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An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA.
As the applications of CRISPR-Cas9 technology diversify and spread beyond the laboratory to diagnostic and therapeutic use, the demands of gRNA synthesis have increased and access to tailored gRNAs is now restrictive. Enzymatic routes are time-consuming, difficult to scale-up and suffer from polymerase-bias while existing chemical routes are inefficient. Here, we describe a split-and-click convergent chemical route to individual or pools of sgRNAs. The synthetic burden is reduced by splitting the sgRNA into a variable DNA/genome-targeting 20-mer, produced on-demand and in high purity, and a fixed Cas9-binding chemically-modified 79-mer, produced cost-effectively on large-scale, a strategy that provides access to site-specific modifications that enhance sgRNA activity and in vivo stability. Click ligation of the two components generates an artificial triazole linkage that is tolerated in functionally critical regions of the sgRNA and allows efficient DNA cleavage in vitro as well as gene-editing in cells with no unexpected off-target effects.
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Optimization of T4 phage engineering via CRISPR/Cas9.
A major limitation hindering the widespread use of synthetic phages in medical and industrial settings is the lack of an efficient phage-engineering platform. Classical T4 phage engineering and several newly proposed methods are often inefficient and time consuming and consequently, only able to produce an inconsistent range of genomic editing rates between 0.03-3%. Here, we review and present new understandings of the CRISPR/Cas9 assisted genome engineering technique that significantly improves the genomic editing rate of T4 phages. Our results indicate that crRNAs selection is a major rate limiting factor in T4 phage engineering via CRISPR/Cas9. We were able to achieve an editing rate of > 99% for multiple genes that functionalizes the phages for further applications. We envision that this improved phage-engineering platform will accelerate the fields of individualized phage therapy, biocontrol, and rapid diagnostics.
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Innovative approach in malaria research: Harnessing CRISPR-Cas9 for antimalarial drug-resistance studies in Africa.
Malaria remains a major global health challenge, particularly in sub-Saharan Africa, where Plasmodium falciparum is increasingly resistant to frontline antimalarial therapies. CRISPR-Cas9, a groundbreaking genome editing tool, has become a transformative force in biomedical research, offering valuable insights into the genetic mechanisms underlying drug resistance. This review provides a comprehensive overview of the CRISPR-Cas9 system, its origin, evolution, and application in antimalarial drug-resistance research, with particular emphasis on African studies. We examine the role of CRISPR in elucidating resistance pathways, validating molecular markers, and enhancing diagnostic strategies. Additionally, a systematic scoping review highlights the geographic scope and focus of CRISPR-related malaria research conducted across Africa. Significantly low application and adoption were observed. Despite existing technological and regulatory barriers, CRISPR holds strong potential for accelerating antimalarial drug discovery and advancing precision medicine. Its strategic application in malaria-endemic regions could significantly bolster efforts toward disease control and eventual elimination.
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[Creation of new glabrous and salt-tolerant rice germplasm along the Yellow River by CRISPR-Cas9-mediated editing of OsSPL10].
The OsSPL10 gene has previously been reported to positively regulate trichome development and negatively regulate salt and drought stress tolerance in rice. However, it is not clear whether this gene can be used for gene editing to create new germplasm of glabrous leaf and salt-tolerant rice. In this study, we created six rice mutants by CRISPR/Cas9-mediated editing of OsSPL10 from 'Xinfeng 2', 'Xinkedao 31', and 'Xindao 25', the main rice cultivars along the Yellow River. Visual observation and scanning electron microscopy verified that the mutants lacked trichomes on the leaves and glumes, and the expression of glabrous marker genes OsHL6, OsGL6, and OsWOX3B in mutants was down-regulated compared with that in the wild type. The net photosynthetic rate, stomatal conductance, and transpiration rate of flag leaves in the mutants were significantly higher than those in the wild type. In addition, the survival rates of the mutants were much higher than that of the wild type after 7 days of treatment with 200 mmol/L NaCl. The results of quantitative real-time polymerase chain reaction (qRT-PCR) further verified that compared with the wild type, the mutants demonstrated down-regulated expression of the salt stress-related gene OsGASR1 and up-regulated expression of OsNHX2 and OsIDS1. Statistical analysis of agronomic traits showed that the mutants had increased plant height and no significant changes in yield-related traits compared with the wild type. The six spl10 mutants created in this study not only had glabrous leaves and glumes but also demonstrated enhanced tolerance to salt stress, serving as new germplasm resources for directional breeding of rice along the Yellow River.
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Benchmarking the PAM compatibility of Cas12a variants for high-throughput yeast genetic variant engineering.
