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      Tissue Specific DNA Repair Outcomes Shape the Landscape of Genome Editing

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          Abstract

          The use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 has moved from bench to bedside in less than 10years, realising the vision of correcting disease through genome editing. The accuracy and safety of this approach relies on the precise control of DNA damage and repair processes to achieve the desired editing outcomes. Strategies for modulating pathway choice for repairing CRISPR-mediated DNA double-strand breaks (DSBs) have advanced the genome editing field. However, the promise of correcting genetic diseases with CRISPR-Cas9 based therapies is restrained by a lack of insight into controlling desired editing outcomes in cells of different tissue origin. Here, we review recent developments and urge for a greater understanding of tissue specific DNA repair processes of CRISPR-induced DNA breaks. We propose that integrated mapping of tissue specific DNA repair processes will fundamentally empower the implementation of precise and safe genome editing therapies for a larger variety of diseases.

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          Most cited references83

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          A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

          Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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            Multiplex genome engineering using CRISPR/Cas systems.

            Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
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              RNA-guided human genome engineering via Cas9.

              Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                03 September 2021
                2021
                : 12
                : 728520
                Affiliations
                [1] 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna, Austria
                [2] 2Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna , Vienna, Austria
                Author notes

                Edited by: Sylvie M. Noordermeer, Leiden University Medical Center, Netherlands

                Reviewed by: Michael Aregger, National Cancer Institute (NCI), United States; Chris Richardson, University of California, Santa Barbara, United States

                *Correspondence: Joanna I. Loizou, joanna.loizou@ 123456meduniwien.ac.at

                These authors have contributed equally to this work

                This article was submitted to Human and Medical Genomics, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2021.728520
                8446275
                34539755
                567d048d-2f51-49a8-a116-62281889b999
                Copyright © 2021 Meyenberg, Ferreira da Silva and Loizou.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 21 June 2021
                : 05 August 2021
                Page count
                Figures: 2, Tables: 0, Equations: 0, References: 85, Pages: 11, Words: 9450
                Funding
                Funded by: Austrian Academy of Sciences 10.13039/501100001822
                Award ID: ÖAW25035
                Award ID: ÖAW25757
                Funded by: ERC Synergy Grant
                Award ID: 855741
                Funded by: FWF Stand Alone Grant
                Award ID: P33024
                Categories
                Genetics
                Review

                Genetics
                crispr-cas9,genome editing,dna double-strand break,homology directed repair,non-homologous end-joining,microhomology mediated end-joining,tissue specific dna repair,tissue stem cells

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