Genome editing in mammalian cells using the CRISPR type I-D nuclease

Osakabe, Keishi; Wada, Naoki; Murakami, Emi; Miyashita, Naoyuki; Osakabe, Yuriko

doi:10.1093/nar/gkab348

Cited by 39 publications

(35 citation statements)

References 65 publications

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“…Classification of subtype has been more complicated (for details, please refer to a review by Makarova et al, 2020) . Recently, we identified that Cas10 is an important component in TiD ( Osakabe et al, 2020 , 2021 ). This diversification of CRISPR–Cas results from evolution in an intensive arms race between bacteria and their phage foes ( Hampton et al, 2020 ).…”

Section: Future Perspectivesmentioning

confidence: 99%

“…Recently, we characterized type I-D (TiD) CRISPR–Cas loci from Microcystis aeruginosa , and successfully developed a genome editing tool, which we named TiD, based on this system ( Osakabe et al, 2020 , 2021 ; Figure1A ; Figure 3B ). Several groups have reported in vitro DNA binding and cleavage capability of several type I-D systems from bacteria such as Sulfolobus islandicus and Synechocystis sp.…”

Section: Introductionmentioning

confidence: 99%

“…Like other type I-based systems, recognition of a longer target sequence (35 or 36 nt) than that of Cas9 (20 nt) suggests that TiD has higher specificity than CRISPR–Cas9. Using TiD, we have successfully induced mutations at target genes in human cells ( Osakabe et al, 2021 ). Interestingly, our results showed that the mutation patterns produced by TiD in both human cells and plants were different from those induced by known Cas proteins such as Cas9, Cas12a, and Cas3: TiD introduced not only small insertion/deletion but also long-range deletions (ranging from 2.5 kb to 18.5 kb), and its direction was not uni-directional, but bi-directional ( Osakabe et al, 2020 , 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Using TiD, we have successfully induced mutations at target genes in human cells ( Osakabe et al, 2021 ). Interestingly, our results showed that the mutation patterns produced by TiD in both human cells and plants were different from those induced by known Cas proteins such as Cas9, Cas12a, and Cas3: TiD introduced not only small insertion/deletion but also long-range deletions (ranging from 2.5 kb to 18.5 kb), and its direction was not uni-directional, but bi-directional ( Osakabe et al, 2020 , 2021 ). Although the mutation patterns induced by genome editing would depend on the host organisms and the presence of active repair pathways, TiD would be a tool that can induce both small indels and long deletions, whereas majority of mutations induced by CRISPR–Cas9 and Cas12 are small indels (they also induce long deletions in some cases), and type I-E CRISPR–Cas can induce only unidirectional long deletions.…”

Section: Introductionmentioning

confidence: 99%

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Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems

Wada

Osakabe

2022

Plant Physiology

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Since its first appearance, CRISPR-Cas9 has been developed extensively as a programmable genome editing tool, opening a new era in plant genome engineering. However, CRISPR-Cas9 still has some drawbacks, such as limitations of the PAM sequence, target specificity, and the large size of the cas9 gene. To combat invading bacterial phages and plasmid DNAs, bacteria and archaea have diverse and unexplored CRISPR-Cas systems, which have the potential to be developed as a useful genome editing tools. Recently, discovery and characterization of additional CRISPR-Cas systems have been reported. Among them, several CRISPR-Cas systems have been applied successfully to plant and human genome editing. For example, several groups have achieved genome editing using CRISPR-Cas type I-D and type I-E systems, which had never been applied for genome editing previously. In addition to higher specificity and recognition of different PAM sequences, recently developed CRISPR-Cas systems often provide unique characteristics that differ from well-known Cas proteins such as Cas9 and Cas12a. For examples, type I CRISPR-Cas10 induces small indels and bi-directional long-range deletions ranging up to 7.2 kb in tomatoes (Solanum lycopersicum L.). Type IV CRIPSR-Cas13 targets RNA, not dsDNA, enabling highly specific knockdown of target genes. In this article, we review the development of CRISPR-Cas systems, focusing especially on their application to plant genome engineering. Recent CRISPR-Cas tools are helping expand our plant genome engineering toolbox.

