ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Transcription factors and their three-dimensional interactions are crucial to gene regulation [1,2]. Many distal transcription factor binding sites have been identified by genome-wide chromatin experiments, such as chromatin immunoprecipitation (ChIP)-chip [3], ChIP-paired-end tag (PET) [4], and ChIP-Seq [5], but it is not clear which of these distal transcription factor binding sites are real and functional in gene regulation, and which are non-functional 'parking spots'. Three-dimensional chromatin interactions have been shown to bring distal transcription factor binding sites into close spatial proximity to gene promoters [6], but global analysis of three-dimensional chromatin interactions has been limited by the lack of techniques for high-resolution and whole-genome analysis.Recently, we developed a global, de novo, high-throughput method, Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), for characterizing the three-dimensional structures of long-range chromatin interactions in the nucleus [7-9], which makes it possible to identify transcriptional binding sites involved in long-range interactions at a genome-wide level. The key features in ChIA-PET analysis (Figure 1a) are that the cross-linked chromatin interaction nodes bound by protein factors are enriched by ChIP, and remote DNA elements tethered together in close spatial distance in these chromatin interaction nodes are connected through proximity ligation with oligonucleotide DNA linkers. We designed linker sequences that not only contain MmeI restriction sites for PET extraction, but also include specific nucleotide barcodes to assess the noise level in ChIA-PET data from random ligation. Upon MmeI digestion, the resulting PET construct contains a 20 bp head tag, a 38 bp linker sequence, and a 20 bp tail tag, which is the template for next generation paired-end sequencing, for example, Illumina paired-end sequencing from the two ends in opposite directions (Figure 1b). Each of th