title: Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins.
abstract: Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions.
authors.affiliation: Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan. hodaka@biken.osaka-u.ac.jp.
authors.forename: Hodaka
authors.initials: H
authors.lastname: Fujii
authors.affiliation: Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan. tf1023jp@biken.osaka-u.ac.jp.
authors.forename: Toshitsugu
authors.initials: T
authors.lastname: Fujita
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism*; D056726:Genetic Association Studies / Q000379:methods; D005818:Genetic Engineering / Q000379:methods; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors
keywords: CRISPR; ChIP; TAL; chromatin; chromatin immunoprecipitation; enChIP; engineered DNA-binding molecule-mediated ChIP; epigenetics; genome function