scholarly journals RNA editing of BFP, a point mutant of GFP, using artificial APOBEC1 deaminase to restore the genetic code

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sonali Bhakta ◽  
Matomo Sakari ◽  
Toshifumi Tsukahara
Keyword(s):  
Rna Editing ◽  
Fluorescent Protein ◽  
Genetic Diseases ◽  
Mrna Level ◽  
Point Mutations ◽  
Artificial Enzyme ◽  
Gene Encoding ◽  
Stem Loop ◽  
Pcr Rflp ◽  
Deaminase Domain

Abstract Many genetic diseases are caused by T-to-C point mutations. Hence, editing of mutated genes represents a promising strategy for treating these disorders. We engineered an artificial RNA editase by combining the deaminase domain of APOBEC1 (apolipoprotein B mRNA editing catalytic polypeptide 1) with a guideRNA (gRNA) which is complementary to target mRNA. In this artificial enzyme system, gRNA is bound to MS2 stem-loop, and deaminase domain, which has the ability to convert mutated target nucleotide C-to-U, is fused to MS2 coat protein. As a target RNA, we used RNA encoding blue fluorescent protein (BFP) which was derived from the gene encoding GFP by 199 T > C mutation. Upon transient expression of both components (deaminase and gRNA), we observed GFP by confocal microscopy, indicating that mutated 199C in BFP had been converted to U, restoring original sequence of GFP. This result was confirmed by PCR–RFLP and Sanger’s sequencing using cDNA from transfected cells, revealing an editing efficiency of approximately 21%. Although deep RNA sequencing result showed some off-target editing events in this system, we successfully developed an artificial RNA editing system using artificial deaminase (APOBEC1) in combination with MS2 system could lead to therapies that treat genetic disease by restoring wild-type sequence at the mRNA level.

scholarly journals RNA Editing as a Therapeutic Approach for Retinal Gene Therapy Requiring Long Coding Sequences

2020 ◽  
Vol 21 (3) ◽  
pp. 777 ◽  
Author(s):  
Lewis E. Fry ◽  
Caroline F. Peddle ◽  
Alun R. Barnard ◽  
Michelle E. McClements ◽  
Robert E. MacLaren
Keyword(s):  
Gene Therapy ◽  
Rna Editing ◽  
Therapeutic Approach ◽  
Genetic Diseases ◽  
Point Mutations ◽  
Transcript Level ◽  
Gene Replacement ◽  
Promising Therapeutic Approach ◽  
Pairing Site ◽  
Large Genes

RNA editing aims to treat genetic disease through altering gene expression at the transcript level. Pairing site-directed RNA-targeting mechanisms with engineered deaminase enzymes allows for the programmable correction of G>A and T>C mutations in RNA. This offers a promising therapeutic approach for a range of genetic diseases. For inherited retinal degenerations caused by point mutations in large genes not amenable to single-adeno-associated viral (AAV) gene therapy such as USH2A and ABCA4, correcting RNA offers an alternative to gene replacement. Genome editing of RNA rather than DNA may offer an improved safety profile, due to the transient and potentially reversible nature of edits made to RNA. This review considers the current site-directing RNA editing systems, and the potential to translate these to the clinic for the treatment of inherited retinal degeneration.

scholarly journals Developing PspCas13b-based enhanced RESCUE system, eRESCUE, with efficient RNA base editing

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Guo Li ◽  
Yihan Wang ◽  
Xiangyang Li ◽  
Yuzhe Wang ◽  
Xingxu Huang ◽  
...  
Keyword(s):  
Genetic Code ◽  
Rna Editing ◽  
Genetic Diseases ◽  
Disease Treatment ◽  
Editing Efficiency ◽  
Base Editing ◽  
Rescue System ◽  
Adenine Deaminase ◽  
Deaminase Domain

