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Int. J. Mol. Sci. 2015, 16(9), 21802-21812; doi:10.3390/ijms160921802

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

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
*
Author to whom correspondence should be addressed.
Academic Editor: Izuho Hatada
Received: 6 August 2015 / Revised: 24 August 2015 / Accepted: 29 August 2015 / Published: 9 September 2015
(This article belongs to the Special Issue Genome Editing)
View Full-Text   |   Download PDF [708 KB, uploaded 9 September 2015]   |  

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. View Full-Text
Keywords: ChIP; chromatin immunoprecipitation; enChIP; engineered DNA-binding molecule-mediated ChIP; chromatin; epigenetics; genome function; CRISPR; TAL ChIP; chromatin immunoprecipitation; enChIP; engineered DNA-binding molecule-mediated ChIP; chromatin; epigenetics; genome function; CRISPR; TAL
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Fujii, H.; Fujita, T. 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. Int. J. Mol. Sci. 2015, 16, 21802-21812.

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