The specificity of exoCasMINI for gene editing.[Tag-seq]
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ABSTRACT:
PROVIDER: PRJNA1142873 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The specificity of hpCasMINI for gene editing.[Tag-seq]
| PRJNA1127530 | ENA
Project description:The exoCasMINI exhibits similar specificity for gene editing. Compared to SpCas9, exoCasMINI also exhibited higher specificity for genomic DNA cleavage at the tested sites.
2025-06-22 | GSE273697 | GEO
Project description:The hpCasMINI exhibits high specificity for gene editing. Compared to SpCas9 and LbCas12a, hpCasMINI also exhibited higher specificity for genomic DNA cleavage at the tested sites.
2024-06-29 | GSE270588 | GEO
Project description:As the ancestor of CRISPR-Cas12 nucleases, TnpB represents the most compact gene editing tool currently available. Recent studies have identified multiple TnpB systems with gene editing activity in mammalian cells, and the potential of TnpB in treating diseases has been demonstrated in animal models. However, the editing characteristics of various TnpB systems, comparable to CRISPR tools, require more extensive investigation. Using a standardized evaluation framework, we conducted a thorough analysis of the editing properties of four TnpB variants alongside representative Cas12 and Cas9 tools. Overall, TnpBs exhibit intermediate editing activity and safety profiles among all tested systems, with ISYmu1 TnpB demonstrating a good performance in both editing activity and specificity. Considering its compact size, potent editing efficiency and high specificity, ISYmu1 TnpB represents a promising candidate for in vivo gene therapy applications.
2025-01-01 | GSE264389 | GEO
Project description:Machine learning-based prediction of the activity and specificity of Cas9 variants in gene editing
2024-08-22 | GSE231840 | GEO
Project description:In this study, we set out to reprogram deaminase context specificity to pinpoint editing. We identified multiple nucleic acid-recognition hotspots in the E. coli tRNA-specific adenosine deaminase (TadA). Strategically sampling these recognition hotspots, we first accessed multipotency for C in TadA and subsequently eliminate its A-deamination activity. We further reprogrammed TadAC context specificity through 16 evolution campaigns, each aimed at a defined NCN context, and isolated hundreds of thousands of context-specific cytosine deaminases. Our panel of 16 NCN-specific deaminases covers the full spectrum of all possible minus1 and plus 1 contexts for a target C, offering on demand deaminase choices for editor customization. Our context-specific CBEs corrected 5,866 of 7,196 disease-associated T:A-to-C:G transitions documented by ClinVar with higher accuracy than existing CBEs, often achieving selective editing of a single cytosine out of multiple cytosines in the protospacer without compromising editing potency. We also showcased the application of context-specific base editing for modeling disease-associated C:G-to-T:A transitions using two cancer driver mutations, KRASG12D and TP53R248Q, each demanding selective editing of one cytosine in two consecutive cytosines (ACC and CCG). These context-specific editors, as expected, showed tightly controlled off-target profiles by rejecting most cytosines at potential off-target sites. Bystander-free, single-nucleobase editing, as enabled by reprogramming deaminase context specificity, complements our current editor portfolio and unlocks new potential in base editing.
2025-04-14 | GSE294219 | GEO
Project description:RNA-guided nucleases (RGNs) based on CRISPR systems permit installing short and large edits within eukaryotic genomes. However, precise genome editing is often hindered due to nuclease off- target activities and the multiple-copy character of the vast majority of chromosomal sequences. Dual nicking RGNs and high-specificity RGNs both exhibit low off-target activities. Here, we report that high-specificity Cas9 nucleases are convertible into nicking Cas9D10A variants whose precision is superior to that of the commonly used Cas9D10A nickase. Dual nicking RGNs based on a selected group of these Cas9D10A variants can yield gene knockouts and gene knock-ins at frequencies similar to or higher than those achieved by their conventional counterparts. Moreover, high-specificity dual nicking RGNs are capable of distinguishing highly similar sequences by “tiptoeing” over pre-existing single base-pair polymorphisms. Finally, high-specificity RNA-guided nicking complexes generally preserve genomic integrity, as demonstrated by unbiased genome-wide high-throughput sequencing assays. Thus, in addition to substantially enlarging the Cas9 nickase toolkit, we demonstrate the feasibility in expanding the range and precision of genome editing procedures. The herein introduced tools and multi-tier high-specificity genome editing strategies might be particularly beneficial whenever predictability and/or safety of genetic manipulations are paramount.
2020-12-08 | GSE153471 | GEO
Project description:We use RNA-seq to study the transcriptome wide specificity profiles of A-to-I RNA editing by split-ADAR2 constructs.
2022-01-19 | GSE158656 | GEO
Project description:Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing
| PRJNA1102325 | ENA
Project description:Ex-vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases by non-homologous end joining (NHEJ) gene disruption or homology-driven repair (HDR) gene correction. Gene editing encompasses delivery of nucleases by electroporation and, when aiming to HDR, of a DNA template often provided by viral vectors. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching similar editing efficiencies. Overall, LNPs may allow efficient and stealthier ex-vivo gene editing in hematopoietic cells for treatment of human diseases.
2024-01-26 | PXD037529 | Pride