AbstractRNA base editing is potential for cellular function research and genetic diseases treating. There are two main RNA base editors, REPAIR and RESCUE, for in vitro use. REPAIR was developed by fusing inactivated Cas13 (dCas13) with the adenine deaminase domain of ADAR2, which efficiently performs adenosine-to-inosine (A-to-I) RNA editing. RESCUE, which performs both cytidine-to-uridine (C-to-U) and A-to-I RNA editing, was developed by fusing inactivated Cas13 (dCas13) with the evolved ADAR2. However, the relatively low editing efficiency of the RESCUE system limits its broad application. Here, we constructed an enhanced RESCUE (eRESCUE) system; this dPspCas13b-RESCUE-NES system was generated by fusing inactivated PspCas13b with the evolved ADAR2. We determined the endogenous mRNA A-to-I and C-to-U editing efficiency mediated by the dPspCas13b-RESCUE-NES system in HEK-293T cells. This new RNA base editor was then used to induce 177Ser/Gly conversion of inhibitor kappa B kinase β (IKKβ) by changing the genetic code from AGU to GGU. The results showed that the eRESCUE editor mediates more efficient A-to-I and C-to-U RNA editing than the RESCUE RNA editor, as was previously reported. The 177Ser/Gly conversion of IKKβ, accomplished by converting the genetic code from AGU to GGU, resulted in a decrease in the phosphorylation of IKKβ and downregulation of downstream IKKβ-related genes. In summary, we developed a more efficient RNA base editor, eRESCUE, which may provide a useful tool for biomedical research and genetic disease treatment.

scholarly journals Investigating REPAIRv2 as a Tool to Edit CFTR mRNA with Premature Stop Codons

2020 ◽  
Vol 21 (13) ◽  
pp. 4781
Author(s):  
Raffaella Melfi ◽  
Patrizia Cancemi ◽  
Roberta Chiavetta ◽  
Viviana Barra ◽  
Laura Lentini ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cell Types ◽  
Good Alternative ◽  
Severe Form ◽  
Full Length ◽  
Compound Heterozygous ◽  
Gene Encoding ◽  
Guide Rna ◽  
Cftr Protein ◽  
Deaminase Domain

Cystic fibrosis (CF) is caused by mutations in the gene encoding the transmembrane conductance regulator (CFTR) protein. Some CF patients are compound heterozygous or homozygous for nonsense mutations in the CFTR gene. This implies the presence in the transcript of premature termination codons (PTCs) responsible for a truncated CFTR protein and a more severe form of the disease. Aminoglycoside and PTC124 derivatives have been used for the read-through of PTCs to restore the full-length CFTR protein. However, in a precision medicine framework, the CRISPR/dCas13b-based molecular tool “REPAIRv2” (RNA Editing for Programmable A to I Replacement, version 2) could be a good alternative to restore the full-length CFTR protein. This RNA editing approach is based on the targeting of the deaminase domain of the hADAR2 enzyme fused to the dCas13b protein to a specific adenosine to be edited to inosine in the mutant mRNA. Targeting specificity is allowed by a guide RNA (gRNA) complementarily to the target region and recognized by the dCas13b protein. Here, we used the REPAIRv2 platform to edit the UGA PTC to UGG in different cell types, namely IB3-1 cells, HeLa, and FRT cells engineered to express H2BGFPopal and CFTRW1282X, respectively.

scholarly journals Site-directed RNA repair of endogenous Mecp2 RNA in neurons

2017 ◽  
Vol 114 (44) ◽  
pp. E9395-E9402 ◽  
Author(s):  
John R. Sinnamon ◽  
Susan Y. Kim ◽  
Glen M. Corson ◽  
Zhen Song ◽  
Hiroyuki Nakai ◽  
...  
Keyword(s):  
Rna Editing ◽  
Protein Function ◽  
Rna Binding ◽  
Catalytic Domain ◽  
Mrna Level ◽  
Gene Encoding ◽  
Rna Repair ◽  
Mecp2 Protein ◽  
Localization Signal

