CRISPR/Cas9: Nature's gift to prokaryotes and an auspicious tool in genome editing

Khanzadi, Manzoor N.; Khan, Abid Ali

doi:10.1002/jobm.201900420

Cited by 28 publications

(16 citation statements)

References 115 publications

(151 reference statements)

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“…CRISPR is a bacterial and archaeal defense mechanism that works in hybrid with CRISPR-associated proteins. These were first discovered inside microorganisms DNA, but were subsequently extended to provide adaptive immune system for microorganisms [13]. CRISPR/Cas systems are easily adapted for genome modification because to their great practicality, comparative simplicity, and robustness [14].…”

Section: Crispr/cas Gene Structurementioning

confidence: 99%

CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered Bio-Based Products

Sharma¹,

Kumawat²,

Pandit³

et al. 2022

Synthetic Genomics - From BioBricks to Synthetic Genomes

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Biogenetic engineering is a significant technology to sensibly manage microbial metabolic product factories. Genome modification methods for efficiently controlling and modifying genes at the genome level have progressed in biogenetic engineering during the last decade. CRISPR is genome editing technology that allows for the modification of organisms’ genomes. CRISPR and its related RNA-guided endonuclease are versatile advanced immune system frameworks for defending against foreign DNA and RNAs. CRISPR is efficient, accessible, and trustworthy genomic modification tool in unparalleled resolution. At present, CRISPR-Cas9 method is expanded to industrially manipulate cells. Metabolically modified organisms are quickly becoming interested in the production of different bio-based components. Here, chapter explore about the control productivity of targeted biomolecules in divergent cells based on the use of different CRISPR-related Cas9.

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Section: Crispr/cas Gene Structurementioning

confidence: 99%

CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered Bio-Based Products

Sharma¹,

Kumawat²,

Pandit³

et al. 2022

Synthetic Genomics - From BioBricks to Synthetic Genomes

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“…Naturally, this currently unavoidable requirement introduces a design constraint when considering new targets: not every sequence will be targetable with a single Cas variant or at all using CRISPR-Cas. This has spurred the search for novel, naturally occurring Cas variants with alternative PAM preferences (e.g., Cas12a, Cas12e, Cas14), as well as re-engineering variants with expanded PAM compatibility or developing possible “PAMless” systems (e.g., SpCas9-NG, xCas9-3.7, and SpRY) [ 77 , 90 , 93 ]. It is worth noting, however, that while the PAM limits targetable sequences (and thus potential applications), the restriction it imposes may assist in reducing off-target activity.…”

Section: Crispr-casmentioning

confidence: 99%

Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies

Castro

Bjelic

Malhotra

et al. 2021

IJMS

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Recent advances in programmable nucleases including meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) have propelled genome editing from explorative research to clinical and industrial settings. Each technology, however, features distinct modes of action that unevenly impact their applicability across the entire genome and are often tested under significantly different conditions. While CRISPR-Cas is currently leading the field due to its versatility, quick adoption, and high degree of support, it is not without limitations. Currently, no technology can be regarded as ideal or even applicable to every case as the context dictates the best approach for genetic modification within a target organism. In this review, we implement a four-pillar framework (context, feasibility, efficiency, and safety) to assess the main genome editing platforms, as a basis for rational decision-making by an expanding base of users, regulators, and consumers. Beyond carefully considering their specific use case with the assessment framework proposed here, we urge stakeholders interested in genome editing to independently validate the parameters of their chosen platform prior to commitment. Furthermore, safety across all applications, particularly in clinical settings, is a paramount consideration and comprehensive off-target detection strategies should be incorporated within workflows to address this. Often neglected aspects such as immunogenicity and the inadvertent selection of mutants deficient for DNA repair pathways must also be considered.

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“…The Cas9 protein acts as a guide to cut the DNA double-strand, and the sgRNA acts as a guide, under the guidance of sgRNA. The Cas9 protein can cut the different target sites through the principle of base complementary pairing to achieve the double-strand break of DNA (Moses et al, 2019;Yang et al, 2020).In addition CRISPR/Cas9 can also be used for gene expression regulation (transcriptional activation/repression), epigenetic modi cations, and genomic imaging (Amjad et al, 2020;Khanzadi and Khan, 2020). This application relies on the resolution of the Cas9 protein structure (Gangopadhyay et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Hippo Kinase Pathway and of Prognosis Significance in primary Low-grade Glioma

Mijiti

Maimaiti

Chen

et al. 2022

Preprint

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Background Lethal genes in low-grade gliomas (LGGs) may have an essential prognostic significance and therefore need to be systematically analyzed. The purpose of this study is to analyze essential genes correlated with cell survival by evaluating CRISPR-cas9 screening data, leading to the identification of novel treatment targets for patients. Methods In this study, genes related to cell viability from the Depmap CRISPR-cas9 screen were intersected to differentially expressed genes (DEGs) between tumor and GTEx normal tissues from TCGA. The LASSO regression method was used to construct a signature that used to anticipate overall survival in patients with LGG. An evaluation of the signature was carried out using both multivariate and univariate Cox regression. Then, we determined which key pathways were modulated by this signature by comparing DEGs between low- and high-risk patients. WGCNA was conducted to identify modules associated with high-risk. In this study, we also performed enrichment analysis to identify pathways mediated by DEGs, overlapping genes, and genes shared in the WGCNA. Finally, we used to western blot, qRT-PCR and IHC to detect the expression of hub genes. Results Using the TCGA database, 145 oncogenes were identified as overexpressed. These genes were intersected with lethal genes identified in the Depmap database, which are enriched in Hippo pathways. A total of 19 genes were used to construct the gene signature by means of LASSO regression. The median risk score (0.752324) was employed to distinguish between low- and high-risk patients. The patients with high-risk characteristics showed a shorter OS duration in the internal training, the internal validation, and the external validation datasets. Ultimately, the Hippo signaling pathway was the predominantly enriched pathway in 145 genes, DEGs, and 3 modular genes in WGCNA. Finally, we found differences of hub genes expression in different clinical samples. Importantly, protein and mRNA expression of REP65 was significantly up-regulated in tumor cells both in the public cohort and our cohort. Conclusion The hippo signaling pathway detected based on CRISPR-cas9 screening is a critical regulator of viability and tumor proliferation and therefore is an innovative new target for treating cancerous brain tumors, including LGG.

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CRISPR/Cas9: Nature's gift to prokaryotes and an auspicious tool in genome editing

Cited by 28 publications

References 115 publications

CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered Bio-Based Products

CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered Bio-Based Products

Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Hippo Kinase Pathway and of Prognosis Significance in primary Low-grade Glioma

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