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Section: Future Perspectivesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems

Wada

Osakabe

2022

Plant Physiology

Self Cite

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“…In type I-C systems, the Cas5 subunit possesses crRNA processing activity and Cas6 is absent (21). Although more complex than the streamlined class 2 systems such as Cas9 and Cas12, type I effectors have been utilised for a growing range of genome editing approaches and are particularly useful for long range genome edits (7,(22)(23)(24)(25).…”

Section: Introductionmentioning

confidence: 99%

Structure and mechanism of the type I-G CRISPR effector

Shangguan

Graham

Sundaramoorthy

et al. 2022

Preprint

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Type I CRISPR systems are the most common CRISPR type found in bacteria. They use a multisubunit effector, guided by crRNA, to detect and bind dsDNA targets, forming an R-loop and recruiting the Cas3 enzyme to facilitate target DNA destruction, thus providing immunity against mobile genetic elements. Subtypes have been classified into families A-G, with type I-G being the least well understood. Here, we report the composition, structure and function of the type I-G Cascade CRISPR effector from Thioalkalivibrio sulfidiphilus, revealing key new molecular details. The unique Csb2 subunit processes pre-crRNA, remaining bound to the 3-prime end of the mature crRNA, and seven Cas7 subunits form the backbone of the effector. Cas3 associates stably with the effector complex via the Cas8g subunit and is important for target DNA recognition. Structural analysis by cryo-Electron Microscopy reveals a strikingly curved backbone conformation with Cas8g spanning the belly of the structure. Type I-G Cascade is one of the most streamlined Class 1 CRISPR effectors. These biochemical and structural insights shed new light on the diversity of type I systems and open the way to applications in genome engineering.

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Efficient, compact, and versatile: Type I‐F2 CRISPR‐Cas system

Ma,

Zhang,

Liu

et al. 2024

mLife

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Type I CRISPR-Cas systems are the most prevalent and versatile among CRISPR-Cas systems, widely distributed across prokaryotes 1 . These systems are composed of multisubunit complexes, known as Cascade (CRISPR-associated complex for antiviral defense), which function by binding to CRISPR RNAs (crRNAs) and targeting complementary DNA sequences for degradation. Type I CRISPR-Cas systems, including subtypes I-A to I-G, have been extensively studied for their potential in genome manipulation [2][3][4][5][6][7][8][9][10][11][12] .Although Type I CRISPR-Cas systems offer significant potential for genome editing and transcriptional regulation, they face notable difficulties when used in eukaryotic cells. The main challenge stems from their considerable size and intricate multi-subunit architecture, which complicate their delivery especially when using viral vectors with strict cargo size limits, such as adeno-associated viruses (AAVs). For example, the Cascade complex of the well-studied Escherichia coli Type I-E CRISPR-Cas3 system consists of five subunits with a total gene size exceeding 4.2 kb 7 . Even the more compact Type I-C Cascade from Neisseria lactamica still comprises four subunits, over 3.2 kb in gene size 13,14 (Figure 1A), which is challenging to package and deliver effectively. Moreover, the assembly of these multiple subunits within cells can be inefficient, leading to reduced activity. Furthermore, the lack of a universal protospacer adjacent motif (PAM) across different Type I CRISPR-Cas systems adds another layer of difficulty, as it limits the range of targetable sequences. These limitations highlight the need for more compact and efficient CRISPR systems, particularly for therapeutic applications that require precise and reliable gene editing.The latest study published in Nature Communications presents a milestone in genome editing and transcriptional regulation within human cells, leveraging the smallest Type I system known to date, the I-F2 subtype 15 . Guo et al. focused on overcoming the limitations of traditional Type I CRISPR-Cas systems by developing a minimal version of the I-F2 subtype, derived from Moraxella osloensis CCUG 350. The I-

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Genome editing in mammalian cells using the CRISPR type I-D nuclease

Cited by 39 publications

References 65 publications

Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems

Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems

Structure and mechanism of the type I-G CRISPR effector

Efficient, compact, and versatile: Type I‐F2 CRISPR‐Cas system

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