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CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]

ABSTRACT: CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]

PROVIDER: PRJNA437656 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR6822180_1.fastq.gz	Fastqsanger.gz
	SRR6822180_2.fastq.gz	Fastqsanger.gz
	SRR6822181_1.fastq.gz	Fastqsanger.gz
	SRR6822181_2.fastq.gz	Fastqsanger.gz
	SRR6822182_1.fastq.gz	Fastqsanger.gz

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CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors

Project description:CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors

| PRJNA437650 | ENA

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]

Project description:CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased precision, such as cytidine deaminase single-base editors, are preferred. We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.

2018-07-06 | GSE111644 | GEO

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]

2018-07-06 | GSE111645 | GEO

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]

2018-07-06 | GSE111643 | GEO

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]

Project description:CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]

| PRJNA437654 | ENA

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]

Project description:CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]

| PRJNA437655 | ENA

CRISPR-SKIP: programmable gene splicing with single base editors.

Project description:CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for off-target mutations, technologies capable of introducing targeted changes with increased precision, such as single-base editors, are preferred. We present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.

| S-EPMC6092781 | biostudies-literature

Incorporating programmable DNA-binding domains enhances the efficiency and flexibility of miniature CRISPR base editors

Project description:The therapeutic application of base editors is currently limited by their large sizes, which are often beyond the packaging capabilities of adeno-associated viral (AAV) vectors. Despite recent progress in mega genome mining that has identified a diverse array of compact CRISPR proteins (e.g. Cas12f, TnpB, and IscB), the resulting miniature base editors are often exhibited reduced activities and a limited targeting scope, leaving a broad spectrum of disease-relevant genetic variants inaccessible. In this study, we have developed a platform, designated as Zinc Finger Proteins (ZFP)-enhanced miniature base editor (zmBE), which integrates programmable DNA-binding domains to enhance the efficiency and expand targeting scope of miniature base editors, including those based on Un1Cas12f1 and OgeuIscB. Utilizing protein language model (PLM) for the design of ZFPs further simplified development and optimization of zmBEs tailored to a specific target. Leveraging these methodologies, we engineered a zmBE that effectively induced the SMN2 exon 7 A6>G conversion and restored SMN2 exon 7 inclusion. Our study thus provides a versatile platform for developing miniature base editors for in vivo therapeutic applications.

2025-04-18 | GSE294498 | GEO

CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-07-06 | GSE111646 | GEO

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [Modifications - validation]

Project description:Base Editing has been touted the most intelligent and precise application of the CRISPR platform so far, merging the simplicity of RNA-guided nucleases with deaminases that allow for the programmable generation of single base substitutions - without introduction of double-strand breaks. Even though the two-component system has been expected to cause off-target substitutions, studies involving cytosine base editors (CBEs) showed that in most cases, relatively few single base off-targets could be detected on DNA. We introduce the concept of multi-dimensional off-targeting, presenting an extensive amount of RNA cytidines being edited by DNA base editors. Epitranscriptomic off-target effects affected different cell lines and were independent of the guide RNAs used, suggesting Cas9-independent activity of the cytidine deaminase rAPOBEC1 on single-stranded RNA. With the help of protein engineering, we developed CBE variants with massively reduced inadvertent mutation of RNA that preserve and enhance DNA base editing capabilities.

2019-03-31 | GSE121667 | GEO

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