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ABSTRACT: NGS of RHO base editor

PROVIDER: PRJNA990454 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25169016_1.fastq.gz	Fastqsanger.gz
	SRR25169016_2.fastq.gz	Fastqsanger.gz
	SRR25169017_1.fastq.gz	Fastqsanger.gz
	SRR25169017_2.fastq.gz	Fastqsanger.gz

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Project description:NGS of gene using adenine base editor systems in rice calli

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Mitochondrial DNA base editing in vivo via viral DdCBE delivery to somatic cells

Project description:We show that delivering the mitochondrial base editor DdCBEs via AAV transduction of somatic cells efficiently produces precise base editing of the intended region.

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Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor

Project description:Even the latest generation of base editor (BE3) causes unwanted indels and non-C-to-T substitutions, compromising the fidelity of base editing outcome. Here we report a enhanced base editing system. The enhanced base edting system decreased the formation of unintended indels and C-to-A/C-to-G substitutions, and increased the frequency of desired C-to-T substitution, thereby improving both the accuracy and efficiency of base editing.

2017-08-29 | GSE98685 | GEO

Knockout of circRNAs by base editing back-splice sites of circularized exons

Project description:Subcellular RNA-seq datasets are used for genome-wide analysis of circRNAs in 293FT cells. Here we knocked out circRNAs by base editor (BE)-mediated nucleotide changes.

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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

Bimodal Adenine and Cytosine CRISPR Base Editing on DNA

Project description:Adenine and cytosine base editors (ABEs and CBEs) represent a new genome editing technology that allows the programmable installation of A-to-G or C-to-T alterations on DNA. We engineered Streptococcus pyogenes Cas9-based adenine and cytosine base editor (SpACE) that enables efficient simultaneous introduction of A-to-G and C-to-T substitutions in the same base editing window on DNA.

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Project description:Evaluation of Cas9 and base editor variants

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Homo sapiens

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

Project description:CRISPR-Cas base editor technology enables targeted nucleotide alterations and is being rapidly deployed for research and potential therapeutic applications. The most widely used base editors induce DNA cytosine (C) deamination with rat APOBEC1 (rAPOBEC1) enzyme, which is targeted by a linked Cas protein-guide RNA (gRNA) complex. Previous studies of cytosine base editor (CBE) specificity have identified off-target DNA edits in human cells. Here we show that a CBE with rAPOBEC1 can cause extensive transcriptome-wide RNA cytosine deamination in human cells, inducing tens of thousands of C-to-uracil (U) edits with frequencies ranging from 0.07% to 100% in 38% - 58% of expressed genes. CBE-induced RNA edits occur in both protein-coding and non-protein-coding sequences and generate missense, nonsense, splice site, 5’ UTR, and 3’ UTR mutations. We engineered two CBE variants bearing rAPOBEC1 mutations that substantially decrease the numbers of RNA edits (reductions of >390-fold and >3,800-fold) in human cells. These variants also showed more precise on-target DNA editing and, with the majority of gRNAs tested, editing efficiencies comparable to those observed with wild-type CBE. Finally, we show that recently described adenine base editors (ABEs) can also induce transcriptome-wide RNA edits. These results have important implications for the research and therapeutic uses of base editors, illustrate the feasibility of engineering improved variants with reduced RNA editing activities, and suggest the need to more fully define and characterize the RNA off-target effects of deaminase enzymes in base editor platforms.

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