CRISPR and Genetic Engineering

This study uses CRISPR/Cas9 to suppress lachrymatory factor synthase in onions, reducing tear-inducing activity but causing growth issues.

The paper analyzes SpCas9 on- and off-target effects in Arabidopsis using high-efficiency multiplex editing and finds high specificity but potential for extensive on-target modifications at complex loci.

The paper demonstrates a method to regulate the Wnt pathway in human pluripotent stem cells by linking a developmental promoter to CRISPR interference, showing reduced CTNNB1 expression and attenuated Wnt gene induction.

The paper evaluates the role of the histone H3 tail in KRAB-DNMT3L-dCas9-mediated gene silencing and finds it does not provide a general functional advantage.

PhAGE enables one-step integration of ~20 kb DNA fragments into E. coli genome, resolving the trade-off between simplicity and insert size in genome engineering.

This study identifies optimal buffer conditions for LbCas12a trans-cleavage activity, showing that while some buffers enhance catalytic efficiency, they also increase nonspecific cleavage, requiring careful optimization for detection performance.

Auto-SMART automates the design of CRISPR/Cas9 repair templates, enabling efficient genome editing by optimizing guide RNA selection and donor template construction.

This paper demonstrates CRISPR-INTEGRATE for targeted genome engineering in plant-pathogenic Pseudomonas, enabling gene disruption and prophage excision with phenotypic effects.

This study compares CRISPR-Cas systems for RNA knockdown in rat sensory neurons, finding hfCas13d provides robust gene silencing with minimal toxicity.

The paper identifies a TldR repressor in Enterococcus faecalis that directly represses OppA, revealing its role in regulating bacterial peptide import and uncovering a conserved structural mechanism inherited from TnpB ancestors.

This paper introduces twin-prime editing to visualize endogenous proteins and track mutant alleles at single-cell resolution in vivo.

This study develops a stochastic model to investigate how CRISPR-Cas systems balance short-term and long-term antiviral defense, revealing three evolutionary regimes and spontaneous division of labor within CRISPR arrays.

The paper identifies human gene modules enriched for genetic interactions using a combinatorial knockout platform and validates their conservation and rewiring across cancer cell lines.

This study evaluates combinatorial CRISPR/Cas12a for locus excision in mammalian cells and finds low efficiency despite targeting intronic regions.

This study shows that reprogrammed gRNAs with mismatches can shift editing outcomes to improve gene knockout efficiency without reducing overall editing efficiency.

The paper generates an iPSC collection with CNM mutations using base editing and evaluates off-target effects via whole genome sequencing.

The paper benchmarks variant effect predictors using MAVE data, identifies reliability ceilings, and shows that correction improves performance in some regions but not others.

The paper demonstrates that inactivating HSD17B11 confers resistance to PAC, enabling efficient CRISPR/Cas9-based gene inactivation through PAC selection.

SEME corrects aberrant splicing in iPSC-CMs by programmable microexon incorporation, restoring filamin C expression in a dilated cardiomyopathy model.

The paper uses automated mini-bioreactors to study the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida, identifying a critical time window for phenotypic impact.

The paper describes a dimeric TIR effector, TSR1, that binds cA3 and degrades it to auto-limit its activity in type III CRISPR-mediated antiviral immunity.

This study develops split suppression gene drives in Aedes aegypti, showing that inheritance efficiency and reproductive fitness costs must be balanced for effective population suppression.

This paper introduces Partita, a high-density CRISPRa platform for comprehensive gene activation studies, demonstrating its utility in identifying cancer dependencies and resistance pathways in vitro and in vivo.

The paper shows that the attachment site, not linker length, determines the activity window of tethered base editors by analyzing geometric models and experimental data.

This study uses electronic genome mapping to analyze how gRNA mismatches affect CRISPR/Cas9 binding specificity across the human genome, revealing key regions for on- and off-target activity.

The paper introduces universal donor plasmids for biallelic degron-tagging in mammalian cells and organoids using Cas9-induced double strand breaks and homology-independent repair.

The paper maps Cas9-induced sister chromatid exchange (SCE) across genomic targets using sci-L3-Strand-seq, showing local SCE enrichment and context-dependent recombination at repetitive loci.

This paper enhances Cas12a's trans-cleavage activity by fusing Sso7d, improving sensitivity and kinetics for nucleic-acid detection.

The paper introduces GEValT, a method for heritable CRISPR gene editing in arthropods via oral viral transduction, enabling efficient gene knock-out and knock-in.

This study demonstrates TIGR-Tas activity in the green alga Chlamydomonas reinhardtii, showing DNA cleavage and indel formation, but notes low efficiency.