CRISPR and Genetic Engineering

Perturbational fitness analysis of CRISPR screens uncovers information-theoretic relation between gene function and selection

This study uses information theory to analyze CRISPR screens and quantifies gene function through geometric measures of selection dynamics and environmental perturbations.

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

PtWAVE improves detection of large indels in genome editing by extending deconvolution range and enhancing accuracy and sensitivity.

SAM-AMP lyases in CRISPR defence and anti-defence

This study investigates the structure and function of a SAM-AMP lyase from Clostridium botulinum, showing its ability to substitute for a phosphodiesterase in providing anti-phage defence.

Genome-wide Chromosome-specific Aneuploidy Engineering and Phenotypic Characterization with CRISPR-Taiji

The paper introduces CRISPR-Taiji to engineer chromosome-specific aneuploidy and characterizes its transcriptomic effects, linking aneuploidy to ccRCC phenotypes.

Controlling False Discovery in CRISPR Screens

This paper introduces Chronos, a module for estimating false discovery rates in CRISPR screens, showing it outperforms existing methods like MAGeCK in controlling false positives.

Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing

This study identifies a trade-off between PAM recognition breadth and CRISPR-Cas9 editing efficiency, proposing a two-step target capture mechanism to improve genome editing.

Make-or-break prime editing for bacterial genome engineering

This paper develops mbPE, a prime editing system for Streptococcus pneumoniae that enables precise genome editing without donor DNA, achieving high selection efficiencies for point mutations, deletions, and insertions.

A CRISPR/SpCas9M-reporting system for efficient and rapid genome editing in Caulobacter crescentus

This paper develops a CRISPR/SpCas9M-reporting system for efficient genome editing in Caulobacter crescentus and related bacteria, achieving up to 80% editing efficiency with minimal off-target effects.

Programmatic design and editing of cis-regulatory elements

The paper introduces Ledidi, a computational method for designing cis-regulatory elements by optimizing continuous sequences guided by deep learning models, validated experimentally for controlling transcriptional outcomes.

Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis

This paper engineers a plant virus to deliver a compact CRISPR-Cas system for transgene-free germline editing in Arabidopsis.

Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences

This paper introduces a deep learning method to classify CRISPR-Cas systems using repeat sequences, improving classification accuracy for subtypes with limited data.

Empirical Simulation and In Silico Evaluation of an Ethically Governed, AI-Enhanced CRISPR Prime Editing Framework for TOR1A Mutation Correction in Dystonia

The paper develops an AI-enhanced CRISPR prime editing framework for correcting TOR1A mutations in dystonia, showing strong predictive performance and identifying key factors influencing editing efficiency.

Electrical charge-mediated transformation for efficient plant genome editing

This paper introduces an electric charge-mediated method for efficient plant genome editing in faba bean, achieving 50% mutation success rate in the PDS gene without DNA vectors.

Multimodal control of Cas13 activity through domain insertion at an allosteric hotspot

This paper develops OptoCas13d and ChemoCas13d variants of RfxCas13d that can be controlled by light or small molecules to modulate RNA cleavage with high spatial and temporal precision.

CRISPR-CISH: An in situ chromogenic DNA repeat detection system for research and life science education

The paper introduces CRISPR-CISH, a chromogenic in situ DNA detection method that uses CRISPR/dCas9 to generate target-specific signals visible under bright-field microscopes.

Development of a highly efficient base editing system for Lactobacilli to improve probiotics and dissect essential functions

The paper develops a base editing system for Lactobacilli to introduce precise point mutations without donor DNA, enabling functional studies and strain improvement.

Redefining paradigms in the archaeal virus-host arms race

The paper analyzes 7,747 archaeal genomes to reveal disparities in antiviral defense systems compared to bacteria, identifying archaeal-specific systems and evolutionary links to eukaryotic immunity.

CRISPR-Cas9 trans-cleavage is hindered by a closed R-loop, an elongated spacer, and an inactive HNH domain

The paper identifies structural factors affecting CRISPR-Cas9 trans-cleavage activity, including R-loop conformation, spacer length, and HNH domain activity.

ChromeCRISPR - A High Efficacy Hybrid Machine Learning Model for CRISPR/Cas On-Target Predictions

The paper develops a hybrid machine learning model, ChromeCRISPR, which outperforms existing models in predicting CRISPR/Cas9 on-target activity by combining CNN and RNN architectures.

Stronger population suppression by gene drive targeting doublesex from dominant female-sterile resistance alleles

This paper describes a gene drive targeting doublesex in Drosophila that generates dominant female-sterile resistance alleles, leading to stronger population suppression in computational models.

Super Recombinator (SuRe): An in vivo recombination system for scalable and efficient transgene assembly at a single genomic locus

SuRe enables efficient integration of multiple transgenes at a single genomic locus by using CRISPR/Cas9 and serine recombinases, allowing up to 4.2 Mbp recombinant products in Drosophila.

A novel method for detection of Cas9 gRNAs using a fluorophore-labeled DNA oligo

The paper introduces a method for detecting Cas9 gRNAs using fluorophore-labeled DNA oligos to improve gene editing design and targeting efficiency.

Reinforced CRISPR interference enables reliable multiplex gene repression in phylogenetically distant bacteria

This paper develops a CRISPRi platform for multiplex gene repression in diverse bacteria, demonstrating its effectiveness in multiple species.

Repair of leukemia-associated single nucleotide variants via interallelic gene conversion

This study demonstrates that CRISPR-mediated interallelic gene conversion can revert heterozygous SNVs in leukemia cells without exogenous templates, improving survival in xenograft models.

CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage

This study investigates how crRNA binding induces structural changes in Cas7-11, revealing its conformational dynamics and how these changes regulate its function.

Activation of SPARDA defense system by filament assembly reveals beta-relay signaling mechanism widespread in prokaryotic Argonautes

The paper reveals a beta-relay signaling mechanism in prokaryotic Argonautes that activates the SPARDA defense system to degrade invading DNA and host DNA, preventing plasmid spread.

Target-induced Argonaute-HNH filaments confer bacterial immunity

The paper shows that short prokaryotic Argonautes (pAgos) activate HNH nuclease effectors after RNA-guided DNA recognition, forming filaments that degrade DNA and confer bacterial immunity.

Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice

This study optimizes the Cre-Lox system for efficient genome modification in mice by analyzing factors like loxP distance, Cre-driver strain, and breeding age.

Targeted control of gene expression using CRISPR-associated endoribonucleases

This paper introduces DREDGE, a method using CRISPR-associated endoribonucleases to regulate gene expression by targeting direct repeats in the 3' untranslated region, achieving up to 90% downregulation in a reversible manner.

Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex

This study reveals the conformational dynamics of the Cas8 protein in the Cascade-TniQ complex, showing how it transitions between open and closed states to facilitate DNA binding and transposition.