CRISPR and Genetic Engineering

tWhEEL: a transcript-aware workflow for quantifying CRISPR knockout feasibility using transcriptome assembly

tWhEEL quantifies CRISPR knockout feasibility by integrating transcriptome data with guide RNA design and functional annotations to prioritize tractable biological functions and organisms.

Prevention of Klebsiella pneumoniae antibiotic resistance plasmid dissemination by prophylactic or simultaneous CRISPR-Cas9 treatment.

This study demonstrates that mobile CRISPR-Cas9 tools can effectively prevent the dissemination of an AMR plasmid from K. pneumoniae to E. coli under various experimental conditions.

A portable C-terminal rheostat calibrates RecE/Redα exonuclease activity for enhanced bacterial recombineering

The paper identifies a highly active RecET recombinase pair for efficient homologous recombination in Streptomyces, enabling large DNA integration with minimal homology arms.

A synthetic genetic switch for tracking T-DNA delivery supports integration-free genome editing in plants

The paper develops T-SWITCH, a synthetic genetic switch that tracks T-DNA delivery and integration in plants, enabling integration-free genome editing.

Planetary-scale metagenomic search reveals new patterns of CRISPR targeting

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

Carboxymethyl Dextran Coated Iron Oxide Magnetic Nanoparticles as Vehicles for CRISPR Ribonucleoproteins

This paper develops CMD-coated magnetic nanoparticles for delivering CRISPR RNPs, demonstrating efficient genome editing in cell lines and a skin disorder model.

PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design

PrEditR is a tool for designing sgRNAs for CRISPR-based base editors, allowing users to target specific amino acids and annotate resulting mutations.

A dCas9 Proximity Reporter for Investigating DNA Linear and Rotational Dynamics

This paper develops a dCas9-based tool to measure DNA sequence proximity and orientation, finding that rotational alignment significantly affects dCas9 interactions.

Efficient recovery of transgene-free edited tobacco using the transgene self-elimination system via de novo regeneration

This study develops a transgene self-elimination system in tobacco using CRISPR/Cas9 and BARNASE cassettes to generate transgene-free edited progeny through de novo regeneration.

Csx15 is a broad specificity ring nuclease bridging CRISPR-Cas and CBASS cyclic nucleotide signaling systems

This study identifies Csx15 as a ring nuclease that degrades cyclic nucleotides from both CRISPR-Cas and CBASS systems, revealing its role in regulating signaling pathways.

Compact CRISPR-based genetic circuitry using a miniature genome-integrated Cas12m protein

A genome-integrated Cas12m in E. coli shows no measurable growth cost, reverses repression faster than dCas9, and supports NOT gates, a two-layer buffer and a two-pathway pigment circuit.

The effects of DNA repair factor-Cas9 fusions on homing gene drive performance

This study evaluates Cas9 fusion proteins in Drosophila to enhance homing gene drive performance by improving HDR and reducing resistance.

Scalable variant-to-function screens using prime editing perturb-seq

This paper introduces PEP-seq, a method linking genetic variants to transcriptomic states, and shows it can detect functional effects of eQTLs and nonsense-mediated decay.

Single-vector AAV delivery of En-ISPmu1 and donor DNA for in vivo targeted genome integration

The paper describes the development of En-ISPmu1, a modified TnpB nuclease, and demonstrates its ability to achieve targeted genome integration in mouse liver with a single AAV vector.

Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii

This paper develops a CRISPR-Cas9 system for Anaerocellum bescii, enabling gene deletions and vector maintenance through thermostable Cas9.

OddCAPS: a simple, low-cost, universal technique for detecting single nucleotide variants

OddCAPS improves dCAPS by using three primers in one PCR reaction to detect SNVs with more engineered base changes and flexibility in restriction enzyme selection.

In Silico Design and Evaluation of CRISPR Cytosine Base Editing Strategy for Potential Correction of the ASPA Variant Associated with Canavan Disease

The paper designs and computationally evaluates a CRISPR base editing strategy to correct the ASPA variant associated with Canavan disease, identifying a candidate sgRNA with favorable editing characteristics and genome-wide specificity.

U6 promoters in Ulva prolifera enable dual small-RNA/mRNA transcription and vector-based CRISPR-Cas9 genome editing

The paper identifies and characterizes U6 promoters in Ulva prolifera, showing their dual transcriptional activity and utility for CRISPR-Cas9 genome editing.

CRISPR-dPCR: A unified multiplex digital PCR framework for quantitative characterization of targeted knock-in

CRISPR-dPCR quantifies CRISPR knock-in by distinguishing integration from donor abundance and background, using multiplex digital PCR with orthogonal strategies.

Spatiotemporal proteomic profiling of genome editing-associated microenvironment

This study develops a Cas9-TurboID platform to map dynamic protein assemblies around genome editing sites and identifies factors that enhance editing efficiency in heterochromatic regions.

A heat-assisted ttLbCas12a workflow incorporating crRNA 3'-tailing enables efficient multiplex biallelic genome editing in hybrid poplar

Averaging in gene perturbation benchmarks hides perturbation-strength variation: Consequences for model evaluation

The paper evaluates how averaging perturbation responses in gene perturbation benchmarks affects the ability to assess perturbation-strength variation, finding that current models fail to reliably recover perturbation identity.

High-throughput Eukaryotic Screening of Putative Anti-CRISPR Proteins against SpyCas9 and SauCas9

The paper screens hundreds of anti-CRISPR homologs to inhibit SpyCas9 and SauCas9, revealing evolutionary patterns and discovering three novel Acr families.

Genome-scale base editing reveals the functional effects of variants in yeast

This study uses genome-scale CRISPR base editing in yeast to assess the functional effects of 308,461 variants, identifying 18,009 with significant growth impacts.

Sequencing-Free Protospacer-Adjacent Motif Discovery for Uncharacterized CRISPR-Cas9 Orthologs via Active Learning

This paper introduces an active learning method to discover PAMs for uncharacterized CRISPR-Cas9 orthologs without sequencing, reducing data requirements and validating it on known and novel Cas9 variants.

Locally deployed AI agents for CRISPR guide discovery from outbreak reports

The paper develops a CRISPR guide-discovery pipeline using locally deployed AI agents and evaluates it with large language models.

PETRO enables robust estimation of on-target perturbation effects in Perturb-seq

PETRO improves Perturb-seq analysis by reducing off-target bias and enabling robust target-level perturbation effect estimation.

Design of synthetic activators for programmable gene expression

This study designs synthetic activators for programmable gene expression by engineering coactivator-binding proteins and demonstrates their enhanced transcriptional activation capabilities.

CRISPRa-mediated activation of Tfeb in a fibril-induced alpha-synuclein aggregation model

The paper uses CRISPRa to activate Tfeb in a rat model of alpha-synuclein aggregation but finds limited protein expression and no additive effects with media treatments.

Multiplex programming of mappable, molecularly tagged genomic deletions

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.