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20:03 EDT 15th September 2019 | BioPortfolio

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Showing "About That Base Editing" PubMed Articles 1–25 of 2,000+

Off-target Editing by CRISPR-guided DNA base editors.

Base editing is a genome editing strategy that induces specific single nucleotide changes within genomic DNA. Two major DNA base editors, Cytosine base editors (CBEs) and Adenine base editors (ABEs), have been developed that consist of a Cas9 protein linked to a deaminase enzyme that catalyzes targeted base conversion directed by a sgRNA. This strategy has been used widely for precise genome editing because, unlike CRISPR-Cas nuclease-based genome editing systems, this strategy does not create double strand...


RNA-Guided Adenosine Deaminases: Advances and Challenges for Therapeutic RNA Editing.

Targeted transcriptome engineering, in contrast to genome engineering, offers a complementary and potentially tunable and reversible strategy for cellular engineering. In this regard, adenosine to inosine (A-to-I) RNA base editing was recently engineered to make programmable base conversions on target RNAs. Similar to the DNA base editing technology, A-to-I RNA editing may offer an attractive alternative in a therapeutic setting, especially for the correction of point mutations. This Perspective introduces ...

Base editing the mammalian genome.

Base editing is a powerful technology that enables programmable conversion of single nucleotides in the mammalian genome. Base editors consist of a partially active Cas9 nuclease (Cas9) tethered to a natural or synthetic DNA modifying enzyme. Though only recently described, BE has already shown enormous potential for basic and translational research, allowing the creation or repair of disease alleles in a variety of cell types and model organisms. In the past 2 years, a vast array of new and modified base e...


Efficient Generation of Pathogenic A-to-G Mutations in Human Tripronuclear Embryos via ABE-Mediated Base Editing.

Base editing systems show their power in modeling and correcting the pathogenic mutations of genetic diseases. Previous studies have already demonstrated the editing efficiency of BE3-mediated C-to-T conversion in human embryos. However, the precision and efficiency of a recently developed adenine base editor (ABE), which converts A-to-G editing in human embryos, remain to be addressed. Here we selected reported pathogenic mutations to characterize the ABE in human tripronuclear embryos. We found effective ...

Expanded targeting scope and enhanced base editing efficiency in rabbit using optimized xCas9(3.7).

Evolved xCas9(3.7) variant with broad PAM compatibility has been reported in cell lines, while its editing efficiency was site-specific. Here, we show that xCas9(3.7) can recognize a broad PAMs including NGG, NGA, and NGT, in both embryos and Founder (F0) rabbits. Furthermore, the codon-optimized xCas9-derived base editors, exBE4 and exABE, can dramatically improve the base editing efficiencies in rabbit embryos. Our results demonstrated that the optimized xCas9 with expanded PAM compatibility and enhanced ...

Base Editing in Crops: Current Advances, Limitations, and Future Implications.

Targeted mutagenesis via genome editing technologies holds great promise in developing improved crop varieties to meet future demands. Point mutations or single nucleotide polymorphisms (SNPs) often determine important agronomic traits of crops. Genome editing-based single-base changes could generate elite trait variants in crop plants which help in accelerating crop improvement. Among the genome editing technologies, base editing has emerged as a novel and efficient genome editing approach which enables di...

Improving Editing Efficiency for the Sequences with NGH PAM Using xCas9-Derived Base Editors.

The development of CRISPR/Cas9-mediated base editors (BEs) provided a versatile tool for precise genome editing. The recently developed xCas9-derived base editors (xBEs) that recognize the NG PAM substantially expand the targeting scope in the genome, while their editing efficiency needs to be improved. Here, we described an improved version of xBEs by fusing the BPNLS and Gam to the N terminus of xBEs (BPNLS-Gam-xBE3 and BPNLS-xABE), and this version of base editor displayed higher targeting efficiency for...

Simplified adenine base editors improve adenine base editing efficiency in rice.

Adenine base editors (ABEs) have been exploited to introduce targeted adenine (A) to guanine (G) base conversions in various plant genomes, including rice, wheat and Arabidopsis. However, the ABEs reported thus far are all quite inefficient at many target sites in rice, which hampers their applications in plant genome engineering and crop breeding. Here, we show that unlike in the mammalian system, a simplified base editor ABE-P1S (Adenine Base Editor-Plant version 1 Simplified) containing the ecTadA*7.10-n...

High Efficient and Precise Base Editing of C•G to T•A in the Allotetraploid Cotton (Gossypium hirsutum) Genome Using a Modified CRISPR/Cas9 System.

The base-editing technique using CRISPR/nCas9 (Cas9 nickase) or dCas9 (deactivated Cas9) fused with cytidine deaminase is a powerful tool to create point mutations. In this study, a novel G. hirsutum-Base Editor 3 (GhBE3) base editing system has been developed to create single base mutations in the allotetraploid genome of cotton (Gossypium hirsutum). A cytidine deaminase sequence (APOBEC) fused with nCas9 and uracil glycosylase inhibitor (UGI) was inserted into our CRISPR/Cas9 plasmid (pRGEB32-GhU6.7). Thr...

An adenine base editor with expanded targeting scope using SpCas9-NGv1 in rice.

The CRISPR/Cas9 genome editing system induces mainly small insertions or deletions at the target site. In contrast, base editors are precise genome editing tools that enable base conversion at a target site without inducing a DNA double-strand break. Two types of base editors have now been developed: cytosine base editors (CBEs)-cytidine deaminase fused with catalytically impaired Cas9-can efficiently convert a C-G base pair to a T-A pair, while adenine base editors (ABEs)-Cas9 nickase (nCas9) plus engineer...

Improved base editor for efficient editing in GC contexts in rabbits with an optimized AID-Cas9 fusion.

