CRISPR and Genetic Engineering

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.

This paper investigates how natural genetic variations affect CRISPR/Cas9 outcomes and introduces a web platform to predict and avoid editing disparities caused by these variations.

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.

This study delivers Cas9 or base editor RNP complexes directly to retinal cells, achieving gene editing in photoreceptors and RPE, but with toxicity at high concentrations.

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

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

This paper develops a split CRISPR-Cas12a system for sensitive, selective, and multiplexed detection of RNA and DNA without reverse transcription, achieving low detection limits and improved specificity.

This study identifies mutations to improve prime editing efficiency in low-dNTP environments by enhancing MMLV-reverse transcriptase and reducing SAMHD1 activity.

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.

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

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.

This paper develops a DNA-free CRISPR/Cas9 system in soybean using iPB-RNP method, achieving genome editing in shoot apical meristems without tissue culture, resulting in 0.4-4.6% mutation transmission to next generation.

MultiGreen improves upon GreenGate by enabling efficient multiplexing and reducing assembly cycles for plant transgenic constructs.

The paper describes a CRISPRa screening method combining multiplex perturbations with sc-RNA-seq to identify cell-type-specific regulatory elements and their target genes.

AssemblyTron automates Golden Gate cloning using open-source lab robots, improving efficiency and reducing errors in complex DNA construct assembly.

The paper experimentally characterizes retrons to determine their RT-DNA sequences, production rates, and editing efficacy across bacterial, phage, and human genomes.

This study shows that inhibiting DNA repair pathways with AZD7648 improves gene insertion efficiency in airway stem cells for CFTR correction, but may introduce toxicity.

The paper investigates the deployment of tethered gene drives in continuous space, finding that drive wave interference must be avoided to ensure successful suppression.

This paper develops a CRISPR/Cas9 system for efficient gene editing and overexpression in the fern Ceratopteris richardii, demonstrating functional effects on stomatal and photosynthetic traits.

The paper develops a pipeline for efficient loss-of-function mutagenesis in NPD genes using base editing in hiPSCs, achieving high reproducibility and confirming neural phenotypes.

SeqVerify is a computational pipeline that analyzes whole genome sequencing data to verify gene editing outcomes and detect abnormalities in cell lines.

This paper engineers Escherichia coli Nissle 1917 to block antibiotic resistance gene transfer using a type I CRISPR-Cas system, showing efficacy in vitro and in zebrafish.

The paper tests a hypothesis about overhang stability affecting ligation efficiency in Golden Gate Assembly and finds that strong overhangs improve efficiency.

This study improves prime editing efficiency in dicots by using novel PE components, achieving heritable edits in tomato and Arabidopsis with 38.2% success.

This study evaluates CRISPR-based gene integration in skeletal muscle using two high-expressing loci, demonstrating high-level therapeutic gene expression in mouse myoblasts.

The paper introduces crispat, a tool for guide assignment in single-cell CRISPR screens, showing differences in results across strategies.

This paper introduces DdCBEs with modified TALE proteins that remove the 5-T constraint, enabling efficient and specific mitochondrial base editing at previously inaccessible sites.

SpacerPlacer reconstructs ancestral CRISPR array evolution, revealing frequent spacer deletions and a decrease in deletion frequency towards both ends of arrays.

This paper develops PRECIS, a method combining prime editing and a synthetic intron reporter to efficiently generate SF3B1 mutant cell lines that recapitulate cancer-related splicing and CNV events.

This paper introduces a scarless gene editing strategy using a cyclical marker system in Chlamydomonas reinhardtii to enable unlimited sequential CRISPR edits.