CRISPR and Genetic Engineering

Genome-wide CRISPR knockout screen reveals the landscape of essential genes across the porcine genome

The paper identifies essential genes in porcine cell lines using CRISPR screening and compares them to human essential genes.

CasGen: A Regularized Generative Model for CRISPR Cas Protein Design with Classification and Margin-Based Optimization

CasGen generates novel Cas9 and Cas12 proteins using a transformer-based model with margin-based regularization, achieving structural similarity and functional integrity.

Machine-Guided Dual-Objective Protein Engineering for Deimmunization and Therapeutic Functions

The paper presents a workflow using machine learning to optimize protein function and reduce immunogenicity in cell and gene therapies.

Gearing up Golden Braid assembly for plant synthetic genomics with RepTiles

The paper introduces RepTiles, a system for generating random DNA segments for synthetic genomics, enabling the construction of ultra-long synthetic DNA in Physcomitrium patens.

Enzymatic Assembly for CRISPR Split-Cas9 System: The Emergence of a Sortase-based Split-Cas9 Technology

This study introduces a Sortase-based split-Cas9 system for precise genome editing, demonstrating its feasibility in E. coli and human cells with reduced off-target effects.

Single component CRISPR-mediated base-editors for Agrobacterium and their use to develop an improved suite of strains

The paper develops CRISPR-mediated base-editors to create disarmed Agrobacterium strains with auxotrophy and recombination deficiency for improved plant transformation.

Cytosolic CRISPR RNA for RNA-targeting CRISPR-Cas systems

This study shows that U1-driven CRISPR RNAs enhance the efficiency of RNA-targeting CRISPR-Cas13 systems for knockdown and editing without modifying Cas13 proteins.

A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency

The paper benchmarks CRISPR sgRNA design algorithms and creates smaller, efficient libraries for loss-of-function screens.

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

GuideScan2 constructs high-specificity CRISPR gRNA databases and enables design of allele-specific gRNAs, reducing off-target effects in gene essentiality screens.

Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system

The paper identifies Cas11b as an internally translated protein in an archaeal CRISPR-Cas system, showing its necessity for effective interference and Cascade complex formation.

Computational modeling of human genetic variants in mice

H2M is a computational pipeline that models human genetic variants in mice by predicting equivalent mutations and creating a database of mutation pairs for functional studies.

Multiplexed in vivo base editing identifies functional gene-variant-context interactions

The paper uses in vivo base editing to systematically analyze the functional impact of genetic variants in cancer models, revealing context-dependent effects and limitations of CRISPR-Cas9.

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

The paper demonstrates that RNA-guided nuclease TnpB enables gene drive in plasmids by biasing the inheritance of insertion sequences.

Circularization of Single-Stranded DNA Donor Template Unleashes the Power of Non-Viral Gene Delivery for Long-Term HSCs editing

This study develops a non-viral gene editing method using circular single-stranded DNA templates and TALEN, showing improved engraftment and long-term gene editing in HSPCs compared to AAV.

Characterization the gene editing with miniature nucleases TnpB, IscB and enIscB in Escherichia coli strains

This study characterizes the genome-editing capabilities of TnpB, IscB, and enIscB in E. coli strains, revealing their activity in specific strains and mechanisms of bacterial escape.

A family of Tn7-like transposons evolved to target CRISPR repeats

The paper identifies a novel group of Tn7-like transposons in Cyanobacteria that target CRISPR arrays, revealing a new interaction between transposons and CRISPR-Cas systems.

Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models

The paper develops PiCTURE and machine learning models to predict RNA off-target effects of CRISPR base editors in tissue-specific transcriptomes, finding higher risks in colon and lungs compared to brain and ovaries.

AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack

This paper shows AcrVIB1 inhibits CRISPR-Cas13b by promoting unproductive crRNA binding and degradation, revealing a mechanism to suppress immune defense.

CRISPR/Cas9-mediated elimination of the LMNA c.745C>G pathogenic mutation enhances survival and cardiac function in LMNA-associated congenital muscular dystrophy

This study uses CRISPR/Cas9 to target a specific mutation in LMNA-associated congenital muscular dystrophy, improving survival and cardiac function in mice.

Enhancing gRNA Transcript levels by Reducing the Scaffold Poly-T Tract for Optimal SpCas9- and SaCas9-mediated Gene Editing

This study shows that shortening the 4T poly-T tract in gRNA scaffolds improves transcript levels and editing efficiency, especially under low vector conditions, for both SpCas9 and SaCas9.

In vivo expansion of gene-targeted hepatocytes through transient inhibition of an essential gene

This paper introduces a method to increase the proportion of correctly repaired hepatocytes in the liver through transient gene inhibition and transgene delivery, achieving a 25% increase in targeted cells and five-fold transgene expression.

A molecular proximity sensor based on an engineered, dual-component guide RNA

This paper introduces P3 editing, a method that links protein-protein proximity to CRISPR-Cas9 dual-component guide RNA formation, enabling genome editing triggered by molecular interactions in human cells.

Low copy CRISPR-Cas13d mitigates collateral RNA cleavage

The paper evaluates collateral RNA cleavage in CRISPR-Cas13d systems and finds that low-copy expression reduces off-target effects while maintaining on-target knockdown.

Rapid enzymatic assay for antiretroviral drug monitoring using CRISPR-Cas12a enabled readout

The paper develops a rapid CRISPR-Cas12a-based assay to measure HIV drug levels, showing it can detect clinically relevant concentrations in complex samples.

Simultaneous single-cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships

The paper introduces CAT-ATAC, a method combining CRISPR, RNA, and ATAC-seq in single cells to identify gene regulatory relationships and validate them with loss-of-function experiments.

Mutational scanning of TnpB reveals latent activity for genome editing

This study identifies activating mutations in TnpB enzymes that enhance genome editing activity across multiple species.

DNA-Dependent Protein Kinase Inhibitors PI-103 and Samotolisib Augment CRISPR/Cas9 Knockin Efficiency in Human T Cells

This study shows that PI-103 and samotolisib enhance CRISPR/Cas9-mediated TCR knockin efficiency in human T cells without affecting viability or phenotype.

Flexibility in PAM Recognition Expands DNA Targeting in xCas9

This study investigates how xCas9 expands DNA targeting by recognizing alternative PAM sequences through increased flexibility in its PAM-interacting region.

Systematic silencing of oncogenic fusion transcripts with ultra-precise CRISPR-Cas13b

This paper introduces CRISPR-PspCas13b as a method to systematically silence oncogenic fusion transcripts, showing effectiveness against drug-resistant cancer drivers.

Frequent, context-dependent effects of human genetic variation on Cas9 activity revealed by population-scale GUIDE-seq-2 and deep combinatorial CHANCE-seq profiling

The paper uses population-scale GUIDE-seq-2 and CHANCE-seq to analyze how genetic variants affect Cas9 activity, finding frequent context-dependent effects on off-target sites.