Schematic of ChIA-PET analysis. (a) The ChIA-PET experimental protocol, which includes chromatin preparation, ChIP, linker ligation, proximity ligation, MmeI restriction digestion, and DNA sequencing. (b) The ChIA-PET constructs prepared for sequencing analysis. Each PET construct involves a pair of tags (20 bp each) and a linker (38 bp) between the tag pairs. This full-length linker is derived from ligation of two half-linkers, A or B, each with a unique barcode nucleotide (CG for half-linker A and AT for half-linker B). The barcode nucleotides are highlighted as red letters. Linkers with AB barcodes are considered to be non-specific chimeric proximity ligation products. (c) Mapping tags of PET sequences to reference genome. The categories of 'self-ligation PETs' and 'inter-ligation PETs' were assigned. (d) Clustering of overlapping PET sequences in the same genomic regions to identify enriched protein binding sites by overlapping 'self-ligation PETs' and long-range chromatin interactions by overlapping 'inter-ligation PETs'.