CRISPR and Genetic Engineering

Mutational scanning by multiplexed genome editing of the essential transcription termination factor Nrd1.

The paper develops a CRISPR-based platform to scan mutations in essential genes, applying it to Nrd1 to identify critical residues in its CTD-interacting domain.

Development of a Toolkit for High-Efficiency, Markerless, and Iterative Genome Editing in Shouchella clausii

The paper develops a genetic toolkit for markerless genome editing in Shouchella clausii, demonstrating its effectiveness in multiple genome modification applications.

Optimized CRISPR/Cas9 Electroporation and Single Cell Cloning Protocol for Generating Pure Cellular Models in Human Immortalized Myoblasts

The paper develops a CRISPR/Cas9 electroporation and single-cell cloning protocol for human myoblasts, achieving high editing success rates and purity.

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads

This study uses long-read sequencing to analyze CRISPR-Cas9 editing outcomes and mosaicism in zebrafish, revealing genetic mosaicism in founder fish and its inheritance to offspring.

Guide RNA library representation results in gene essentiality prediction bias in genome-wide CRISPR screens

This study shows that gRNA library representation bias affects gene essentiality predictions in CRISPR screens, with library choice being the most significant factor.

CRISPR/Cas13-mediated Dynamin 2 reduction therapy in a canine model of DNM2-related centronuclear myopathy

This study demonstrates that CRISPR/Cas13-mediated reduction of DNM2 expression can alleviate CNM symptoms in a canine model.

MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA

MitoScribe records graded molecular signals into mitochondrial DNA, enabling high-resolution tracking of cellular states during differentiation.

Diversity and abundance of ring nucleases in type III CRISPR-Cas loci

The paper analyzes type III CRISPR-Cas loci across 38,742 prokaryotic genomes to identify and characterize ring nucleases that regulate cyclic oligoadenylate levels.

Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent

The paper tests a synthetic CRISPR-Cas system in Pseudomonas aeruginosa against 13 phages and finds nutrient-dependent protection efficacy.

An RNA-mediated DNA melting mechanism for CRISPR-Cas9

This study identifies an RNA-mediated DNA melting mechanism in CRISPR-Cas9 using simulations and experiments, showing RNA bases intercalate to promote strand separation.

Transient ATM inhibition enhances knock-in efficiency in hematopoietic stem cells by attenuating the DNA damage response

This study shows that transient ATM inhibition improves knock-in efficiency in mouse hematopoietic stem cells by reducing DNA damage response and apoptosis.

High-fidelity CRISPR genome editing of single-nucleotide mutation with near-complementary guide RNA via enhanced target binding kinetics

This paper introduces a CRISPR-Cas9 editing strategy using near-complementary sgRNAs to specifically target single-nucleotide mutations without relying on PAM sequences, demonstrating its effectiveness on a cancer-related mutation.

High-throughput Experimental Validation of Synonymous Mutation Neutrality in the Human Genome

The paper validates that synonymous mutations in the human genome rarely affect fitness, occurring 165-fold less frequently than non-synonymous mutations.

PyVADesign: a Python-based cloning tool for one-step generation of large mutant libraries

PyVADesign is a Python tool that streamlines the design and ordering of dsDNA fragments for generating large mutant libraries, with automated primer design.

A Compact Base Editor Rescues AATD-associated Liver and Lung Disease in Mouse Models

This paper demonstrates that a compact ABE corrects the PiZ mutation in AATD mouse models, reducing liver disease and improving lung function.

De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems

This paper engineers de novo RNA-guided transposition systems using TnpB-family proteins, showing improved specificity and efficiency compared to naturally evolved systems.

CRISPR-Cas9 target-strand nicking provides phage resistance by inhibiting replication

This study shows that Cas9 nicking of the target DNA strand can provide sufficient phage resistance, while non-target nicking does not enhance protection beyond Cas9 binding.

Restricted edition of ALS is required during co-edition in order to maintain normal tomato development

The paper evaluates the effects of co-editing ALS with a reporter gene in tomato, showing that the desired mutation has minimal impact on plant growth but additional mutations cause reduced vigor and altered metabolites.

An integrated enzymatic and computational pipeline for quantifying off-target base-editing

The paper introduces a combined enzymatic and computational pipeline to identify off-target base-editing sites in human cells on a genome-wide scale.

Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins

This paper introduces RENDER, a method for transient delivery of CRISPR-based epigenome editors as ribonucleoproteins to modulate gene expression in human cells, achieving durable epigenetic silencing.

CHARACTERIZATION OF RECOMBINASE ACTIVITY ACROSS CELLULAR GROWTH PHASES

This study examines how the serine recombinase Bxb1 functions in different growth phases of E. coli, showing that recombination efficiency peaks in exponential phase but persists in stationary phase.

Insulated piggyBac and FRT vectors for engineering transgenic homozygous and heterozygous eHAP cells

The paper develops insulated vectors for transgene expression in eHAP cells, enabling efficient transfection and expression, and demonstrates their use in generating transgenic heterozygous diploid cells.

Structure-guided engineering of type I-F CASTs for targeted gene insertion in human cells

This paper engineers type I-F CAST systems for targeted gene insertion in human cells by combining structural insights with rational design to improve efficiency and PAM flexibility.

Robust fluorescent labeling and tracking of endogenous non-repetitive genomic loci

This paper develops a method to fluorescently label and track non-repetitive genomic loci in live human cells, showing gene-specific chromatin dynamics independent of transcription.

Optimized R2 Retroelement Complexes Enable Precise and Efficient DNA Insertion into Plant Genomes

This paper develops an optimized R2 retroelement system for precise DNA insertion into plant genomes, achieving up to 24% efficiency for 2-5 kb payloads.

EASY-CRISPR: a toolbox for high-throughput single-step custom genetic editing in bacteria

EASY-CRISPR enables high-throughput, single-step genetic editing in E. coli using optimized guide RNAs and repair templates to construct genetic tools and mutant libraries.

A genome-scale CRISPR deletion screen in Chinese Hamster Ovary cells reveals essential regions of the coding and non-coding genome

This study uses a genome-scale CRISPR deletion screen in CHO cells to identify essential genomic regions, revealing 427 previously unannotated or poorly characterized regions critical for cell survival.

Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli

The paper identifies cellular factors influencing DGR activity in E. coli through reconstitution and screens, revealing mutagenic contexts and orientation preferences that enhance editing efficiency.

Integrating multiplexing into confineable gene drives effectively overrides resistance in Anopheles stephensi

The paper assesses two multiplexing strategies for CRISPR/Cas9-based gene drives in Anopheles stephensi to overcome target site resistance.

Editing of ADA2 Point Mutation in Human Hematopoietic Stem Cells

This paper edits the ADA2 p.R169Q mutation in human hematopoietic stem cells using CRISPR-Cas9 and HDR, showing improved efficiency with NHEJ inhibitors but increased chromosomal deletions.