CRISPR and Genetic Engineering

Genetically modified primary airway-epithelial cell culture models to study virus-host interactions of emerging respiratory viruses

This paper describes protocols for generating genetically modified airway epithelial cell cultures to study virus-host interactions of emerging respiratory viruses.

Self-extending DNA recording with stochastic and programmed writing

This paper introduces a method for self-extending DNA recording that combines stochastic and programmed writing, enabling the accumulation of cellular histories with joint cellular and tissue readout.

Splicing-guaranteed artificial introns enable efficient homology-directed repair at internal exons and streamlined cell engineering

This paper introduces ARI-HDR, a method for efficient internal-exon editing using splicing-guaranteed artificial introns, achieving over 80% editing efficiency in human genes.

Aminoacylated tRNA tails trigger auxiliary bacterial immunity

The paper shows that cleaved aminoacylated tRNA tails trigger auxiliary bacterial immunity by activating Adt1, leading to mRNA cleavage and cellular dormancy.

Base Editing as a Therapeutic Strategy for Autosomal Dominant Tubulointerstitial Kidney Disease caused by Pathogenic UMOD Variants

This paper evaluates base editing strategies for treating ADTKD-UMOD by correcting pathogenic UMOD variants and inactivating mutant alleles, showing efficient correction and expression modulation in cell models.

A cold-adapted Cas9 nuclease from the deep ocean

This paper characterizes DO1Cas9, a cold-adapted Cas9 nuclease from the deep ocean, showing improved activity under cold conditions and broader organismal applicability.

Targeted RNA degradation of HIV-1 TAR element at 5'UTR by CRISPR-Cas13X blocks HIV-1 lytic reactivation

This study uses CRISPR-Cas13X to target HIV-1 TAR RNA, inhibiting viral reactivation and reducing viral load in infected cells.

Using Polycistronic gRNAs and a tRNA Cleavage System in CRISPR-Based Genome Editing of Toxoplasma gondii

This paper improves CRISPR-based genome editing in Toxoplasma gondii by optimizing gRNA expression and introducing a tRNA-based polycistronic system for multiplexed editing.

Experimental Methods for CRISPR Enzyme Assays with Fluorescence Readout

The paper presents a standardized experimental protocol and analysis framework for fluorescence-based CRISPR enzyme assays to improve reproducibility and consistency in kinetic measurements.

High temperature ligation enables in vitro assembly of eukaryotic genes

This paper introduces High Temperature (HighT) assembly, a DNA assembly method that improves accuracy and yield by ligating DNA at higher temperatures, and demonstrates its application in constructing synthetic genes and genomic regions.

One-Entry Golden Seamless Cloning with a Reusable Donor Streamlines Plant Gene Functional Analysis

The paper introduces a cloning system that simplifies gene cloning and distribution across vectors with reduced background and increased efficiency.

Probabilistic Modelling of Base Editing Efficiency and Bystander Outcome Composition

The paper introduces crispAIBE, a probabilistic framework for predicting base editing efficiency and bystander allele composition, achieving high correlation and coverage on benchmark datasets.

CRISCross: Integration of Epigenetic Information for Deep-Learning-Based Prediction of CRISPR-Cas9 Off-Targets Across Cell Types

CRISCross improves CRISPR-Cas9 off-target prediction by integrating epigenetic features with sequence data across cell types, showing better performance than sequence-only models.

Cytos MPS: an automated multimodal pooled screening platform for protein, morphology and transcriptomics

Cytos MPS integrates CRISPR guide identity, morphology, transcriptomics, and protein data to reveal multimodal phenotypes from perturbations.

tRNA-derived second messengers confer bacterial immunity

The paper identifies a bacterial immune pathway where tRNA cleavage generates second messengers that trigger cell death via RNA-guided nuclease activity.

A quick and efficient method enabling lncRNA functional studies in the marine diatom Phaeodactylum tricornutum using a multiplexed CRISPR-Cas9 editing approach

This paper develops a CRISPR-Cas9 method to generate lncRNA knockouts in the diatom Phaeodactylum tricornutum, demonstrating its utility in studying lncRNA function under phosphate stress.

A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

High-throughput in vivo DNA data encoding by multiplexed conjugationand orthogonal base editing

The paper introduces a system for high-throughput in vivo DNA data encoding using bacterial conjugation and base editing, successfully encoding and retrieving binary data with high accuracy.

An integration-free CRISPR platform for genetic dissection of respiratory virus host dependencies in human nasal epithelium

The paper develops an integration-free CRISPR platform to study host dependencies of respiratory viruses in human nasal epithelium, showing ACE2 and TMPRSS2 are critical for SARS-CoV-2 and hCoV-NL63 infection.

Asymmetric DNA targeting by RNA-guided TIGR-Tas systems

This study investigates how TIGR-Tas systems recognize and cleave DNA targets, revealing asymmetric target engagement and coordinated cleavage across both RNA-DNA heteroduplexes.

High-efficiency targeted integration of extrachromosomal arrays in C. elegans using PhiC31 integrase

The paper introduces PhIAT, a method using PhiC31 integrase to efficiently integrate extrachromosomal arrays into C. elegans chromosomes, enabling stable genomic modifications.

Acquisition of novel arrays via horizontal gene transfer rewire CRISPR-mediated defense in Pseudomonas aeruginosa

This study identifies an isolated CRISPR array in Pseudomonas aeruginosa that is horizontally transferred and contributes to CRISPR-mediated immunity through recombination with mobile genetic elements.

Overexpressing FLP Recombinase Can Cause Synaptic Trafficking Defects in C. elegans

This study shows that high expression of FLP recombinase in C. elegans causes synaptic trafficking defects, highlighting potential cytotoxicity of tyrosine recombinases at high doses.

Engineered mRNA-packaging virus-like particles enable efficient and precise mitochondrial base editing in vitro and in vivo

This study develops mtBE-VLPs for transient mitochondrial base editing, achieving high efficiency and reduced off-target effects in vitro and in vivo.

Programming primary human T cells to deliver gene editing machinery

This study engineers primary human T cells to deliver gene editing machinery using retroviral-based delivery vehicles, demonstrating efficient editing of diverse target cells.

Transposon end recognition and pairing by I-F3 CRISPR-associated transposase

This study determines how the I-F3 CRISPR-associated transposase recognizes and pairs transposon ends for transposition using cryo-EM and biochemical analyses.

Systematic mapping of chimera-permissive sites by CRISPR-guided PAM scanning

This paper uses CRISPR-guided PAM scanning to identify chimera-permissive sites in proteins, enabling the design of functional chimeras with preserved activity.

Structural basis of directionality control in large serine integrases

The paper reports structural insights into how large serine integrases control directionality during DNA integration and excision using recombination directionality factors.

AGROtools: A comprehensive modular cloning toolset for Agrobacterium strain engineering

AGROtools simplifies Agrobacterium strain engineering by providing a modular cloning toolkit that enables efficient genetic modifications and marker removal.

Protocol for Non-viral HDR-based CRISPR/Cas9 platform for small custom editing in primary T cells

This paper presents a non-viral HDR-based CRISPR/Cas9 protocol for editing primary T cells with up to 80% HDR efficiency, targeting small pathogenic variants in patient and healthy donor cells.