CRISPR and Genetic Engineering

Highly enhanced transgene integration in human pluripotent stem cells by serine integrase BxbI

This study enhances transgene integration in human pluripotent stem cells using BxbI integrase with codon optimization and other modifications, achieving up to 20-fold higher efficiency.

Redirecting DNA repair for efficient CRISPR-Cas-based gene targeting in tomato

This study improves CRISPR-Cas gene targeting efficiency in tomato by suppressing nonhomologous end-joining and enhancing homologous recombination.

CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

This paper compares CRISPR-Cas9 and Cas12a systems for genome editing and large fragment deletions in Aspergillus niger, showing Cas12a's higher efficiency with single gRNA and both systems achieving 100% efficiency with two gRNAs.

Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection

This paper designs artificial CRISPR-Cas13a guide RNAs using model-directed algorithms, showing improved sensitivity and variant discrimination in nucleic acid detection.

Large Serine Integrase Off-Target Discovery with Deep Learning for Genome Wide Prediction

The paper introduces IntQuery, a deep learning model that predicts LSI off-target activity genome-wide using data from Cryptic-seq.

CRISPR/Cas9-based somatic knock-in of reporters in the avian embryo in ovo

The paper demonstrates an efficient CRISPR/Cas9 method for somatic knock-in of reporters in avian embryos, enabling dynamic monitoring of protein distribution and labeling of neural sub-populations.

Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes

The paper develops a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and uses it to explore the function of genetic variants in both coding and non-coding regions.

Tunable, proteolytic dosage control of CRISPR-Cas systems enables precise gene therapy for dosage sensitive disorders

This paper introduces an IFFL-based CRISPR-Cas system to reduce gene expression variability, demonstrating improved dosage control for RAI1 in a mouse model.

The mechanism of bacterial defense system DdmDE from Lactobacillus casei

This study reveals the mechanism of the DdmDE system in Lactobacillus casei, showing how it degrades plasmids through a guided helicase-nuclease activity.

CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation

CRISPR-GEM predicts optimal CRISPR target genes by modeling gene regulatory networks using MLPs trained on differential gene expression data.

Optimizing a CRISPR-Cas13d gene circuit for tunable target RNA downregulation with minimal collateral RNA cutting

This paper develops MONARCH gene circuits to optimize CRISPR-Cas13d for tunable RNA downregulation with minimal off-target effects in human and green monkey cells.

An optimized somatic embryo transformation system assisted homozygous edited rubber tree generation method mediated by CRISPR/Cas9

This study develops a CRISPR/Cas9-based method to generate homozygous edited rubber tree plants by optimizing somatic embryo transformation and subculture procedures.

CRISPR/Cas-based genome editing for cyanophage of Anabeana sp.

This study uses CRISPR-Cas12a to delete genes in cyanophages, reducing genome size by 6.6% and identifying nonessential genes for propagation.

Filament formation activates protease and ring nuclease activities of CRISPR SAVED-Lon

The paper characterizes the CRISPR SAVED-Lon system, showing that filament formation activates protease and ring nuclease activities, leading to growth arrest in E. coli.

Systematic empirical evaluation of individual base editing targets: validating therapeutic targets in USH2A and comparison of methods

The paper evaluates base editing efficiency for USH2A mutations using in vitro screening and a mouse model, showing high correction rates and comparing methods.

Enrichment of allelic editing outcomes by Prime Editing in iPS cells

This study compares Cas9 and Prime Editing (PE) in human iPS cells, showing PE's superior precision and demonstrating how sorting by PE expression affects allelic editing outcomes.

An all-in-one AAV vector for cardiac-specific gene silencing by an adenine base editor

This study shows that single-AAV delivery of base editors can achieve effective cardiac gene silencing with higher success rates than dual-AAV systems.

Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording

The paper designs and characterizes diverse genomic parts for precise genome editing and molecular recording in mammalian cells.

Impact of Essential Genes on the Success of Genome Editing Experiments Generating 3,313 New Genetically Engineered Mouse Lines

The paper analyzes 3,313 genetically engineered mouse lines to identify gene essentiality as the main factor affecting Cas9-based genome editing success.

Early zygotic engineering promotes targeted large transgene integration and direct production of fully transgenic animals

The paper describes a method to achieve high-efficiency targeted transgene integration in zygotes, producing non-mosaic transgenic animals without requiring mosaic breeding.

Megabase-scale Transgene De-Duplication to Generate a Functional Single-Copy Full-Length Humanized DMD Mouse Model

The paper generates a single-copy humanized DMD mouse model by deleting a duplicated transgene to improve the accuracy of CRISPR therapy testing.

Optimization of methods for rapid and robust generation of cardiomyocyte-specific crispants in zebrafish using the cardiodeleter system

The paper optimizes methods to generate cardiomyocyte-specific CRISPR mutants in zebrafish using the cardiodeleter system, enabling rapid and robust gene deletion with detailed protocols.

Expanding the CRISPR toolbox by engineering Cas12a orthologs of metagenomic discovery

The paper identifies and characterizes new Cas12a orthologs from metagenomic data, leading to variants with improved PAM recognition and editing efficiency for CRISPR applications.

Single cell variation and rapid emergence of phenotypic heterogeneity in cell lines- a cautionary tale for devotees of CRISPR-Cas9.

This study shows that CRISPR-Cas9-generated cell lines exhibit significant phenotypic heterogeneity, including variable susceptibility to viral infections, highlighting potential experimental artifacts in gene editing studies.

Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication

This study examines the CRISPRi effects of the Type IV-A1 CRISPR-Cas system in Pseudomonas oleovorans and Escherichia coli using synthetic crRNAs, revealing long-range gene repression and plasmid targeting.

Assessment of drive efficiency and resistance allele formation of a homing gene drive in the mosquito Aedes aegypti

This study evaluates the efficiency and resistance allele formation of two CRISPR/Cas9-based gene drives in Aedes aegypti, finding one drive achieves super-Mendelian inheritance rates.

Cytotoxicity of Activator Expression in CRISPR-based Transcriptional Activation Systems

This study shows that CRISPRa systems can cause cytotoxicity, limiting their use in research and genetic screens.

Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability

The paper constructs CRISPRi libraries to knock down essential genes in S. pombe, revealing metabolic pathway interactions and enabling functional studies of essential genes.

Tailoring a CRISPR/Cas-based Epi-editor for Decreased Cytotoxicity and Enzymatic Specificity

This paper engineers modified p300 variants fused to dCas9 to reduce cytotoxicity and enhance enzymatic specificity in CRISPR-based epi-editing.

A massively parallel in vivo assay of TdT mutants yields variants with altered nucleotide insertion biases

The paper develops a high-throughput assay to profile and engineer TdT variants, identifying variants with altered nucleotide insertion biases that enhance DNA recording capabilities.