CRISPR and Genetic Engineering

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

This study characterizes AcrIF11, an ADP-ribosyltransferase that inhibits CRISPR-Cas systems with high potency and specificity, and shows its reversibility through macrodomain enzymes.

Weighted Off-target and Efficiency Scoring Reveal Genome Composition-Dependent Optimal CRISPR/Cas9 Guide Design

This paper introduces a computational method to optimize CRISPR/Cas9 guide design by integrating genome composition, PAM diversity, and weighted off-target scoring to improve specificity and efficiency.

PAM adenine methylation and flanking sequence regulate SaCas9 activity in bacteria

This study uses machine learning to predict SaCas9 activity in bacteria, revealing that PAM adenine methylation and flanking sequences significantly influence activity.

Exploring the deletion landscape of S. aureus Cas9 with SABER

The paper introduces SABER, a method to efficiently map tolerated deletions in SaCas9, enabling the design of minimal CRISPRi effectors.

Genome-wide high-density CRISPR interference screens reveal condition-specific metabolic vulnerabilities in Pseudomonas aeruginosa PAO1

The paper uses CRISPRi screens to identify metabolic vulnerabilities in P. aeruginosa PAO1 under different conditions, revealing key genes for targeting chronic infections.

T cell correction pipeline for Inborn Errors of Immunity

This paper presents a T cell gene correction pipeline using CRISPR/Cas9 and HDR to correct monogenic mutations in IEI models, achieving up to 80% bi-allelic editing with no detectable off-target effects.

Pythia: Non-random DNA repair allows predictable CRISPR/Cas9 integration and gene editing

The paper introduces Pythia, a tool that uses deep learning to predict CRISPR/Cas9 integration and editing outcomes by leveraging non-random DNA repair patterns.

Kingdom-Wide CRISPR Guide Design with ALLEGRO

ALLEGRO designs universal CRISPR sgRNA libraries targeting multiple fungal species, validated experimentally across three fungi and extended to others.

ONE-STEP tagging: a versatile method for rapid site-specific integration by simultaneous reagent delivery

ONE-STEP tagging enables rapid, efficient, and scalable protein tagging in diverse cell types through CRISPR-Cas9 and Bxb1 integrase, with high integration efficiency and multiplexing capabilities.

A compact vector for scarless gene editing in E. coli

The paper introduces pCASKD, a single-plasmid system for scarless gene editing in E. coli, demonstrating efficient knock-in and knock-out edits with reduced false positives and faster workflow.

AI-generated small binder improves prime editing

The paper uses AI to generate a small MLH1 binder that enhances prime editing efficiency by disrupting MMR, resulting in the highest PE efficiency to date.

CRISPRi-seq in Haemophilus influenzae reveals genome-wide and medium-specific growth determinants

This paper introduces a CRISPRi-seq platform in Haemophilus influenzae to study gene fitness and essentiality, revealing medium-specific growth determinants and introducing a genome annotation resource.

Python-based automation of INDIGO webserver using Selenium: A high throughput analysis of Sanger sequence data to detect allelic variations created by CRISPR/Cas9-mediated genome editing of crop plants

Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae

The paper develops plasmids for CRISPR-Cas9 genome editing in yeast using retron-mediated amplification of repair templates, achieving high editing efficiencies.

Escape from antimicrobial CRISPR-Cas9 in E. coli ST131 depends on the genetic context of the target gene.

This study investigates CRISPR-Cas9 antimicrobial activity against E. coli ST131 and identifies two escape mechanisms, showing that genetic context of the target gene influences escape frequency.

The stress of carrying CRISPR-Cas

This study investigates the CRISPR-Cas system in Streptococcus anginosus, finding that it imposes metabolic and fitness costs, impairing stress response and potentially explaining its low prevalence in this species.

Protective antigen-mediated delivery of an anti-CRISPR proteinfor precision genome editing

This paper develops a protein-based delivery system for anti-CRISPR proteins to precisely control Cas9 activity, reducing off-target effects and improving genome editing specificity.

A platform for the systematic interrogation of genetic interactions in human cells: 26 gene by genome-wide double knockout screens as a proof of concept

The paper introduces a method for systematically studying genetic interactions in human cells using CRISPR/Cas9 screens and demonstrates its effectiveness through 26 gene by genome-wide knockout screens.

Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy

This study uses long-read sequencing to analyze genomic and transcriptomic changes in AAV-CRISPR therapy for DMD, revealing complex editing outcomes and developing new methods for detection.

CRISPR-GPT for Agentic Automation of Gene Editing Experiments

CRISPR-GPT automates CRISPR-based gene-editing design and analysis by integrating LLMs with domain expertise, demonstrating effectiveness in gene knockout and activation experiments.

Split Cas12a protospacer engineering enables ultra-specific, PAM-free detection

The paper describes engineering Cas12a to enable PAM-free, ultra-specific detection by splitting the target DNA duplex and improving structural selectivity and nucleotide specificity.

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

The paper develops a CRISPR/Cas13d-based method to specifically knockdown RNA isoforms and provides computational tools for experimental design and analysis.

Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair

This study determines the structural basis for how a domesticated reverse transcriptase evolved to function in DNA repair by revealing key structural adaptations in its apoenzyme and DNA synthesis complexes.

Optimized iMAP CRISPR Perturbation Illuminates Context-Specific Functions of RNA Modification Factors

The paper optimizes the iMAP CRISPR platform to reduce recombination bias, profiles RNA modification factors across mouse tissues, and identifies context-specific functions with therapeutic implications.

Dopamine receptor 1 specific CRISPRa mice exhibit disrupted behaviors and striatal baseline cellular activity

This paper shows that CRISPR-dCas9 systems can cause behavioral and cellular changes in mice even without targeting specific genes, highlighting the need for validation.

A rapid and efficient red-light-activated Cre recombinase system for genome engineering in mammalian cells and transgenic mice

This paper introduces REDMAPCre, a red-light-activated Cre recombinase system that enables rapid and efficient DNA recombination in mammalian cells and mice.

Engineering circular guide RNA and CRISPR-Cas13d-encoding mRNA for the RNA editing of Adar1 in triple-negative breast cancer immunotherapy

This study develops circular guide RNAs (cgRNAs) and Cas13d-encoding mRNA for efficient RNA editing of Adar1 in triple-negative breast cancer, showing improved stability and therapeutic efficacy.

Systematic Mapping of Bacterial CRISPRa Design Rules and Implications for Synergistic Gene Activation

This study systematically maps bacterial CRISPRa design rules and finds no synergistic activation, highlighting mechanistic differences from eukaryotic systems.

Effect of Caenorhabditis elegans U6 Promoters on CRISPR/Cas9-Mediated Gene Editing Efficiency

This study evaluates C. elegans U6 promoters' impact on CRISPR/Cas9 gene editing efficiency, identifying four superior promoters that enhance editing outcomes.

Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown

The paper identifies cognate recombination directionality factors (RDFs) for large serine recombinases using AlphaFold2-multimer and experimental validation.