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Graph-CRISPR: a gene editing efficiency prediction model based on graph neural network with integrated sequence and secondary structure feature extraction.
Clustered regularly interspaced short palindromic repeats (CRISPR) gene-editing technology has transformed molecular biology. Predicting editing efficiency is crucial for optimization, and numerous computational models have been created. However, many current models struggle to generalize across diverse editing systems, often experiencing performance drops with varying conditions or systems. Additionally, most models focus on ribonucleic acid (RNA) sequence and thermodynamic features, overlooking the importance of secondary structure information. Here, we present the first graph-based model (Graph-CRISPR) that integrates both sequence and secondary structure features of single guide RNA enhancing editing efficiency prediction. Tests show Graph-CRISPR consistently surpasses baseline models across systems like CRISPR-Cas9, prime editing, and base editing. It also demonstrates strong resilience, maintaining robust performance under varying experimental conditions. This work highlights the potential of integrating sequence and structural information through graph-based modeling to enhance predictive accuracy and adaptability in gene editing applications. The datasets and source codes are publicly available at: https://github.com/MoonLBH/Graph-CRISPR.
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Genome editing for plant research and crop improvement.
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel (insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.
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Prime editing promises to be a cut above CRISPR.
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CRISPR tool enables next-generation gene-editing techniques.
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Accurate analysis of genuine CRISPR editing events with ampliCan.
We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, and off-target read detection and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated data sets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.
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The Moral Choices on CRISPR Babies.
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Highly efficient base editing in human tripronuclear zygotes.
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CRISPR: express delivery to any DNA address.
The sudden emergence and worldwide adoption of CRISPR gene-editing technology confronts humanity with unprecedented opportunities and choices. CRISPR's transformative impact on our future understanding of biology, along with its potential to unleash control over the most fundamental of biological processes, is predictable by already achieved applications. Although its origin, composition, and function were revealed only recently, close to 3000 CRISPR-based publications have appeared including insightful and diversely focused reviews referenced here. Adding further to scientific and public awareness, a recent symposium addressed the ethical implications of interfacing CRISPR technology and human biology. However, the magnitude of CRISPR's rapidly emerging power mandates its broadest assessment. Only with the participation of a diverse and informed community can the most effective and humanity-positive CRISPR applications be defined. This brief review is aimed at those with little previous exposure to the CRISPR revolution. The molecules that constitute CRISPR's core components and their functional organization are described along with how the mechanism has been harnessed to edit genome structure and modulate gene function. Additionally, a glimpse into CRISPR's potential to unleash genetic changes with far-reaching consequences is presented.
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Perturbing proteomes at single residue resolution using base editing.
Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
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The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs.
Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action were elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.
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