Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1015647 | ENA |
REPOSITORIES: ENA
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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.
2020-07-02 | GSE137411 | GEO
Project description:Programmable base editing of RNA enables rewriting the genetic codes on specific sites. Current tools for specific RNA editing dependent on the assembly or recruitment of the guide RNA into an RNA/protein complex, which may cause delivery barrier and low editing efficiency. Here we report a new set of tools, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. The REWIRE system contains a human-originated programmable RNA-binding domain (PUF domain) to specifically recognize target sequence and different deaminase domains to achieve A-to-I or C-to-U editing. By utilizing this system, we have achieved editing efficiencies up to 80% in A-to-I editing and 65% in C-to-U editing, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. We applied the REWIREs to correct disease-associated mutations and modify mitochondrial RNAs, and further optimized the REWIREs to improve the editing efficiency and minimize off-target effects. As a single-component base editing system originated from human proteins, REWIRE presents a precise and efficient RNA-editing platform with broad applicability in basic research and gene therapy.
2022-09-20 | GSE155734 | GEO
Project description:RNA base editing applies endogenous or engineered adenosine deaminases to introduce adenosine-to-inosine changes into a target RNA in a highly programmable manner. Recently, notable success was achieved for the repair of disease-causing guanosine-to-adenosine mutations by means of RNA base editing. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory sites of post-translational modification (PTM), like phosphorylation and/or acetylation sites. We demonstrate the feasibility of PTM interference (PTMi) on more than 70 PTM sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects. Specifically, we demonstrate both negative and positive regulation of the JAK/STAT pathway by PTMi. To identify potent regulatory sites for PTMi, we applied an improved version of the SNAP-ADAR tool, which achieved high editing efficiency over a broad codon scope with tight control of bystander editing. The transient nature of RNA base editing enables the fast, dose-dependent (thus partial) and reversible manipulation of PTM sites, which is a key advantage over DNA editing approaches, where genetic compensation or lethality can conceal a phenotype. In summary, PTM interference might become a valuable field of application of RNA base editing in basic biology and medicine.
2024-04-19 | GSE264114 | GEO
Project description:Programmable nucleases and designer-recombinases are prominent genome editing tools that hold great potential for the treatment of human genetic disorders. However, both of these tools alone are not optimal for clinical applications. We present an approach that combines the ease of targeting of programmable nucleases with editing safety and accuracy of site-specific recombinases. We find that insertional fusions of zinc-finger DNA-binding domains (ZFDs) into the coding sequence of designer-recombinases generate conditional enzymes that are inactive, unless the ZFD binds its target site placed in the vicinity of the recombinase binding site. This induced-fit activity is transferable to a recombinase with relaxed specificity, representing the prototype of a new class of genome editing enzymes that opens exciting perspectives for flexible, seamless, and precise genome surgery.
2023-12-19 | GSE243676 | GEO
Project description:Dissecting primer editing by proofreading polymerases
| PRJNA673973 | ENA
Project description:CRISPR technologies have begun to revolutionize T cell therapies; however, conventional CRISPR/Cas9 genome-editing tools are limited in their safety, efficacy, and scope. To address these challenges, we developed MEGA (Multiplexed Effector Guide Arrays), a platform for programmable and scalable regulation of the T cell transcriptome using the RNA-guided, RNA-targeting activity of CRISPR/Cas13d. MEGA enables quantitative, reversible, and massively-multiplexed gene knockdown in primary human T cells without targeting or cutting genomic DNA. Applying MEGA to a model of CAR T cell exhaustion, we robustly suppressed inhibitory receptor upregulation and uncovered paired regulators of T cell function through combinatorial CRISPR screening. We additionally implemented druggable regulation of MEGA to control CAR activation in a receptor-independent manner. Lastly, MEGA enabled multiplexed disruption of immunoregulatory metabolic pathways to enhance CAR T cell fitness and anti-tumor activity in vitro and in vivo. MEGA offers a versatile synthetic toolkit for applications in cancer immunotherapy and beyond.
2023-11-06 | GSE246823 | GEO