The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Stephen Moore - One of the best experts on this subject based on the ideXlab platform.
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adar2 mislocalization and widespread RNA Editing aberrations in c9orf72 mediated als ftd
Acta Neuropathologica, 2019Co-Authors: Stephen Moore, Eric Alsop, Ileana Lorenzini, Alexander Starr, Benjamin E Rabichow, Emily Mendez, Jennifer Levy, Camelia Burciu, Rebecca ReimanAbstract:The hexanucleotide repeat expansion GGGGCC (G4C2)n in the C9orf72 gene is the most common genetic abnormality associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent findings suggest that dysfunction of nuclear-cytoplasmic trafficking could affect the transport of RNA binding proteins in C9orf72 ALS/FTD. Here, we provide evidence that the RNA Editing enzyme adenosine deaminase acting on RNA 2 (ADAR2) is mislocalized in C9orf72 repeat expansion mediated ALS/FTD. ADAR2 is responsible for adenosine (A) to inosine (I) Editing of double-stranded RNA, and its function has been shown to be essential for survival. Here we show the mislocalization of ADAR2 in human induced pluripotent stem cell-derived motor neurons (hiPSC-MNs) from C9orf72 patients, in mice expressing (G4C2)149, and in C9orf72 ALS/FTD patient postmortem tissue. As a consequence of this mislocalization we observe alterations in RNA Editing in our model systems and across multiple brain regions. Analysis of Editing at 408,580 known RNA Editing sites indicates that there are vast RNA A to I Editing aberrations in C9orf72-mediated ALS/FTD. These RNA Editing aberrations are found in many cellular pathways, such as the ALS pathway and the crucial EIF2 signaling pathway. Our findings suggest that the mislocalization of ADAR2 in C9orf72 mediated ALS/FTD is responsible for the alteration of RNA processing events that may impact vast cellular functions, including the integrated stress response (ISR) and protein translation.
Tadafumi Kato - One of the best experts on this subject based on the ideXlab platform.
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measuring RNA Editing of serotonin 2c receptor
Biochemistry, 2011Co-Authors: Kazuya Iwamoto, Miki Bundo, Kiyoto Kasai, Tadafumi KatoAbstract:Pre-mRNA of serotonin 2C receptor (HTR2C, 5-hydroxytryptamine (serotonin) receptor 2C) undergoes A-to-I type RNA Editing, which is a post-transcriptional event leading to the change of genomically encoded information. RNA Editing generates various HTR2C isoforms, each of which has distinctive receptor activity. Postmortem, animal, and pharmacological studies have suggested that the altered RNA Editing of HTR2C is involved in the pathophysiology of mental disorders, although results remain inconsistent. Here we review the techniques used for estimation of RNA Editing of HTR2C. Among the techniques reported so far, a high-throughput sequencing-based method would be the most powerful method of choice for the large-scale experiments. Several different methods that were previously developed, such as pyrosequencing and capillary electrophoresis, should be suitable for validation as well as for rapid screening or exploratory purposes.
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serotonin receptor 2c and mental disorders genetic expression and RNA Editing studies
RNA Biology, 2009Co-Authors: Kazuya Iwamoto, Miki Bundo, Tadafumi KatoAbstract:Serotonin receptor 2C (HTR2C) is one of the attractive candidate genes for studying pathophysiology of mental disorders. Here we overviewed the genetic, expression, and RNA Editing studies suggesting the close relationship between HTR2C and major mental disorders including schizophrenia, bipolar disorder, and major depression. We especially focused on the human studies as well as with reference to relevant cellular and animal models. Possible significance of genetic variations affecting expression and RNA Editing and appropriate animal models that mimic human mental disorders were discussed.
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estimating RNA Editing efficiency of five Editing sites in the serotonin 2c receptor by pyrosequencing
RNA, 2005Co-Authors: Kazuya Iwamoto, Miki Bundo, Tadafumi KatoAbstract:: Accumulating evidence suggests that altered RNA Editing of the serotonin 2C receptor (HTR2C) is involved in the pathophysiology of mental disorders and the action of antidepressants. Estimating RNA Editing of HTR2C in various samples is a first step to understanding its pathophysiological roles. Here, we developed a high-throughput quantification method of RNA Editing efficiency by pyrosequencing. By optimizing the dispensation order, the RNA Editing efficiency of all five RNA Editing sites including consecutively ordered sites in HTR2C was obtained. More importantly, our method made it possible to determine the content of partial HTR2C isoforms, which enabled us to monitor possible functional changes of HTR2C. This method was validated in both oligonucleotide and RT-PCR product templates, and showed good correlation with conventional cloning-sequencing analysis. Our method could be a valuable tool in the rapid assessment of RNA Editing status, including assessment of natural variations, alterations in disease tissues, and responses to drugs.