Rett syndrome (RTT) is a debilitating neurological disorder caused by mutations in the gene encoding the transcription factor Methyl CpG Binding Protein 2 (MECP2). A distinct disorder results from MECP2 gene duplication, suggesting that therapeutic approaches must restore close to normal levels of MECP2. Here, we apply the approach of site-directed RNA editing to repair, at the mRNA level, a disease-causing guanosine to adenosine (G > A) mutation in the mouse MeCP2 DNA binding domain. To mediate repair, we exploit the catalytic domain of Adenosine Deaminase Acting on RNA (ADAR2) that deaminates A to inosine (I) residues that are subsequently translated as G. We fuse the ADAR2 domain, tagged with a nuclear localization signal, to an RNA binding peptide from bacteriophage lambda. In cultured neurons from mice that harbor an RTT patient G > A mutation and express engineered ADAR2, along with an appropriate RNA guide to target the enzyme, 72% of Mecp2 mRNA is repaired. Levels of MeCP2 protein are also increased significantly. Importantly, as in wild-type neurons, the repaired MeCP2 protein is enriched in heterochromatic foci, reflecting restoration of normal MeCP2 binding to methylated DNA. This successful use of site-directed RNA editing to repair an endogenous mRNA and restore protein function opens the door to future in vivo applications to treat RTT and other diseases.

scholarly journals In vivoRNA targeting of point mutations via suppressor tRNAs and adenosine deaminases

2017 ◽  
Author(s):  
Dhruva Katrekar ◽  
Prashant Mali
Keyword(s):  
Mouse Model ◽  
Rna Editing ◽  
Unnatural Amino Acids ◽  
Stop Codon ◽  
Genetic Diseases ◽  
Point Mutations ◽  
Premature Stop Codon ◽  
Dystrophin Gene ◽  
Multiple Challenges

ABSTRACTPoint mutations underlie many genetic diseases. In this regard, while programmable DNA nucleases have been used to repair mutations, their use for gene therapy poses multiple challenges: one, efficiency of homologous recombination is typically low in cells; two, an active nuclease presents a risk of introducing permanent off-target mutations; and three, prevalent programmable nucleases typically comprise elements of non-human origin raising the potential ofin vivoimmunogenicity. In light of these, approaches to instead directly target RNA, and use of molecular machinery native to the host would be highly desirable. Towards this, we engineered and optimized two complementary approaches, referred together hereon astRiAD, based on the use oftRNAsin codon suppression andadenosinedeaminases in RNA editing. Specifically, by delivering modified endogenous tRNAs and/or the RNA editing enzyme ADAR2 and an associated guiding RNA (adRNA) via adeno-associated viruses, we enabled premature stop codon read-through and correction in themdxmouse model of muscular dystrophy that harbors a nonsense mutation in the dystrophin gene. We further demonstrated inducible restoration of dystrophin expression by pyrolysyl-tRNA mediated incorporation of unnatural amino acids (UAAs) at the stop codon. Additionally, we also engineered ADAR2 mediated correction of a point mutation in liver RNA of thespfashmouse model of ornithine transcarbamylase (OTC) deficiency. Taken together, our results establish the use of suppressor tRNAs and ADAR2 forin vivoRNA targeting, and this integrated tRiAD approach is robust, genomically scarless, and potentially non-immunogenic as it utilizes effector RNAs and human proteins.

Genetic code restoration by artificial RNA editing of Ochre stop codon with ADAR1 deaminase

2018 ◽  
Vol 31 (12) ◽  
pp. 471-478 ◽  
Author(s):  
Sonali Bhakta ◽  
Md Thoufic Anam Azad ◽  
Toshifumi Tsukahara
Keyword(s):  
Genetic Code ◽  
Rna Editing ◽  
Fluorescent Protein ◽  
Catalytic Domain ◽  
Stop Codon ◽  
Direct Sequencing ◽  
Genetic Diseases ◽  
Site Directed Mutagenesis ◽  
Sequencing Analysis

