Development of Toolboxes for Precision Genome/Epigenome Editing and Imaging of Epigenetics

Abstract

Zinc finger (ZF) proteins are composed of repeated ββα modules and coordinate a zinc ion. ZF domains recognizing specific DNA target sequences can be substituted for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methyltransferases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the CRISPR-Cas9 system has expanded the range of possibilities for genome-editing technologies. In addition, these DNA binding domains can also be utilized to build a toolbox for epigenetic controls by fusing them with protein- or DNA-modifying enzymes. Here, our research on epigenome editing including the development of artificial zinc finger recombinase (ZFR), split DNA methyltransferase, and fluorescence imaging of histone proteins by ZIP tag-probe system is introduced. Advances in the ZF, TALE, and CRISPR-Cas9 platforms have paved the way for the next generation of genome/epigenome engineering approaches.

Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis

“…With the dawn of new site- and cell specific epigenetic modulators like modified CRISPR, zinc finger proteins and transcription-activator-like-effectors [31–33], the identification of potential genomic sites for antiepileptogenic intervention is of utmost importance.…”

The past, present, and future of artificial zinc finger proteins: design strategies and chemical and biological applications

“…The major site-specific nucleases are ZF nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9. These technologies have a much wider range of applications compared to conventional genetic engineering and gene therapy and are being intensively studied [ 87 – 92 ]. Here, we will introduce ZFNs, which have been at the center of genome editing research since the early stages of its development.…”

“…8 ). Some attempts have been made to “correct” and normalize mutated chromosomes using ZFNs for practical use in gene therapy [ 87 , 93 , 94 ]. Sangamo successfully altered DNA sequences by inducing homologous recombination between chromosomes and extrachromosomal DNA at specific sites of DNA double-strand breaks on chromosomes by ZFNs.…”

Chemical and Light Inducible Epigenome Editing

“…Several DNA-targeting technical platforms have been developed that have been or can potentially be applied to locus-specific epigenome editing [37,[40][41][42][43]. Three most commonly used techniques for DNA targeting in cells include zinc finger proteins (ZFPs), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeats (CRISPR) systems.…”