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altered RNA Editing of serotonin 2c receptor in a rat model of depression
Neuroscience Research, 2005Co-Authors: Kazuya Iwamoto, Noriaki Nakatani, Miki Bundo, Takeo Yoshikawa, Tadafumi KatoAbstract:Abstract Altered RNA Editing of serotonin 2C receptor ( HTR2C ) has been suggested to be involved in the pathophysiology of major depression. Here we examined RNA Editing status of HTR2C in the learned helplessness (LH) rats, one of well-established animal models of depression. LH rats showed the significantly increased RNA Editing of site E, and tendency for increased RNA Editing of other Editing sites. Treatment with fluoxetine, a selective serotonin reuptake inhibitor, or imipramine, a tricyclic antidepressant, affected the RNA Editing status of the LH rats. Although, these antidepressants differentially altered RNA Editing status, they commonly reduced RNA Editing efficiency of site E. We further revealed that altered RNA Editing in the LH rats and by antidepressants was not explained by altered expression of RNA Editing enzymes or their substrates (adenosine deaminases that act on RNA, HTR2C , and spliced form of HTR2C ). These results suggest that alteration of RNA Editing of HTR2C may play a role in the pathophysiology of depression and action of antidepressants.
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RNA Editing of serotonin 2c receptor in human postmortem brains of major mental disorders
Neuroscience Letters, 2003Co-Authors: Kazuya Iwamoto, Tadafumi KatoAbstract:Abstract The importance of serotonin 2C receptor (HTR2C) in mental disorders has been implicated by studies of HTR2C-deficient mice and linkage and association studies. Recent studies have revealed that RNA Editing of HTR2C is involved in mental disorders. Here we examined RNA Editing efficiencies of site A and D of HTR2C in the prefrontal cortex samples of patients with bipolar disorder, schizophrenia, and major depression as well as control subjects by using primer extension combined with denaturing high performance liquid chromatography. Postmortem samples were donated by the Stanley Foundation Brain Collection. We could not find significant alterations of RNA Editing efficiencies of these sites in patients. However, we found trends for increased RNA Editing efficiencies of site D in depressive patients (P=0.08) and site A in suicide victims (P=0.07). These findings are in accordance with the previous findings, and suggest that altered RNA Editing of HTR2C may have some significance in major depression and suicide.
Ronald B. Emeson - One of the best experts on this subject based on the ideXlab platform.
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Mutations underlying Episodic Ataxia type-1 antagonize Kv1.1 RNA Editing.
Scientific Reports, 2017Co-Authors: Elizabeth A. Ferrick-kiddie, Joshua J. C. Rosenthal, Gregory D. Ayers, Ronald B. EmesonAbstract:: Adenosine-to-inosine RNA Editing in transcripts encoding the voltage-gated potassium channel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from inactivation. Numerous Kv1.1 mutations have been associated with the human disorder Episodic Ataxia Type-1 (EA1), characterized by stress-induced ataxia, myokymia, and increased prevalence of seizures. Three EA1 mutations, V404I, I407M, and V408A, are located within the RNA duplex structure required for RNA Editing. Each mutation decreased RNA Editing both in vitro and using an in vivo mouse model bearing the V408A allele. Editing of transcripts encoding mutant channels affects numerous biophysical properties including channel opening, closing, and inactivation. Thus EA1 symptoms could be influenced not only by the direct effects of the mutations on channel properties, but also by their influence on RNA Editing. These studies provide the first evidence that mutations associated with human genetic disorders can affect cis-regulatory elements to alter RNA Editing.
Toshiharu Shikanai - One of the best experts on this subject based on the ideXlab platform.
