If a PET does not fit into these criteria, then the PET most likely resulted from a ligation product between two DNA fragments and referred to as an inter-ligation PET. The two tags of an inter-ligation PETs do not have fixed tag orientations, might not be found on the same strands, might have any genomic span, and might not map to the same chromosome. If the two tags of an inter-ligation PET are mapped in the same chromosome but with a span > 3 Kb in any orientation, then these PETs are called intrachromosomal inter-ligation PETs. PETs which are mapped to different chromosomes are called interchromosomal inter-ligation PETs. Figure 7. Proposed mechanism showing how distal regulatory elements can initiate long-range chromatin interactions involving promoter regions of target genes. The interactions form DNA loop structures with multiple TFBS at the anchoring center. Small loops might package genes near the anchoring center in a tight sub-compartment, which could increase the local concentration of regulatory proteins for enhanced transcriptional activation. This mechanism might also enhance transcription efficiency, allowing RNA pol II to cycle the tight circular gene templates. The large interaction loops are more likely to link together distant genes at either end of the loop residing near anchor sites for coordinated regulation, or could separate genes in long loops to prevent their activation. Adapted from Fullwood et al. (2009). Advantages of the ChIA-PET method  Weaknesses  Fullwood et al. (2009), used ChIA-PET to detect and map the chromatin interaction network mediated by estrogen receptor alpha (ER-alpha) in human cancer cells. The resulting global chromatin interactome map revealed that remote ER-alpha-binding sites were also anchored to gene promoters through long-range chromatin interactions suggesting that ER-alpha functions by extensive chromatin looping in order to bring genes together for coordinated transcriptional regulation. Software typically used in a ChIA-PET experiment  ELAND  Maps ChIP enriched DNA fragments to the reference human genome. RepeatMasker  In-silico masking of repetitive elements. Monte Carlo simulation  Used to estimate the false discovery rates. PET-Tool  A software suite for processing and managing of Paired-End di-Tag sequence data. ChIA-PET Tool  A software suite for processing ChIA-PET data.ChIA-PET Tool web site ChIA-PET Tool paper  Chromatin immunoprecipitation:  ChIP-Seq, ChIP-PET, ChIP-SAGE, ChIP-CHIP.