@article{3a0968f32e9a44e185a5f4bdeb52b90c,
title = "CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9",
abstract = "Cis-regulatory elements (CREs) play a pivotal role in spatiotemporal control of tissue-specific gene expression, yet the molecular composition of the vast majority of CREs in native chromatin remains unknown. In this article, we describe the clustered regularly interspaced short palindromic repeats (CRISPR) affinity purification in situ of regulatory elements (CAPTURE) approach to simultaneously identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 (dCas9) protein and programmable single guide RNAs (sgRNAs), this approach allows for high-resolution and locus-specific isolation of protein complexes and long-range chromatin looping associated with single copy CREs in mammalian cells. Unbiased analysis of the compositional structure of developmentally regulated or disease-associated CREs identifies new features of transcriptional regulation. Hence, CAPTURE provides a versatile platform to study genomic locus-regulating chromatin composition in a mammalian genome.",
keywords = "CRISPR, DNA looping, chromatin, cis-regulatory elements, enhancer",
author = "Xin Liu and Yuannyu Zhang and Yong Chen and Mushan Li and Zhen Shao and Zhang, {Michael Q.} and Jian Xu",
note = "Funding Information: Due to space limitations, we apologize for not being able to cite all the relevant references. We thank B. Chen and H. Chen (University of California, San Francisco) for sharing reagents and protocols, and F. Zhou (Fudan University) for helpful advice regarding peptide preparation and mass spectrometry. This work was supported by the National Institutes of Health (NIH) grant R01MH102616, the Cecil H. and Ida Green Endowment, the National Natural Science Foundation of China (NSFC) grants (91519326, 31671384 to M.Q.Z.), the National Institutes of Health (NIH)/National Funding Information: Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) grants K01DK093543, R03DK101665, and R01DK111430, Cancer Prevention and Research Institute of Texas (CPRIT) grants (RR140025 and RP180504), the American Cancer Society (IRG-02-196) award, the Harold C. Simmons Comprehensive Cancer Center at University of Texas Southwestern Medical Center (UT South-western), the Welch Foundation grant I-1942-20170325, an American Society of Hematology Scholar Award (to J.X.), and a Hamon Center for Regenerative Science and Medicine (CSRM) fellowship at University of Texas Southwestern Medical Center (UT Southwestern) and the American Heart Association (AHA) postdoctoral fellowship (18POST34060219) to X. L. Publisher Copyright: {\textcopyright} 2018 John Wiley & Sons, Inc.",
year = "2018",
month = jul,
doi = "10.1002/cpmb.64",
language = "English (US)",
volume = "123",
journal = "Current Protocols in Molecular Biology",
issn = "1934-3639",
publisher = "John Wiley and Sons Inc.",
number = "1",
}