Abstract Site directed mutagenesis is a very effective approach to recode genetic information. Proper linking of the catalytic domain of the RNA editing enzyme adenosine deaminase acting on RNA (ADAR) to an antisense guide RNA can convert specific adenosines (As) to inosines (Is), with the latter recognized as guanosines (Gs) during the translation process. Efforts have been made to engineer the deaminase domain of ADAR1 and the MS2 system to target specific A residues to restore G→A mutations. The target consisted of an ochre (TAA) stop codon, generated from the TGG codon encoding amino acid 58 (Trp) of enhanced green fluorescent protein (EGFP). This system had the ability to convert the stop codon (TAA) to a readable codon (TGG), thereby restoring fluorescence in a cellular system, as shown by JuLi fluorescence and LSM confocal microscopy. The specificity of the editing was confirmed by polymerase chain reaction-restriction fragment length polymorphism, as the restored EGFP mRNA could be cleaved into fragments of 160 and 100 base pairs. Direct sequencing analysis with both sense and antisense primers showed that the restoration rate was higher for the 5′ than for the 3′A. This system may be very useful for treating genetic diseases that result from G→A point mutations. Successful artificial editing of RNA in vivo can accelerate research in this field, and pioneer genetic code restoration therapy, including stop codon read-through therapy, for various genetic diseases.

Genetic and Biochemical Markers of Ovarian Function and Their Impact on Women Reproductive Status

2020 ◽  
Vol 71 (10) ◽  
pp. 212-217
Author(s):  
Adina-Elena Tanase ◽  
Roxana Popescu ◽  
Mircea Onofriescu ◽  
Roxana Daniela Matasariu
Keyword(s):  
Ovarian Function ◽  
Rflp Analysis ◽  
Fsh Receptor ◽  
Gene Encoding ◽  
Female Population ◽  
Fshr Gene ◽  
Pcr Rflp ◽  
Regulation Mechanisms ◽  
American Society ◽  
Dependent Mechanism

Endometriosis is a disease very common nowadays affecting 1-2% of the female population, by estrogen-dependent mechanism. The identification of mutations in the gene encoding for the FSH receptor (FSHR) has been reported since 1995. Physiology teaches us that follicle-stimulating hormone (FSH) is a hormone that is vital in the steroidogenesis regulation mechanisms, while FSH receptor (FSHR) activation helps to promote folliculogenesis and estrogensynthesis. Therefore, studies to show if there are any correlations between endometriosis and FSHR are acquired. Genotyping of FSHR gene polymorphisms were performed using PCR - Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. We analysed a total of 78 patients, 44 infertile patients with endometriosis and 34 controls (non-infertile, pregnant patients). The endometriosis group included women with diagnosis of endo-metriosis confirmed by laparoscopy and /or laparotomy and histological evidence of disease with the endometriosis staging according to American Society for Reproductive Medicine (ASRM). Corroborated with the severity of endometriosis, A919G and A2039G tests found that 71.4% of the M (GG) results were associated with primary infertility, not statistically significant (p=0.994) and 42.9% of the total M results had moderate or severe forms of endometriosis (p = 0.185). The genetic involvement in different pathologies such as endometriosis, has yet to be understood, but knowing more about its mechanism, will help physician target the disease at a more profound level.

Artificial RNA Editing with ADAR for Gene Therapy

2020 ◽  
Vol 20 (1) ◽  
pp. 44-54 ◽  
Author(s):  
Sonali Bhakta ◽  
Toshifumi Tsukahara
Keyword(s):  
Gene Therapy ◽  
Genetic Code ◽  
Molecular Mechanism ◽  
Rna Editing ◽  
Comparative Studies ◽  
Genetic Diseases ◽  
Adenosine Deaminases ◽  
Family Protein ◽  
Hydrolytic Deamination

