Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1107439 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Base editors (BEs) shed new light on correcting disease-related T-to-C mutations. However, current rat APOBEC1-based BEs are less efficient in editing cytosines in highly-methylated regions or in GpC context. By screening a variety of APOBEC/AID deaminases, we showed that human APOBEC3A-conjugated BE and its engineered forms can mediate efficient C-to-T base editing in all examined contexts, including regions with high-methylation levels and GpC dinucleotides, which extends base editing scope.
2018-08-20 | GSE114999 | GEO
Project description:RNA-programmable deaminases, known as base editors (BEs), enable precise single base conversions on genomic DNA and hold great promise for therapeutic application in patients. Recent studies, however, have raised serious concern with regard to off-target effects, questioning translatability of BEs to the clinic. Here we analyze transcriptome- and genome-wide off-target effects following AAV-mediated delivery of cytosine base editors (CBEs) in vivo in an unbiased manner. We show that low expression of CBEs allows sufficient on-target editing to cure a disease phenotype with no increase in off-target effects compared to untreated controls. To further improve safety of in vivo base editing, we developed a lipid nanoparticle (LNP)-mediated delivery system to transiently express BEs. We reach up to 21% on-target editing with no detectable transcriptome- or genome-wide off-target effects, and are able to reverse the disease phenotype of a phenylketonuria mouse model. These results have important implications, underlining the feasibility of transient in vivo base editing for therapeutic use in patients.
2020-08-24 | GSE148349 | GEO
Project description:Genome-wide knockout or knockdown screens have become powerful tools for the investigation of genotype-to-phenotype relationships. In bacteria, these screens commonly rely on transcriptional repression by dCas9, gene knockouts through Cas9 editing or random transposon mutagenesis, but depending on the technique, suffer from incomplete gene silencing, low editing efficiencies or they require massive library sizes. Here, we take a distinct approach with base editing to introduce premature stop codons or mutate start codons in Escherichia coli using a ScCas9 nickase derived base editor (ScBE3) that exhibits flexible PAM recognition. We then derive guide design rules by applying machine learning to a gene essentiality screen conducted in E. coli. For further improvement, we combined base-editing with Cas9-induced cleavage of the unedited cell fraction. The efficiency of this dual system was validated through a screen of conditionally essential E. coli genes. This improved setup that decouples the gene editing from the screening leads to more efficient guide depletion and confirmed previously published conditionally essential genes. Overall, base editing represents a useful tool for genome-wide knockout screens in bacteria and will eventually enable genome-wide knockout screens in a broader range of bacterial species to study their diverse genetics.
2024-02-05 | GSE225335 | GEO