title: ChIA-PET analysis of transcriptional chromatin interactions.
abstract: Long-range chromatin contacts between specific DNA regulatory elements play a pivotal role in gene expression regulation, and a global characterization of these interactions in the 3-dimensional (3D) chromatin structure is imperative in understanding signaling networks and cell states. Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a method which converts functional chromatin structure into millions of short tag sequences. Combining Chromatin Immunoprecipitation (ChIP), proximity ligation and high-throughput sequencing, ChIA-PET provides a global and unbiased interrogation of higher-order chromatin structures associated with specific protein factors. Here, we describe the detailed procedures of the ChIA-PET methodology, unraveling transcription-associated chromatin contacts in a model human cell line.
authors.affiliation: Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
authors.forename: Jingyao
authors.initials: J
authors.lastname: Zhang
authors.forename: Huay Mei
authors.initials: HM
authors.lastname: Poh
authors.forename: Su Qin
authors.initials: SQ
authors.lastname: Peh
authors.forename: Yee Yen
authors.initials: YY
authors.lastname: Sia
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.forename: Fabianus Hendriyan
authors.initials: FH
authors.lastname: Mulawadi
authors.forename: Yufen
authors.initials: Y
authors.lastname: Goh
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fullwood
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D002843:Chromatin / Q000235:genetics* / Q000648:ultrastructure; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D003432:Cross-Linking Reagents / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004843:Epistasis, Genetic; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013010:Sonication; D013388:Succinimides / Q000737:chemistry
chemical_list: D002843:Chromatin; D003432:Cross-Linking Reagents; D013388:Succinimides; C028722:ethylene glycolylbis(succinimidyl succinate); D004247:DNA