Cytidine base editors, which are composed of a cytidine deaminase fused to clustered regularly interspaced short palindromic repeat-associated protein 9 (Cas9) nickase, enable the efficient conversion of the C·G base pair to T·A in various organisms. However, the currently used rat apolipoprotein B mRNA-editing enzyme, catalytic polypeptide 1(rA1)-based BE3 is often inefficient in target Cs that are immediately downstream of a G (GC context). Here, we observed that, with an 11-nt editing window, an optimi...

Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG.

Engineered SpCas9 variants, namely xCas9 and Cas9-NG, have shown promising potential on improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9 (xCas9-3.7, the most effective xCas9 variant in mammalian cells), for targeted mutagenesis at all 16 possible NGN PAM combinations in duplicates. xCas9 mostly exhibited equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at the canonical NGG PAM...

Genome engineering in rice using Cas9 variants that recognize NG PAM sequences.

CRISPR-Cas9 genome editing relies on sgRNA-target DNA base pairing and a short downstream PAM sequence to recognize target DNA. The strict PAM requirement hinders the applications of CRISPR-Cas9 system since it restricts the targetable sites in the genomes. xCas9 and SpCas9-NG are two recently engineered SpCas9 variants that can recognize more relaxed NG PAMs, which have great potential in addressing the issue of PAM constraint. Here, we use stable transgenic lines to evaluate the efficacies of xCas9 and Sp...

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.

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 transcripto...

Cas9-NG greatly expands the targeting scope of genome-editing toolkit by recognizing NG and other atypical PAMs in rice.

The CRISPR technologies enabling precise genome manipulation are valuable for the gene function study and molecular crop breeding. However, the requirement of a protospacer adjacent motif (PAM), such as NGG, TTN, etc., for Cas protein recognition restricts the targetable genomic loci in applications. Very lately, Cas9-NG which recognizes a minimal NG PAM was reported to expand the targeting space in genome editing in human cells, but little is known about its applications in plants. Here, we evaluated the n...

Base editor correction of COL7A1 in recessive dystrophic epidermolysis bullosa patient-derived fibroblasts and iPSCs.

Genome editing represents a promising strategy for therapeutic correction of COL7A1 mutations that cause recessive dystrophic epidermolysis bullosa (RDEB). DNA cleavage followed by homology-directed repair (HDR) using an exogenous template has previously been used to correct COL7A1 mutations. HDR rates can be modest and the double-strand DNA breaks that initiate HDR commonly result in accompanying undesired insertions and deletions (indels). To overcome these limitations, we applied an A•T→G•C adenine...

Increasing Cytosine Base Editing Scope and Efficiency With Engineered Cas9-PmCDA1 Fusions and the Modified sgRNA in Rice.

Base editors that do not require double-stranded DNA cleavage or homology-directed repair enable higher efficiency and cleaner substitution of targeted single nucleotides in genomic DNA than conventional approaches. However, their broad applications are limited within the editing window of several base pairs from the canonical NGG protospacer adjacent motif (PAM) sequence. In this study, we fused the D10A nickase of several Cas9 (SpCas9) variants with cytidine deaminase 1 (PmCDA1) and uracil DNA glycosyla...

Gene Editing Based Hearing Impairment Research and Therapeutics.

Hearing impairment affects 1 in 500 newborns worldwide and nearly one out of three people over the age of 65 (WHO, 2019). Hereditary hearing loss is the most common type of congenital deafness; genetic factors also affect deafness susceptibility. Gene therapies may preserve or restore natural sound perception, and have rescued deafness in multiple hereditary murine models. CRISPR-Cas9 and base editors (BEs) are newly developed gene-editing technologies that can facilitate gene studies in the inner ear and p...

Off-target challenge for base editor-mediated genome editing.

Effects of providing manuscript editing through a combination of in-house and external editing services in an academic hospital.

English editing services are effective for improving manuscript quality as well as providing learning opportunities for non-native English-speaking authors. Herein, we describe the effects of a combined system of in-house and external editing services for handling large volumes of editing requests and providing personalized editing service in academic hospitals.

The G3-U70-independent tRNA recognition by human mitochondrial alanyl-tRNA synthetase.

Alanyl-tRNA synthetases (AlaRSs) from three domains of life predominantly rely on a single wobble base pair, G3-U70, of tRNAAla as a major determinant. However, this base pair is divergent in human mitochondrial tRNAAla, but instead with a translocated G5-U68. How human mitochondrial AlaRS (hmtAlaRS) recognizes tRNAAla, in particular, in the acceptor stem region, remains unknown. In the present study, we found that hmtAlaRS is a monomer and recognizes mitochondrial tRNAAla in a G3-U70-independent manner, re...

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture.

Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and desc...

Clinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers.

RNA editing is a post-transcriptional process that alters the nucleotide sequences of certain transcripts, in vertebrate most often converting adenosines to inosines. Multiple studies have recently implicated RNA editing in cancer development; however, most studies have focused on recoding RNA editing events. The function and clinical relevance of noncoding RNA (ncRNA) editing events in cancers have not been systematically examined.

Metabolic editing: small measures, great impact.

Metabolic pathways are tightly regulated at the transcriptional and post-translational level, often relying on protein-protein interactions or post-translational protein modifications. Whereas these principles have been established already for a long time, the number of experimentally established cases is expected to rise exponentially in the near future as a result of recent advances in protein-based detection methods. Interactions and modifications are often dependent on only short amino-acid sequences th...

Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.

A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes on the RNA editing process. We performed comprehensive phenotypic, transcriptomics, proteomics, and RNA binding screens on worms mutated in a single ADAR gene. We found that ADR-1 mutants exhibit more-severe phenotypes than ADR-2, and some of them are a res...


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