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conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA Editing
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Kenji Okuda, Kazuo Shinozaki, Fumiyoshi Myouga, Reiko Motohashi, Toshiharu ShikanaiAbstract:The pentatricopeptide repeat (PPR) proteins form one of the largest families in higher plants and are believed to be involved in the posttranscriptional processes of gene expression in plant organelles. It has been shown by using a genetic approach focusing on NAD(P)H dehydrogenase (NDH) activity that a PPR protein CRR4 is essential for a specific RNA Editing event in chloroplasts. Here, we discovered Arabidopsis crr21 mutants that are specifically impaired in the RNA Editing of the site 2 of ndhD (ndhD-2), which encodes a subunit of the NDH complex. The CRR21 gene encodes a member of the PPR protein family. The RNA Editing of ndhD-2 converts the Ser-128 of NdhD to leucine. In crr21, the activity of the NDH complex is specifically impaired, suggesting that the Ser128Leu change has important consequences for the function of the NDH complex. Both CRR21 and CRR4 belong to the E+ subgroup in the PLS subfamily that is characterized by the presence of a conserved C-terminal region (the E/E+ domain). This E/E+ domain is highly conserved and exchangeable between CRR21 and CRR4, although it is not essential for the RNA binding. Our results suggest that the E/E+ domain has a common function in RNA Editing rather than of recognizing specific RNA sequences.
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conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA Editing
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Kenji Okuda, Kazuo Shinozaki, Fumiyoshi Myouga, Reiko Motohashi, Toshiharu ShikanaiAbstract:The pentatricopeptide repeat (PPR) proteins form one of the largest families in higher plants and are believed to be involved in the posttranscriptional processes of gene expression in plant organelles. It has been shown by using a genetic approach focusing on NAD(P)H dehydrogenase (NDH) activity that a PPR protein CRR4 is essential for a specific RNA Editing event in chloroplasts. Here, we discovered Arabidopsis crr21 mutants that are specifically impaired in the RNA Editing of the site 2 of ndhD (ndhD-2), which encodes a subunit of the NDH complex. The CRR21 gene encodes a member of the PPR protein family. The RNA Editing of ndhD-2 converts the Ser-128 of NdhD to leucine. In crr21, the activity of the NDH complex is specifically impaired, suggesting that the Ser128Leu change has important consequences for the function of the NDH complex. Both CRR21 and CRR4 belong to the E+ subgroup in the PLS subfamily that is characterized by the presence of a conserved C-terminal region (the E/E+ domain). This E/E+ domain is highly conserved and exchangeable between CRR21 and CRR4, although it is not essential for the RNA binding. Our results suggest that the E/E+ domain has a common function in RNA Editing rather than of recognizing specific RNA sequences.
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RNA Editing in plant organelles machinery physiological function and evolution
Cellular and Molecular Life Sciences, 2006Co-Authors: Toshiharu ShikanaiAbstract:In plants, RNA Editing is a process for converting a specific nucleotide of RNA from C to U and less frequently from U to C in mitochondria and plastids. To specify the site of Editing, the cis-element adjacent to the Editing site functions as a binding site for the trans-acting factor. Genetic approaches using Arabidopsis thaliana have clarified that a member of the protein family with pentatricopeptide repeat (PPR) motifs is essential for RNA Editing to generate a translational initiation codon of the chloroplast ndhD gene. The PPR motif is a highly degenerate unit of 35 amino acids and appears as tandem repeats in proteins that are involved in RNA maturation steps in mitochondria and plastids. The Arabidopsis genome encodes approximately 450 members of the PPR family, some of which possibly function as trans-acting factors binding the cis-elements of the RNA Editing sites to facilitate access of an unidentified RNA Editing enzyme. Based on this breakthrough in the research on plant RNA Editing, I would like to discuss the possible steps of co-evolution of RNA Editing events and PPR proteins.
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a pentatricopeptide repeat protein is essential for RNA Editing in chloroplasts
Nature, 2005Co-Authors: Emi Kotera, Toshiharu Shikanai, Masao TasakaAbstract:RNA Editing is a process of RNA maturation involved in the insertion, deletion or modification of nucleotides1. In organellar transcripts of higher plants, specific cytidine residues are converted into uridine residues. In many cases, Editing results in the restoration of conserved amino acid residues, a process that is essential for protein function in plastids2,3. Despite the technical breakthrough in establishing systems in vivo4 and in vitro5 for analysing RNA Editing, its machinery still remains to be identified in higher plants. Here we introduce a genetic approach and report the discovery of a gene responsible for the specific RNA Editing event in the chloroplast.
Anna A Kliuchnikova - One of the best experts on this subject based on the ideXlab platform.
