CRISPR and Genetic Engineering

The paper compares different dCas9-VP64 constructs for CRISPR activation and identifies superior variants that enhance gene activation efficiency.

The paper was withdrawn due to duplicate submission and is not intended for citation.

This study shows that Cas9 expression levels significantly affect the efficiency and speed of large-scale pooled CRISPR screens, with higher Cas9 expression improving performance.

This paper introduces CRISPR-VAE, a framework that explains gRNA efficiency predictions and generates efficient gRNA sequences for CRISPR-Cas12a.

This study compares methods for knocking-in large DNA fragments using CRISPR, finding that HDR with CRISPR is the most reliable and effective approach.

This study shows that combining CbAgo with RecBexo-C enables efficient in vitro cleavage of double-stranded DNA at specific sequences, generating custom single-stranded overhangs for DNA ligation.

The paper develops a system for gene editing in bacteria using SpCas9/sgRNA ribonucleoprotein complexes and demonstrates its application via homologous recombination.

This study uses CRISPR-Cas9 to induce systematic chromosome rearrangements in human cells, resulting in genome and transcriptome changes similar to those in tumors.

The paper characterizes MbpAgo, a pAgo from Mucilaginibacter paludis that preferentially cleaves RNA over DNA, and demonstrates its temperature tolerance and guide flexibility.

This paper demonstrates a tethered gene drive system in Drosophila that confines homing drives to target populations, enabling controlled modification or suppression.

This study introduces SITE-Seq, a method to detect off-target sites in genome-edited rice, and shows it identifies mutations not found by in silico tools.

This paper introduces a Donorguide technology that improves HDR efficiency and precision by fusing an ssDNA template to tracrRNA, showing enhanced results in vitro and in vivo.

The paper develops a system to modulate R-loops at specific loci using a chimaera protein and applies it to study R-loop functions in cis and trans.

The paper shows bacterial CRISPR-Cas systems increase at ~45°C due to reduced grazing risk and increased viral lysis pressure.

This paper corrects a pathogenic mutation in iPSCs from a Christianson syndrome patient using CRISPR/Cas9, resulting in functional NHE6 protein expression.

The paper maps CRISPR spacers and identifies PAM sequences, revealing strand targeting preferences and shared CRISPR components across systems.

The paper introduces a paired-guide RNA CRISPR-Cas9 system to identify protein-coding and lncRNA genes involved in human B-cell to macrophage transdifferentiation, identifying 26 potential novel genes.

The paper introduces TIARS, a method to detect precise CRISPR/Cas9 edits using restriction-fragment length polymorphisms, and validates it in zebrafish for atp7a gene mutations.

The paper introduces a method to profile off-target specificity of CRISPR enzymes using ssDNA mapping, applicable to both catalytically dead and active Cas9 variants.

ONE-seq identifies population-specific off-target effects of CRISPR gene editors using global human genome sequence diversity.

The paper describes a reporter system to quantify durable CRISPR-based gene silencing and reports a single CRISPR protein capable of producing long-lasting gene repression.

This study demonstrates that long-term tissue-specific Cas9 expression in mice does not cause detrimental health effects or metabolic changes, supporting its use for gene-specific studies.

The paper demonstrates a CRISPRa/i toolbox for manipulating the Cacna1h gene promoter to study CaV3.2 channelopathies in neuronal cells and tissues.

This study identifies and characterizes prokaryotic Argonautes (pAgos) as programmable endonucleases, showing their ability to cleave DNA in vitro with guide RNA/DNA and potential for gene editing.

The paper evaluates two AID systems for chromatin protein degradation in mammalian cells, finding that AtAFB2 is more efficient and robust than OsTIR1 with proper puromycin selection.

BEdeepon predicts base editor efficiencies and outcome sequences using deep learning models trained on high-throughput screening data.

BEdeepoff predicts off-target editing efficiencies for ABE and CBE base editors using deep learning models trained on high-throughput screening data.

This paper describes the generation of two transgenic mouse lines for in vivo epigenome editing using CRISPR-based systems to activate or repress gene expression.

Chronos infers gene knockout fitness effects by explicitly modelling cell proliferation dynamics after knockout, using longitudinal readouts and correcting several known screen biases.

This study uses CRISPR-Cas9 to target MCPyV T antigen in Merkel cell carcinoma, showing reduced T antigen expression in cell lines.