Editing mutated genes is a potential way for the treatment of genetic diseases. G-to-A mutations are common in mammals and can be treated by adenosine-to-inosine (A-to-I) editing, a type of substitutional RNA editing. The molecular mechanism of A-to-I editing involves the hydrolytic deamination of adenosine to an inosine base; this reaction is mediated by RNA-specific deaminases, adenosine deaminases acting on RNA (ADARs), family protein. Here, we review recent findings regarding the application of ADARs to restoring the genetic code along with different approaches involved in the process of artificial RNA editing by ADAR. We have also addressed comparative studies of various isoforms of ADARs. Therefore, we will try to provide a detailed overview of the artificial RNA editing and the role of ADAR with a focus on the enzymatic site directed A-to-I editing.

scholarly journals Versatile CRISPR/Cas9 Systems for Genome Editing in Ustilago maydis

2021 ◽  
Vol 7 (2) ◽  
pp. 149
Author(s):  
Sarah-Maria Wege ◽  
Katharina Gejer ◽  
Fabienne Becker ◽  
Michael Bölker ◽  
Johannes Freitag ◽  
...  
Keyword(s):  
Genome Editing ◽  
Cell Biology ◽  
Gene Deletion ◽  
Fluorescent Protein ◽  
Point Mutations ◽  
Model Organism ◽  
Ustilago Maydis ◽  
Genomic Locus ◽  
Targeted Gene Deletion ◽  
Molecular Cell Biology

The phytopathogenic smut fungus Ustilago maydis is a versatile model organism to study plant pathology, fungal genetics, and molecular cell biology. Here, we report several strategies to manipulate the genome of U. maydis by the CRISPR/Cas9 technology. These include targeted gene deletion via homologous recombination of short double-stranded oligonucleotides, introduction of point mutations, heterologous complementation at the genomic locus, and endogenous N-terminal tagging with the fluorescent protein mCherry. All applications are independent of a permanent selectable marker and only require transient expression of the endonuclease Cas9hf and sgRNA. The techniques presented here are likely to accelerate research in the U. maydis community but can also act as a template for genome editing in other important fungi.

scholarly journals Mechanism of Aurora-B Degradation and Its Dependency on Intact KEN and A-Boxes: Identification of an Aneuploidy-Promoting Property

2005 ◽  
Vol 25 (12) ◽  
pp. 4977-4992 ◽  
Author(s):  
Hao G. Nguyen ◽  
Dharmaraj Chinnappan ◽  
Takeshi Urano ◽  
Katya Ravid
Keyword(s):  
Chromosome Segregation ◽  
Fluorescent Protein ◽  
Point Mutations ◽  
Degradation Pathway ◽  
Aurora B ◽  
Stable Form ◽  
Wild Type ◽  
Green Fluorescent ◽  
Critical Regions

ABSTRACT The kinase Aurora-B, a regulator of chromosome segregation and cytokinesis, is highly expressed in a variety of tumors. During the cell cycle, the level of this protein is tightly controlled, and its deregulated abundance is suspected to contribute to aneuploidy. Here, we provide evidence that Aurora-B is a short-lived protein degraded by the proteasome via the anaphase-promoting cyclosome complex (APC/c) pathway. Aurora-B interacts with the APC/c through the Cdc27 subunit, Aurora-B is ubiquitinated, and its level is increased upon treatment with inhibitors of the proteasome. Aurora-B binds in vivo to the degradation-targeting proteins Cdh1 and Cdc20, the overexpression of which accelerates Aurora-B degradation. Using deletions or point mutations of the five putative degradation signals in Aurora-B, we show that degradation of this protein does not depend on its D-boxes (RXXL), but it does require intact KEN boxes and A-boxes (QRVL) located within the first 65 amino acids. Cells transfected with wild-type or A-box-mutated or KEN box-mutated Aurora-B fused to green fluorescent protein display the protein localized to the chromosomes and then to the midzone during mitosis, but the mutated forms are detected at greater intensities. Hence, we identified the degradation pathway for Aurora-B as well as critical regions for its clearance. Intriguingly, overexpression of a stable form of Aurora-B alone induces aneuploidy and anchorage-independent growth.

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