title: Chromatin interaction analysis using paired-end tag sequencing.
abstract: Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a technique developed for large-scale, de novo analysis of higher-order chromatin structures. Cells are treated with formaldehyde to cross-link chromatin interactions, DNA segments bound by protein factors are enriched by chromatin immunoprecipitation, and interacting DNA fragments are then captured by proximity ligation. The Paired-End Tag (PET) strategy is applied to the construction of ChIA-PET libraries, which are sequenced by high-throughput next-generation sequencing technologies. Finally, raw PET sequences are subjected to bioinformatics analysis, resulting in a genome-wide map of binding sites and chromatin interactions mediated by the protein factor under study. This unit describes ChIA-PET for genome-wide analysis of chromatin interactions in mammalian cells, with the application of Roche/454 and Illumina sequencing technologies.
authors.affiliation: Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fullwood
authors.forename: Yuyuan
authors.initials: Y
authors.lastname: Han
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D002843:Chromatin