CRISPR and Genetic Engineering

Automated plasmid design for marker-free genome editing in budding yeast

The paper introduces PIPOline, a computational tool for designing plasmids for marker-free genome editing in budding yeast, and demonstrates its application for gene tagging and deletion.

A comprehensive benchmark for multiple highly efficient base editors with broad targeting scope

The paper benchmarks multiple base editors and develops a model to predict editing efficiency, validating edits for disease-associated variants and identifying cancer-related SNVs.

KOnezumi-AID: A Software to Automate the Design of Multiplex Knockouts Using Target-AID

KOnezumi-AID automates gRNA design for Target-AID-mediated gene knockouts, enabling efficient and safe multiplex knockout strategies in mouse and human genomes.

High-accuracy crRNA array assembly strategy for multiplex CRISPR

This paper introduces a high-accuracy CRISPR array assembly strategy that enables efficient assembly of multiple crRNAs in a single reaction, improving the practicality of multiplex CRISPR applications.

Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells

This study shows that gene editing of HSCs without ex vivo culture reduces genotoxicity while maintaining therapeutic efficacy for beta-hemoglobinopathy treatment.

Mitochondrial adenine base editing of mouse somatic tissues via adeno-associated viral delivery

This study tests mitochondrial adenine base editing in mouse tissues via AAV delivery, finding low and modestly increasing editing efficiency over time.

Efficient in situ epitope tagging of rice genes by nuclease-mediated prime editing

This study develops and validates an efficient method for in situ epitope tagging of rice genes using prime editing, demonstrating its utility for gene function studies and genetic improvement.

Degron-modified Cas12a enhances single-cell CRISPR screening

This paper develops a degron-modified Cas12a system to enable accurate single-cell detection of pre-crRNAs, enhancing Perturb-seq capabilities for multiplex guide expression.

A scalable method for modulating plant gene expression using a multispecies genomic model and protoplast-based massively parallel reporter assay

The paper introduces a scalable method to upregulate plant gene expression using a genomic model and MPRA, identifying functional cis-regulatory elements without prior knowledge.

SspA is a transcriptional regulator of CRISPR adaptation in E. coli

This study identifies SspA as a transcriptional regulator of CRISPR adaptation in E. coli using a CRISPRi-based screen and proposes a model of independent cellular control of adaptation and interference by SspA.

Crackling Cloud: an event-driven, cloud-based CRISPR-Cas9 guide RNA design tool

Crackling Cloud is a cloud-based tool for designing CRISPR-Cas9 guide RNAs, offering scalability and accessibility without requiring local high-performance computing resources.

Cardiac Applications of CRISPR/AAV-Mediated Precise Genome Editing

This study applies CASAAV-HDR to model cardiomyopathies and perform functional genomics in mouse cardiomyocytes, showing its utility for disease modeling and enhancer analysis.

CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise.

The paper shows that CRISPR-based methods for studying miRNA binding sites in isogenic cell lines are unreliable due to high variability between replicates.

RecombiCraft Library construction: A novel method for DNA Library cloning and expansion using non-enzymatic single-step DNA recombination and liquid culture

This paper introduces RecombiCraft, a method for DNA library construction in E. coli using SLiCE and liquid culture, which minimizes sequence bias and reduces costs.

The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity

This study shows that the Cas10 nuclease activity in type III-A CRISPR-Cas systems relieves host dormancy to enable spacer acquisition and retention, enhancing broad-spectrum immunity.

Fluorescence-based CRISPR interference system for controlled genetic repression and live single-cell imaging in mycobacteria

The paper develops and validates fluorescence-based CRISPRi tools for gene repression and live single-cell imaging in mycobacteria.

Spacer acquisition in type VI CRISPR-Cas systems associated with reverse transcriptase-Cas1 fusion proteins

This study shows that type VI-B CRISPR-Cas systems with RT-Cas1 fusion proteins can acquire spacers from RNA, functioning independently of other systems.

CRISPR-Cas13d as a molecular tool to achieve targeted gene expression knockdown in chick embryos

This paper adapts the CRISPR-Cas13d system for targeted gene expression knockdown in chick embryos, demonstrating effective PAX7 knockdown comparable to morpholino.

A genome-scale single cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

The paper presents a genome-scale CRISPRi perturbation map in human pluripotent stem cells using single-cell RNA sequencing to study trans gene regulation across diverse genetic backgrounds.

SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping

SPLICER improves exon skipping by editing both splice acceptor and donor sites, reducing aberrant splicing and enabling therapeutic applications in Alzheimer's disease.

Engineered transcription-associated Cas9 targeting in eukaryotic cells

This paper introduces a method to temporally control Cas9 DNA targeting by coupling it with transcription through engineered RNA binding, enabling selective gene editing in yeast and human cells.

Engineered CRISPR-Base Editors as a Permanent Treatment for Familial Dysautonomia

This paper develops a CRISPR base editing strategy to correct the FD-causing mutation in human cells and mice, achieving up to 70% on-target correction and functional restoration.

A programmable, selection-free CRISPR interference system in Staphylococcus aureus

This paper develops a selection-free CRISPRi system in S. aureus that silences virulence genes without antibiotic selection or exogenous inducers, validated in vitro and in vivo.

Successful delivery of CRISPR-Cas9 with a baculovirus vector for insect brain targets

The paper successfully delivers CRISPR-Cas9 via a baculovirus vector to knock down AmOctβ2R in honey bee brain neurons, leading to appetite suppression.

The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations

The paper investigates how DNA repair genes influence Cas9-induced mutations by analyzing mutational outcomes across 2,838 synthetic targets in mouse cells, revealing gene-specific roles and improving predictive models.

Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens

The paper introduces Exorcise, a tool to reannotate CRISPR libraries to user-defined genomes, improving targeting accuracy and reducing bias in screens.

Enhanced in vivo gene knockout with undetectable off-targets using multiplexed Cas12a sgRNAs

The paper presents a Cas12a-based system using multiplexed sgRNAs to achieve efficient and specific gene knockouts in Drosophila with minimal off-target effects.

A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs

This paper develops a versatile platform for optogenetic and chemogenetic control of CRISPR-Cas9 and Cas12 across multiple orthologs using engineered anti-CRISPR proteins.

Barcoding Notch signaling in the developing brain

The paper introduces SABER-seq, a CRISPR-Cas-based method to record Notch signaling in zebrafish brains, and identifies cell types influenced by Notch signaling.

DNA-guided CRISPR/Cas12 for RNA targeting

This study introduces {Psi}DNA, a DNA-based guide for Cas12 enzymes that enables specific and efficient RNA targeting, achieving 100% accuracy in detecting HCV RNA.