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

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

PROVIDER: PRJNA437655 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR6822152_1.fastq.gz	Fastqsanger.gz
	SRR6822152_2.fastq.gz	Fastqsanger.gz
	SRR6822153_1.fastq.gz	Fastqsanger.gz
	SRR6822153_2.fastq.gz	Fastqsanger.gz
	SRR6822154_1.fastq.gz	Fastqsanger.gz

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

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 | GSE111645 | GEO

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]

2018-07-06 | GSE111644 | 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 [RNA-seq]

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

| PRJNA437656 | 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

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

Targeted exon skipping with AAV-mediated split adenine base editors.

Project description:Techniques for exclusion of exons from mature transcripts have been applied as gene therapies for treating many different diseases. Since exon skipping has been traditionally accomplished using technologies that have a transient effect, it is particularly important to develop new techniques that enable permanent exon skipping. We have recently demonstrated that this can be accomplished using cytidine base editors for permanently disabling the splice acceptor of target exons. We now demonstrate the application of adenine-deaminase base editors to disrupt the conserved adenosine within splice acceptor sites for programmable exon skipping. We also demonstrate that by altering the amino acid sequence of the linker between the adenosine deaminase domain and the Cas9 nickase or by coupling the adenine base editor with a uracil glycosylase inhibitor, the DNA editing efficiency and exon skipping rates improve significantly. Finally, we developed a split base editor architecture compatible with adeno-associated viral packaging. Collectively, these results represent significant progress towards permanent in vivo exon skipping through base editing and, ultimately, a new modality of gene therapy for the treatment of genetic diseases.

2019-09-12 | GSE120125 | GEO

Protein language models-assisted optimization of a Uracil-N glycosylase variant enables programmable T-to-S base editing

Project description:Current base editors use DNA deaminases, including cytidine deaminase in cytidine base editor (CBE) or adenine deaminase in adenine base editor (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for base editors capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel base editors, but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.

2024-01-23 | GSE253655 | GEO

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