachromosomal (both tags of each PET are from the same chromosome) or interchromosomal (the tags are from different chromosomes). Singleton PETs are presumed experimental noise, and overlapping PET clusters are considered enriched putative binding sites or interaction events (
To test the ChIA-PET strategy, we constructed two ChIA-PET libraries from independent ERα ChIP-enriched oestrogen-treated MCF-7 chromatin preparations, and generated two replicate pilot datasets (IHM001H and IHM001N) using Roche/454 pyrosequencing. Our analysis showed that both ChIA-PET libraries produced comparable putative binding sites and interactions. To assess levels of false positive chromatin interactions, we created a negative control ChIP-PET library (IHM043) from the same ChIP sample, wherein the DNA was reverse cross-linked before proximity ligation. We also analyzed a previously reported cloning-based ChIP-PET library (SHC007)8 (link). Both libraries generated abundant binding sites but no interactions. As an additional control, we used IgG, which binds to chromatin nonspecifically, to perform a mock ChIA-PET analysis (IHM062), and only a few binding sites and interactions were identified (
In proximity ligation-based analyses including 3C, the level of non-specific chimeric DNA ligations between different chromatin complexes can be high and thus may confound data analysis. To address this, we designed linker nucleotide barcodes in the ChIA-PET method to specifically identify such chimeric ligation PETs in another ERα ChIA-PET replicate. Linker barcoding analysis suggests that chimeric ligations are random and do not overlap with each other to form false positive interactions (
Together, these libraries indicate that the prevalent chromatin interactions (