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ABSTRACT: ABE-mismatch

PROVIDER: PRJNA820057 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18490880_1.fastq.gz	Fastqsanger.gz
	SRR18490880_2.fastq.gz	Fastqsanger.gz
	SRR18490881_1.fastq.gz	Fastqsanger.gz
	SRR18490881_2.fastq.gz	Fastqsanger.gz
	SRR18490882_1.fastq.gz	Fastqsanger.gz

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Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells

Project description:Background The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigated the potential off-target structural variations associated with CRISPR/Cas9, ABE and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. Results The results showed that both Cas9 and ABE generated off-target structural variations (SVs) in mouse embryos, while CBE induced rare SVs. In addition, off-target large deletions were detected in 32.74% of primary human T cells transfected with Cas9 and 9.17% of cells transfected with ABE. Moreover, Cas9-induced aneuploid cells activated the P53 and apoptosis pathways, whereas ABE-associated aneuploid cells significantly upregulated cell cycle-related genes and arrested in G0 phase. A percentage of 16.59% and 4.29% aneuploid cells were still observable at 3 weeks post transfection of Cas9 or ABE. These off-target phenomena in ABE were universal as observed in other cell types such as B cells and Huh7. Furthermore, the off-target SVs were significantly reduced in cells treated with high-fidelity ABE (ABE-V106W). Conclusions This study raises urgent need for minimizing the off-target SVs of CRISPR/Cas9 and ABE.

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Enhanced solvent titer in the fermentation of Clostridium beijerinckii through application of metabolic controls

Project description:Clostridium beijerinckii is an anaerobic strain and well known for acetone-ethanol-butanol (ABE) fermentation using carbohydrates derived from cellulose or starch. During ABE fermentation, various byproducts are formed, mainly including acids (acetate, butyrate and lactate) and gas (hydrogen and carbon dioxide). recently, we found that Clostridium beijerinckii is able to produce a new product that had never been reported before and tightly regulated by pH and nitrogen source.

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Project description:To alleviate the ABE-mediated cytosine editing activity, we engineered the commonly-used version of adenosine deaminase, TadA7.10. We found that the D108Q mutation also reduces cytosine deamination activity in two recently-developed versions of ABE, ABE8e and ABE8s, and has a synergistic effect with V106W, a key mutation that reduces off-target RNA editing.

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