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Specific targeting of plasmids with Argonaute enables genome editing

ABSTRACT: Specific targeting of plasmids with Argonaute enables genome editing

PROVIDER: PRJNA826095 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18735661.fastq.gz	Fastqsanger.gz
	SRR18735662.fastq.gz	Fastqsanger.gz
	SRR18735663.fastq.gz	Fastqsanger.gz
	SRR18735664.fastq.gz	Fastqsanger.gz
	SRR18735665.fastq.gz	Fastqsanger.gz

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Specific targeting of plasmids with Argonaute enables genome editing

Project description:Prokaryotic Argonaute nuclease induces DNA interference between plasmid and chromosomal DNA to promote genome recombineering

2022-04-17 | GSE200694 | GEO

Specific targeting of plasmids with Argonaute enables genome editing.

Project description:Prokaryotic Argonautes (pAgos) are programmable nucleases involved in cell defense against invading DNA. In vitro, pAgos can bind small single-stranded guide DNAs to recognize and cleave complementary DNA. In vivo, pAgos preferentially target plasmids, phages and multicopy genetic elements. Here, we show that CbAgo nuclease from Clostridium butyricum can be used for genomic DNA engineering in bacteria. We demonstrate that CbAgo loaded with plasmid-derived guide DNAs can recognize and cleave homologous chromosomal loci, and define the minimal length of homology required for this targeting. Cleavage of plasmid DNA at an engineered site of the I-SceI meganuclease increases guide DNA loading into CbAgo and enhances processing of homologous chromosomal loci. Analysis of guide DNA loading into CbAgo also reveals off-target sites of I-SceI in the Escherichia coli genome, demonstrating that pAgos can be used for highly sensitive detection of double-stranded breaks in genomic DNA. Finally, we show that CbAgo-dependent targeting of genomic loci with plasmid-derived guide DNAs promotes homologous recombination between plasmid and chromosomal DNA, depending on the catalytic activity of CbAgo. Specific targeting of plasmids with Argonautes can be used to integrate plasmid-encoded sequences into the chromosome thus enabling genome editing.

| S-EPMC10164558 | biostudies-literature

Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

Project description:To investigate the possible consequences of APOBEC1 editing for miRNA targeting, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) of the Argonaute (Ago) proteins (Chi et al., 2009) was performed in BMDMs derived from wild-type and Apobec1-/- littermates.

2017-11-21 | GSE58798 | GEO

Stabilising features of cefotaximase harbouring plasmids enables persistence in UK livestock

Project description:Stabilising features of cefotaximase harbouring plasmids enables persistence in UK livestock

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SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease

Project description:SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease

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SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease [miSeq]

Project description:Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular and cellular biology, medicine and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings preventing their broader implementation including transient effects in the case of oligonucleotides or limiting PAM motifs, sequence context preferences for deaminases, and undesirable cryptic splicing in the case of gene editing tools. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused with different deaminases for simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing not only improves exon skipping rates but also reduces aberrant outcomes such as cryptic splicing and intron retention. SPLICER enables editing of exon splice sites with high efficiency, including many exons refractory to splicing reprogramming by the native SpCas9 BEs. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which contains the amino acid residues responsible for the formation of Aβ plaques in Alzheimer’s disease. SPLICER enabled precise and highly efficient exon skipping, which reduced the formation of Aβ42 peptides in vitro while inducing DNA editing and exon skipping in vivo within a humanized mouse model of Alzheimer’s disease. Overall, SPLICER is a widely applicable and highly efficient toolbox for exon skipping with broad therapeutic applications.

2023-12-10 | GSE246586 | GEO

Light induced targeting enables proteomics on endogenous condensates

Project description:Light induced targeting enables proteomics on endogenous condensates

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SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease [miSeq]

Project description:SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease [miSeq]

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