CRISPR and Genetic Engineering

Prime editing outperforms homology-directed repair as a tool for CRISPR-mediated variant knock-in in zebrafish

This study compares CRISPR-mediated homology-directed repair (HDR) and prime editing (PE) for precise genetic variant knock-in in zebrafish, finding PE achieves higher editing efficiency and fewer off-target effects.

Kinetic mechanism for fidelity of CRISPR-Cas9 variants

The paper develops a kinetic model of CRISPR-Cas9 substrate selection and cleavage, showing specificity improvements arise from kinetic changes, not binding affinity.

Widespread and Abundant CRISPR-Cas Systems in the Deep Ocean

The paper identifies a high abundance of CRISPR-Cas systems in deep ocean microbiomes, highlighting their diversity and potential for bioprospecting.

A highly efficient CRISPR-Cas9-based gene editing system in oat (Avena sativa)

This paper reports the first successful CRISPR-Cas9 gene editing in oat, achieving up to 41.1% efficiency in three genes and revealing developmental phenotypes in mutants.

From lab to field: analyses of genome-edited bacterial blight resistant rice

The paper evaluates genome-edited rice lines resistant to bacterial blight, showing no performance defects and absence of foreign DNA in offspring.

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

The paper introduces CiBER-seq, a CRISPRi platform that improves the sensitivity and scope of genome-wide screens by normalizing expression reporters against control promoters, and validates its ability to capture post-transcriptional and post-translational regulation.

When good guides go bad: empirical evaluation of all unique Cas9 targets in E. coli reveal widespread functionality and rules for gRNA design

The paper evaluates nearly 500,000 unique gRNAs in E. coli, finding most are functional and identifying rules to improve gRNA design.

A resource and computational approach for quantifying gene editing allelism at single-cell resolution

The paper constructs a single-cell DNA sequencing atlas and introduces GUMM, a computational workflow, to accurately infer gene editing allelism despite technical artifacts.

Non-canonical cleavage expands prime editing in 5' direction

This paper expands prime editing capabilities by utilizing non-canonical cleavage to enable editing in the 5' direction of a classic nick site.

Single-stranded HDR templates with truncated Cas12a binding sequences improve knock-in efficiencies in primary human T cells

This study improves CRISPR-Cas12a knock-in efficiency in human T cells by using single-stranded DNA templates with double-stranded Cas-target-sequences, achieving up to 90% knock-in rates for transgene inserts.

Sequential Amino Acid Mutagenesis-Driven De Novo Evolution of Adenine Deaminases Enables Efficient In Vivo Base Editing in Primate

This paper develops hpABE5.20, a base editor with improved precision and reduced off-target effects through sequential amino acid mutagenesis and AI-based structural prediction.

Fusions of catalytically inactive RusA to FokI nuclease coupled with PNA enable programable site-specific double-stranded DNA breaks

The paper develops a new programmable site-specific nuclease system, PC-FIRA, that enables precise double-strand DNA breaks with high specificity and efficiency.

Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9

This paper uses CRISPR-Cas9 to induce targeted loss of heterozygosity in Candida albicans and validates its role in antifungal resistance.

Efficient Cas9 nuclease-based editing in skeletal muscle via lipid nanoparticle delivery

SORT LNPs enable efficient Cas9-mediated repair of a pathogenic allele in skeletal muscle in a mouse model of LGMDR7.

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression

The paper demonstrates that RNA thermometers can reduce Cas9-induced cell death by controlling its expression through temperature-dependent regulation.

SANTON: Sequencing Analysis Toolkits for Off-target Nomination

SANTON is a toolkit for analyzing off-target sequencing data from gene-editing technologies, identifying more potential off-target sites than previous studies.

A Hot-Swappable Genetic Switch: Building an inducible and trackable functional assay for the essential gene MEDIATOR 21

The paper develops a genetic switch system to study the essential gene MED21 in Arabidopsis by inducibly ablating its expression in non-essential tissues and enabling post-embryonic analysis.

Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells

This study develops a CRISPRa-based method to rapidly verify gene editing in human pluripotent stem cells without differentiation.

A census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system

The paper identifies AcrIE9 as an inhibitor of E. coli K12 Type IE CRISPR-Cas system through a census of anti-CRISPR proteins in Enterobacterales.

DSB repair kinetics impair CRISPR-Cas9 editing in human embryos

This study shows that CRISPR-Cas9 editing in human embryos is limited by slow DSB repair kinetics, leading to mosaicism and chromosomal abnormalities.

mtgRNA-db: An annotated database of multi-target CRISPR-Cas9 guide-RNAs in the human genome

The paper creates a database of multi-target CRISPR-Cas9 guide-RNAs with on- and off-target scores and provides a web tool for selecting these guide-RNAs.

TOP-SECRETS enables Cas9 nucleases to discriminate SNVs outside of PAMs

TOP-SECRETS enables Cas9 to distinguish SNVs outside PAMs by generating gRNA variants that improve discrimination between healthy and disease-associated SNVs.

Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection

The paper compares sequence search tools for detecting CRISPR spacer-target interactions and finds significant differences in their performance.

Promoter replacement by genome editing creates gain-of-function traits in Arabidopsis

This paper uses CRISPR-Cas9 to replace the FT promoter in Arabidopsis, leading to early flowering without foreign DNA.

GeneFix-AI: AI-Powered CRISPR-Cas9 System for Real-Time Detection and Correction of Mutations in Non-Human Species

GeneFix-AI predicts and corrects genetic mutations in non-human species using AI to automate CRISPR-Cas9 workflows.

CRISMER: A transformer-based Interpretable Deep Learning Approach for Genome-wide CRISPR Cas-9 Off-Target Prediction and Optimization

CRISMER improves CRISPR-Cas9 off-target prediction and optimization using a hybrid deep learning model, achieving higher accuracy and fewer parameters than existing methods.

Structural basis of unidirectional DNA recombination by the ΦC31 serine integrase

This paper reports structures of ΦC31 integrase in complexes with DNA recombination sites, elucidating the structural basis of its unidirectional recombination mechanism.

In vivo production of an anti-HIV antibody from primate hematopoietic cells by non-viral knock-in

This study shows non-viral gene editing in primate hematopoietic stem cells can produce anti-HIV antibodies in vivo with detectable titers.

Insights on the regulation and function of the CRISPR/Cas transposition system located in the pathogenicity island VpaI-7 from Vibrio parahaemolyticus RIMD2210633.

The paper characterizes the CRISPR/Cas transposition system in Vibrio parahaemolyticus, showing it is transcriptionally active and potentially more efficient in its natural host than in E. coli.

CRISPR-based environmental biosurveillance assisted via artificial intelligence design of guide-RNAs

The paper develops CORSAIR, a CRISPR-based environmental biosurveillance system using AI-designed guide-RNAs for rapid, field-deployable eDNA detection of invasive species.