Saccharomyces cerevisiae is an important organism for basic research and applied biotechnology. Genome editing techniques, particularly CRISPR/Cas9 from Streptococcus pyogenes, have greatly facilitated saturation genome editing in yeast to understand mutant functions on a large scale. However, Cas9 is restricted by its targeting preference for G-rich protospacer-adjacent motif (PAM) sequences. To broaden the targeting scope, we established an efficient homology-integrated CRISPR/Cas12a system to install genetic variants through homologous recombination by targeting T-rich PAMs. We benchmarked the PAM compatibility of PAM-relaxed Cas12a variants and identified the improved LbCas12a (impLbCas12a) as the most efficient and PAM-relaxed variant in S. cerevisiae, showing high editing purity and an editing window centering the double-strand break. We show that our system can be used to perform targeted saturation mutagenesis to reveal functional variants not captured previously. By using a homology-integrated CRISPR RNA array, we utilized the multiplexing capability of CRISPR/Cas12a to realize multiplex genetic variant installation. Our system enriches the yeast genetic variant engineering toolbox, complementing the commonly used CRISPR/Cas9 system.IMPORTANCECRISPR/Cas9 has facilitated yeast functional genomics by generating a large number of precise genetic variants in a very short period of time. This enabled the interrogation of reconstituted natural genetic variants across different genetic backgrounds or entirely synthetic mutations to discover novel or improved functions. However, Cas9 only targets a limited genomic sequence space due to its preference for G-rich PAM sequences. In this study, we close this gap by developing a CRISPR/Cas12a-based system to engineer user-defined genetic variants targeting T-rich PAM sequences. Our system adopts a homology-integrated design and the most PAM-relaxed Cas12a characterized in yeast to date. These features collectively enabled the creation of genetic variant libraries and multiplex edited strains. This genome editing tool can be used together with Cas9-based tools to interrogate a greater genomic sequence space.
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Computation and deep-learning-driven advances in CRISPR genome editing.
Genome editing with CRISPR-Cas systems is revolutionizing medicine, molecular biology and biotechnology. In this Review, we discuss the contributions of deep learning-based structure prediction algorithms, physics-based simulations, neural networks, graph neural networks and generative models, including diffusion and large language models, in engineering and optimizing CRISPR systems and in understanding their mechanistic basis. We highlight the challenges and limitations to the transformative effects of computational modeling and tools in the context of the development of programmable genome editors for biomedicine and biotechnology.
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Highly efficient gene editing of Feline herpesvirus 1 using CRISPR/Cas9 combined with FACS.
Feline herpesvirus 1 (FHV-1) is a major causative agent of feline viral rhinotracheitis and ocular lesions. Due to its large DNA genome, the construction of recombinant FHV-1 viruses presents considerable challenges for conventional methodologies. In this study, we implemented an integrated strategy combining CRISPR/Cas9-mediated gene editing with fluorescence-activated cell sorting (FACS) to enable the rapid and efficient generation of recombinant FHV-1 viruses. Specifically, the thymidine kinase (tk) gene was disrupted by inserting a monomeric Cherry (mCherry) reporter gene, and the glycoprotein E (gE) gene was similarly interrupted through the incorporation of a green fluorescent protein (GFP) reporter. The CRISPR/Cas9 system enables precise, site-specific genomic modifications, while FACS allows for effective enrichment and isolation of the desired recombinant viral populations. This combined approach significantly reduces the time required for recombinant virus generation from weeks to days, thereby offering substantial potential to expedite vaccine development and advance functional genomics research.
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Synthetic threads through the web of life.
CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Excitement over the breakthroughs these tools have enabled in biology and medicine is balanced, justifiably, by concern over how their applications might go wrong in open environments. We do not know how genomic processes (including regulatory and epigenetic processes), evolutionary change, ecosystem interactions, and other higher order processes will affect traits, fitness, and impacts of edited organisms in nature. However, anticipating the spread, change, and impacts of edited traits or organisms in heterogeneous, changing environments is particularly important with "gene drives on the horizon." To anticipate how "synthetic threads" will affect the web of life on Earth, scientists must confront complex system interactions across many levels of biological organization. Currently, we lack plans, infrastructure, and funding for field science and scientists to track new synthetic organisms, with or without gene drives, as they move through open environments.
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Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity.
Virus-mediated expression of CRISPR/Cas9 is commonly used for genome editing in animal brains to model or treat neurological diseases, but the potential neurotoxicity of overexpressing bacterial Cas9 in the mammalian brain remains unknown. Through RNA sequencing (RNA-seq) analysis, we find that virus-mediated expression of Cas9 influences the expression of genes involved in neuronal functions. Reducing the half-life of Cas9 by tagging with geminin, whose expression is regulated by the cell cycle, maintains the genome editing capacity of Cas9 but significantly alleviates neurotoxicity. Thus, modification of Cas9 by shortening its half-life can help develop CRISPR/Cas9-based therapeutic approaches for treating neurological disorders.
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Predicting CRISPR/Cas9 Repair Outcomes by Attention-Based Deep Learning Framework.
As a simple and programmable nuclease-based genome editing tool, the CRISPR/Cas9 system has been widely used in target-gene repair and gene-expression regulation. The DNA mutation generated by CRISPR/Cas9-mediated double-strand breaks determines its biological and phenotypic effects. Experiments have demonstrated that CRISPR/Cas9-generated cellular-repair outcomes depend on local sequence features. Therefore, the repair outcomes after DNA break can be predicted by sequences near the cleavage sites. However, existing prediction methods rely on manually constructed features or insufficiently detailed prediction labels. They cannot satisfy clinical-level-prediction accuracy, which limit the performance of these models to existing knowledge about CRISPR/Cas9 editing. We predict 557 repair labels of DNA, covering the vast majority of Cas9-generated mutational outcomes, and build a deep learning model called Apindel, to predict CRISPR/Cas9 editing outcomes. Apindel, automatically, trains the sequence features of DNA with the GloVe model, introduces location information through Positional Encoding (PE), and embeds the trained-word vector matrixes into a deep learning model, containing BiLSTM and the Attention mechanism. Apindel has better performance and more detailed prediction categories than the most advanced DNA-mutation-predicting models. It, also, reveals that nucleotides at different positions relative to the cleavage sites have different influences on CRISPR/Cas9 editing outcomes.
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