CRISPR/Cas9-mediated targeted knock-in of large constructs using nocodazole and RNase HII

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Abstract

On-target integration of large cassettes via homology-directed repair (HDR) has several applications. However, the HDR-mediated targeted knock-in suffered from low efficiency. In this study, we made several large plasmids (12.1–13.4 kb) which included the CRISPR/Cas9 system along with a puromycin transgene as part of the large DNA donor (5.3–7.1 kb insertion cassettes) and used them to evaluate their targeted integration efficiency into a transgenic murine embryonic fibroblast (MEF) cell line carrying a single copy of a Venus transgene. We established a detection assay by which HDR events could be discriminated from the error-prone non-homologous end-joining (NHEJ) events. Improving the plasmid quality could considerably leverage the cell toxicity impediment of large plasmids. The use of the TILD (targeted integration with linearized dsDNA) cassettes did not improve the HDR rate compared to the circular plasmids. However, the direct inclusion of nocodazole into the electroporation solution significantly improved the HDR rate. Also, simultaneous delivery of RNase HII and the donor plasmids into the electroporated cells considerably improved the HDR events. In conclusion, the results of this study showed that using cell synchronization reagents in the electroporation medium can efficiently induce HDR rate in the mammalian genome.

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Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Alexis Komor, Yongjoo Kim, Michael Packer … (2016)

Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 1,2 Although most genetic diseases arise from point mutations, current approaches to point mutation correction are inefficient and typically induce an abundance of random insertions and deletions (indels) at the target locus from the cellular response to dsDNA breaks. 1,2 Here we report the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting “base editors” convert cytidines within a window of approximately five nucleotides (nt), and can efficiently correct a variety of point mutations relevant to human disease. In four transformed human and murine cell lines, second- and third-generation base editors that fuse uracil glycosylase inhibitor (UGI), and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favor desired base-editing outcomes, resulting in permanent correction of ∼15-75% of total cellular DNA with minimal (typically ≤ 1%) indel formation. Base editing expands the scope and efficiency of genome editing of point mutations.

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Search-and-replace genome editing without double-strand breaks or donor DNA

Andrew Anzalone, Peyton B. Randolph, Jessie Davis … (2019)

Summary Most genetic variants that contribute to disease 1 are challenging to correct efficiently and without excess byproducts 2–5 . Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed >175 edits in human cells including targeted insertions, deletions, and all 12 types of point mutations without requiring double-strand breaks or donor DNA templates. We applied prime editing in human cells to correct efficiently and with few byproducts the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay-Sachs disease (requiring a deletion in HEXA), to install a protective transversion in PRNP, and to precisely insert various tags and epitopes into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle can correct up to 89% of known genetic variants associated with human diseases.

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Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

Kärt Tomberg, Michael Kosicki, Allan Bradley (2018)

CRISPR-Cas9 is poised to become the gene editing tool of choice in clinical contexts. Thus far, exploration of Cas9-induced genetic alterations has been limited to the immediate vicinity of the target site and distal off-target sequences, leading to the conclusion that CRISPR-Cas9 was reasonably specific. Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors and a human differentiated cell line. Using long-read sequencing and long-range PCR genotyping, we show that DNA breaks introduced by single-guide RNA/Cas9 frequently resolved into deletions extending over many kilobases. Furthermore, lesions distal to the cut site and crossover events were identified. The observed genomic damage in mitotically active cells caused by CRISPR-Cas9 editing may have pathogenic consequences.

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Author and article information

Contributors

Wilfried A. Kues: Wilfried.kues@fli.de

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 15 February 2023

Publication date PMC-release: 15 February 2023

Publication date Collection: 2023

Volume: 13

Electronic Location Identifier: 2690

Affiliations

[1 ]GRID grid.417834.d, Biotechnology/Stem Cell Physiology, , Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, ; Höltystr. 10, 31535 Neustadt, Germany

[2 ]GRID grid.411463.5, ISNI 0000 0001 0706 2472, Department of Animal Science, Isfahan (Khorasgan) Branch, , Islamic Azad University, ; Tehran, Iran

[3 ]GRID grid.1008.9, ISNI 0000 0001 2179 088X, School of Biosciences, Royal Parade, , The University of Melbourne, ; Melbourne, VIC Australia

Article

Publisher ID: 29789

DOI: 10.1038/s41598-023-29789-1

PMC ID: 9931768

PubMed ID: 36792645

SO-VID: 11fed70a-1b73-494e-977d-00a1f47bcd81

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 23 August 2022

Date accepted : 10 February 2023

Funding

Funded by: Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit (4246)

Open Access :

Open Access funding enabled and organized by Projekt DEAL.

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ScienceOpen disciplines: Uncategorized

Keywords: molecular engineering,dna recombination,dna

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ScienceOpen disciplines: Uncategorized

Keywords: molecular engineering, dna recombination, dna

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CRISPR/Cas9-mediated targeted knock-in of large constructs using nocodazole and RNase HII

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Abstract

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Most cited references 39

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Search-and-replace genome editing without double-strand breaks or donor DNA

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

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Cited by 5

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