Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System

Stem Cells International, Jul 2018

Epigenetics classically refers to the inheritable changes of hereditary information without perturbing DNA sequences. Understanding mechanisms of how epigenetic factors contribute to inheritable phenotype changes and cell identity will pave the way for us to understand diverse biological processes. In recent years, the emergence of CRISPR/Cas9 technology has provided us with new routes to the epigenetic field. In this review, novel epigenetic techniques utilizing the CRISPR/Cas9 system are the main contents to be discussed, including epigenome editing, temporal and spatial control of epigenetic effectors, noncoding RNA manipulation, chromatin in vivo imaging, and epigenetic element screening.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

http://downloads.hindawi.com/journals/sci/2018/7834175.pdf

Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System

Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System Nina Xie,1,2 Yafang Zhou,1,2 Qiying Sun,1,2 and Beisha Tang1,3,2 1Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China 2National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan 410078, China 3Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China Correspondence should be addressed to Beisha Tang; moc.361@8937gnatsb Received 4 November 2017; Revised 4 February 2018; Accepted 27 March 2018; Published 8 July 2018 Academic Editor: Changwon Park Copyright © 2018 Nina Xie et al. 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. Abstract Epigenetics classically refers to the inheritable changes of hereditary information without perturbing DNA sequences. Understanding mechanisms of how epigenetic factors contribute to inheritable phenotype changes and cell identity will pave the way for us to understand diverse biological processes. In recent years, the emergence of CRISPR/Cas9 technology has provided us with new routes to the epigenetic field. In this review, novel epigenetic techniques utilizing the CRISPR/Cas9 system are the main contents to be discussed, including epigenome editing, temporal and spatial control of epigenetic effectors, noncoding RNA manipulation, chromatin in vivo imaging, and epigenetic element screening. 1. Introduction Epigenetics classically refers to the inheritable changes of hereditary information without perturbing DNA sequences. DNA methylation, demethylation, hydroxyl-methylation, histone modification, chromatin remodeling, gene imprinting, and noncoding RNA are the central mechanisms involved. They play important roles in diverse biological processes including gene regulation, iPSC reprogramming and maintenance, genomic imprinting, X-chromosome inactivation, aging, neurodegeneration, autoimmune modulation, and tumorigenesis [1–4]. Adapted from a natural immune defense system in bacteria, the clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 (Cas9) system, abbreviated as the CRISPR/Cas9 system, is a site-specific genome editing tool that could be implemented to target and mutate specific genomic regions in eukaryotic cells, especially in mammalian cells [5]. The rationale is described below: the in vivo CRISPR/Cas9 system comprises two core components, a Cas9 nuclease and a guide RNA sequence. The guide RNA is programmable. By changing the sequences of guide RNA, researchers could target Cas9 nuclease to almost any locus in the genome precisely. After being delivered into the cell of interest, guide RNA will direct Cas9 nuclease to the target via complementary matching with the corresponding genomic DNA sequence. Flanking by a NGG protospacer adjacent motif (PAM) is a prerequisite for a piece of DNA sequence to be a qualified target. Once guide RNA finds its target, the Cas9 nuclease will transit from the binding state to the cutting state with the help of PAM, subsequently generating a double-stranded break (DSB). Depending on the presence of a repair template, the DSB will be rejoined either by the nonhomologous end joining (NHEJ) or the homology-directed repair (HDR) mechanism. The former is more error-prone, while the latter is more precise [6–11]. Briefly, by designing specific guide RNA sequence and inducing appropriate downstream repair mechanism, researchers can utilize this method to achieve genome modifications flexibly. Notably, since the emergence of CRISPR/Cas9 technology, diverse applications have been explored beyond genome editing. Here, we will focus on the new toolkit that CRISPR/Cas9 has provided to us for epigenetic research. 1.1. Epigenome Editing Epigenome editing refers to the targeted rewriting of epigenetic markers [1, 12]. On the one hand, it could be used to selectively modify epigenetic marks at a given locus to explore mechanisms of how targeted epigenetic alterations would affect transcription regulation and cause subsequent phenotype changes. For example, it has been reported that inducing histone methylation or acetylation at the Fosb locus in the mice brain reward region, nucleus accumbens, could affect relevant transcription network and thus control behavioral responses evoked by drug and stress [13–15]. On the other hand, epigenome editing has the potential for epigenetic treatment, especially for the disorders with abnormal gene imprinting or epigenetic marks. Targeted epigenetic silencing or reactivation of the mutant allele could be a potential therapeutic approach for diseases such as Rett syndrome and Huntington’s disease [12, 16–19]. DNA-binding protein domains, such as zinc finger (ZFN) or transcription activator-like effector nuc (...truncated)


This is a preview of a remote PDF: http://downloads.hindawi.com/journals/sci/2018/7834175.pdf

Nina Xie, Yafang Zhou, Qiying Sun, Beisha Tang. Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System, Stem Cells International, 2018, 2018, DOI: 10.1155/2018/7834175