Open AccessChromatin Interaction Analysis Using Paired‐End Tag Sequencing
Author(s) -
Fullwood Melissa J.,
Han Yuyuan,
Wei ChiaLin,
Ruan Xiaoan,
Ruan Yijun
Publication year - 2010
Publication title -
current protocols in molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.533
H-Index - 42
eISSN - 1934-3647
pISSN - 1934-3639
DOI - 10.1002/0471142727.mb2115s89
Subject(s) - chromatin , chia pet , dna sequencing , chromatin immunoprecipitation , chip sequencing , computational biology , biology , chromosome conformation capture , dna , genome , genetics , microbiology and biotechnology , chromatin remodeling , gene , transcription factor , promoter , enhancer , gene expression
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. Curr. Protoc. Mol. Biol . 89:21.15.1‐21.15.25. © 2010 by John Wiley & Sons, Inc.