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proteome wide analysis of adar mediated messenger RNA Editing during fruit fly ontogeny
Journal of Proteome Research, 2020Co-Authors: Anna A Kliuchnikova, Anton O Goncharov, Lev I Levitsky, Mikhail A Pyatnitskiy, Svetlana E Novikova, Ksenia G Kuznetsova, Mark V Ivanov, Irina Y Ilina, Tatyana E FarafonovaAbstract:Adenosine-to-inosine RNA Editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. In particular, it involves Editing of mRNA codons with the resulting amino acid substitutions. We identified such sites for developmental proteomes of Drosophila melanogaster at the protein level using available data for 15 stages of fruit fly development from egg to imago and 14 time points of embryogenesis. In total, 40 sites were obtained, each belonging to a unique protein, including four sites related to embryogenesis. The interactome analysis has revealed that the majority of the Editing-recoded proteins were associated with synaptic vesicle trafficking and actomyosin organization. Quantitation data analysis suggested the existence of a phase-specific RNA Editing regulation with yet unknown mechanisms. These findings supported the transcriptome analysis results, which showed that a burst in the RNA Editing occurs during insect metamorphosis from pupa to imago. Finally, targeted proteomic analysis was performed to quantify Editing-recoded and genomically encoded versions of five proteins in brains of larvae, pupae, and imago insects, which showed a clear tendency toward an increase in the Editing rate for each of them. These results will allow a better understanding of the protein role in physiological effects of RNA Editing.
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proteome wide analysis of adar mediated messenger RNA Editing during fruit fly ontogeny
bioRxiv, 2020Co-Authors: Anna A Kliuchnikova, Anton O Goncharov, Lev I Levitsky, Mikhail A Pyatnitskiy, Svetlana E Novikova, Ksenia G Kuznetsova, Mark V Ivanov, Irina Y Ilina, Tatyana E Farafonova, Victor G ZgodaAbstract:Adenosine-to-inosine RNA Editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. Some of its functions are enforced through Editing of mRNA codons with the resulting amino acid substitutions. We identified these sites originated from the RNA Editing for developmental proteomes of Drosophila melanogaster at the protein level using available proteomic data for fifteen stages of fruit fly development from egg to imago and fourteen time points of embryogenesis. In total, 42 sites each belonging to a unique protein were found including four sites related to embryogenesis. The interactome analysis has revealed that most of the edited proteins are associated with synaptic vesicle trafficking and actomyosin organization. Quantitation data analysis suggested the existence of phase-specific RNA Editing regulation by yet unknown mechanisms. These results support transcriptome analyses showing that a burst in RNA Editing occurs during insect metamorphosis from pupa to imago. Further, targeted proteomics was employed to quantify edited and genomically encoded versions of five proteins in brains of larvae, pupae, and imago insects showing a clear trend towards an increase in Editing rate for all of them. Our results may help to reveal the protein functions in physiological effects of RNA Editing. SignificanceAdenosine-to-inosine RNA Editing has multiple effects on body functions in many multicellular organisms from insects and molluscs to humans. Recent studies show that at least some of these effects are mediated by changes in protein sequences due to Editing of codons in mRNA. However, it is not known how exactly the edited proteins can participate in RNA Editing-mediated pathways. Moreover, most studies of edited proteins are based on the deduction of protein sequence changes from analysis of transcriptome without measurements of proteins themselves. Earlier, we explored for the first time the edited proteins of Drosophila melanogaster proteome. In this work, we continued the proteome-wide analysis of RNA editome using shotgun proteomic data of ontogeny phases of this model insect. It was found that non-synonymous RNA Editing, which led to translation of changed proteins, is specific to the life cycle phase. Identification of tryptic peptides containing edited protein sites provides a basis for further direct and quantitative analysis of their Editing rate by targeted proteomics. The latter was demonstrated in this study by multiple reaction monitoring experiments which were used to observe the dynamics of Editing in selected brain proteins during developmental phases of fruit fly. HighlightsO_LIProteogenomic approach was applied to shotgun proteomics data of fruit fly ontogeny for identification of proteoforms originating from adenosine-to-inosine RNA Editing. C_LIO_LIEdited proteins identified at all life cycle stages are enriched in annotated protein-protein interactions at statistically significant level with many of them associated with actomyosin and synaptic vesicle functions. C_LIO_LIProteome-wide RNA Editing event profiles were found specific to life cycle phase and independent of the protein abundances. C_LIO_LIA majority of RNA Editing events at the protein level was observed after metamorphosis in late pupae to adult insects, which was consistent with transcriptome data. C_LIO_LITargeted proteomic analysis of five selected edited sites and their genomic counterparts in brains for three phases of the fruit fly life cycle have demonstrated a clear increase in Editing rate of up to 80% for the endophilin A protein in adult flies. C_LI
