Publications
ThesisJan 2017

The CRISPR Enzyme Cpf1 as a Tool for Gene Regulation

Morrison, K
Product Used
NGS
Abstract
Clustered regularly-interspaced short palindromic repeats (CRISPR), a bacterial immune system fully characterized less than a decade ago, has become indispensable in the fields of biology over the past several years as it has been engineered into a tool for the targeted modification of DNA. In particular, the RNA-guided, single-enzyme CRISPR/Cas9 system has been used extensively to introduce mutations and create fusion proteins with targetable functions. However, the new CRISPR enzyme Cpf1 provides a much more robust tool for researchers, with the novel ability to process pre-CRISPR RNAs (pre-crRNAs) independently and to generate staggered cuts in double-stranded DNA. These capabilities, among other nuances of the system, open the door to multiplexed gene targeting and streamlined experimental design. Already, this new system has been used to introduce mutations to various ends, but it has only just begun to be used for gene regulation. To develop Cpf1 into a scalable tool for such studies, the DNA and RNA catalytic domains in three Cpf1 species (Acidaminococcus sp. (As), Francisella novicida (Fn), Lachnospiraceae bacterium (Lb)) were mutated. The results of an analysis of the catalytic function of these mutants verified previous studies that identified the necessary catalytic residues for DNase function (As: E993; Fn: E1006; Lb: E925) and RNase function (As: H800; Fn: H843; Lb: H759). Furthermore, I show that the deoxyribonuclease-dead “dCpf1” mutants can be fused to activator and repressor domains, and introduced into mammalian HEK293T cells with only slightly reduced levels of expression and with nuclear localization maintained. Activation of CXCR4 expression in the HEK293T cell line with designed crRNA guides was not observed, underscoring the complexity of regulatory studies in mammalian systems. These results advance Cpf1 as a tool for precisely controlling the regulation of endogenous genes, identify potential pitfalls for future resolution and will serve to guide researchers in the quest to expand the capabilities of Cpf1.
Product Used
NGS

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