CRISPR and Genetic Engineering

Comprehensive deletion scan of anti-CRISPR AcrIIA4 reveals essential and dispensable domains for Cas9 inhibition

The paper develops a high-throughput method to identify essential and dispensable domains in AcrIIA4 by generating and testing precise deletions, revealing that PAM binding inhibition is key while catalytic domain interaction is dispensable.

A sequential event-responsive fluorescent reporter for inducible Cre and Flp combinatorial recombination

The paper introduces Rubik, a fluorescent reporter that tracks Cre and Flp recombination sequences and enables optogenetic control through temporal recombination events.

Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models

The paper introduces CHOOSER, a foundation model-based framework for discovering CRISPR-Cas systems with self-processing pre-crRNA capability, identifying 11 novel homologs and validating one for functional use.

A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening

The paper benchmarks a high-efficiency prime editing platform for multiplexed dropout screening of genetic variants, identifying negative growth phenotypes for nonsense mutations and splice-disrupting synonymous mutations.

High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors

The paper uses high-throughput variant libraries and machine learning to identify design rules for improving retron gene editors in both yeast and human genome editing.

Towards optimizing diversifying base editors for high-throughput studies of single-nucleotide variants

The paper evaluates how base editor design features affect editing efficiency and mutation patterns in mammalian cells, identifying DivA-BE as the most effective variant.

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes

This paper introduces append editing, a method that uses ADP-ribosylation to achieve distinct genome editing outcomes in bacteria and eukaryotes.

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

The paper shows CRISPR-Cas12a bends DNA to destabilize base pairs during target recognition, similar to CRISPR-Cas9 but with different hybridization directionality.

Open-ended molecular recording of sequential cellular events into DNA

This paper introduces peCHYRON, a DNA recorder that sequentially records cellular events in mammalian cells using prime editing, enabling durable, high-information, and temporally resolved molecular recording.

Accurate prediction of CRISPR editing outcomes in somatic cell lines and zygote with few-shot learning

This paper introduces inDecay, a few-shot learning system for predicting CRISPR editing outcomes in cell lines and zygotes, achieving high accuracy with minimal data.

Establishment of CRISPR/Cas9-based knock-in in a hemimetabolous insect: targeted gene tagging in the cricket Gryllus bimaculatus

The paper establishes a CRISPR/Cas9 method for targeted gene knock-in in the cricket Gryllus bimaculatus, enabling functional genetic studies in a hemimetabolous insect.

Repeat mediated excision of gene drive elements for restoring wild-type populations

This paper demonstrates a gene drive mitigation strategy using Repeat Mediated Excision of a Drive Element (ReMEDE) to replace drive alleles with wild-type alleles in Drosophila melanogaster.

Ecological drivers of CRISPR immune systems

This study investigates how ecological factors like prokaryotic density and diversity influence the distribution of CRISPR-Cas immune systems in different environments.

Evolutionarily guided transcription factor design programs novel T cell states

This paper designs novel transcription factors using evolutionary principles to generate T cell states with enhanced functionality.

PreciCE: Precision engineering of cell fates via data-driven multi-gene control of transcriptional networks

The paper introduces a method to control cell fates by modulating multiple genes using CRISPR tools and machine learning, demonstrating its effectiveness in stem cell differentiation.

Development of compact transcriptional effectors using high-throughput measurements in diverse contexts

The paper develops HT-recruit to measure transcriptional effector function across contexts and identifies context-dependent effectors for CRISPR-based transcription control.

Low RT-based Genome Editing Fidelity in Mouse Hepatocytes: Challenges and Solutions

The paper identifies low fidelity in RT-based genome editing in non-dividing mouse hepatocytes and proposes solutions using neonatal mice and transgenic models.

Characterisation of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina

This study characterizes the transcriptomic effects of Cas13bt3 in retinal cells and demonstrates its efficacy in silencing VEGFA mRNA in human retinal organoids and mouse models.

Rational Design of Enhanced Nme2Cas9 and Nme2SmuCas9 Nucleases and Base Editors

The paper enhances Nme2Cas9 and Nme2SmuCas9 nucleases and base editors for improved efficiency and vector compatibility through mutagenesis and deaminase linker optimization.

Phage CRISPR-like regulatory RNAs silence multilayered bacterial immune systems

The paper identifies viral crlRNAs that suppress bacterial immunity by reprogramming Cas proteins and demonstrates their potential for mammalian genome editing.

Hijacking and recording intracellular RNAs in human cells using eukaryotic reprogrammed tracrRNAs

The paper introduces CHEETAH, a system using reprogrammed tracrRNAs to capture and record intracellular RNAs in human cells, demonstrating its ability to self-edit, selectively record viral RNA fragments, and enable multiplexed, time-resolved recording.

Combinatorial effector targeting (COMET) for transcriptional modulation and locus-specific biochemistry

The paper introduces COMET, a high-throughput screening platform for identifying transcriptional modulators by testing combinatorial dCas9-based fusion proteins, and finds over 5800 significant hits that modulate transcription.

Improving the suppressive power of homing gene drive by co-targeting a distant-site female fertility gene

This paper introduces a two-target gene drive design that improves suppression efficiency by combining homing and fitness cost elements, showing success in Drosophila but highlighting remaining challenges.

Crosstalk between three CRISPR-Cas types enables primed type VI-A adaptation in Listeria seeligeri

The paper shows that Listeria seeligeri's type VI-A CRISPR system uses a type II-C Cas1-2 integrase and priming from a type I-B system for DNA spacer acquisition.

Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors

The paper evaluates near-PAMless base editors and develops a predictive model to forecast editing outcomes, expanding the scope of gene editing.

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

The paper develops a deep mutational scanning pipeline for anti-CRISPR proteins in E. coli, revealing their mutational tolerance and redundancy, and validates findings in mammalian cells.

Bystander base editing interferes with visual function restoration in Leber congenital amaurosis

The paper shows that bystander base editing with ABE8e impairs visual function restoration in LCA model mice by causing structural and functional disruptions in RPE65.

CRISPR-GRIT: Guide-RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans

CRISPR-GRIT enables precise multiplexed genome editing in C. albicans by integrating repair templates into guide RNAs, overcoming the need for co-transformation.

Engineering Resilient Gene Drives Towards Sustainable Malaria Control: Predicting, Testing and Overcoming Target Site Resistance

The paper presents a pipeline to discover and engineer gene drives that overcome resistance in malaria mosquitoes, showing that new resistant alleles can emerge and designing drives that target multiple sites to suppress populations.

Engineered Bxb1 variants improve integrase activity and fidelity

The paper develops Bxb1 variants with improved integrase activity and fidelity, enhancing in vivo efficiency and reducing off-target effects.