1
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Belur NR, Bustos BI, Lubbe SJ, Mazzulli JR. Nuclear aggregates of NONO/SFPQ and A-to-I-edited RNA in Parkinson's disease and dementia with Lewy bodies. Neuron 2024; 112:2558-2580.e13. [PMID: 38761794 PMCID: PMC11309915 DOI: 10.1016/j.neuron.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 03/06/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
Neurodegenerative diseases are commonly classified as proteinopathies that are defined by the aggregation of a specific protein. Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are classified as synucleinopathies since α-synuclein (α-syn)-containing inclusions histopathologically define these diseases. Unbiased biochemical analysis of PD and DLB patient material unexpectedly revealed novel pathological inclusions in the nucleus comprising adenosine-to-inosine (A-to-I)-edited mRNAs and NONO and SFPQ proteins. These inclusions showed no colocalization with Lewy bodies and accumulated at levels comparable to α-syn. NONO and SFPQ aggregates reduced the expression of the editing inhibitor ADAR3, increasing A-to-I editing mainly within human-specific, Alu-repeat regions of axon, synaptic, and mitochondrial transcripts. Inosine-containing transcripts aberrantly accumulated in the nucleus, bound tighter to recombinant purified SFPQ in vitro, and potentiated SFPQ aggregation in human dopamine neurons, resulting in a self-propagating pathological state. Our data offer new insight into the inclusion composition and pathophysiology of PD and DLB.
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Affiliation(s)
- Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Steven J Lubbe
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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2
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Erdmann EA, Forbes M, Becker M, Perez S, Hundley HA. ADR-2 regulates fertility and oocyte fate in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565157. [PMID: 37961348 PMCID: PMC10635048 DOI: 10.1101/2023.11.01.565157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Here, we report that loss of ADR-2, a member of the Adenosine DeAminase acting on RNA (ADAR) family of RNA binding proteins and the sole adenosine-to-inosine RNA editing enzyme in C. elegans, can improve fertility in multiple genetic backgrounds. First, we show that loss of RNA editing by ADR-2 restores normal embryo production to subfertile animals that transgenically express a vitellogenin (yolk protein) fusion to green fluorescent protein. Using this phenotype, a high-throughput screen was designed to identify RNA binding proteins that when depleted yield synthetic phenotypes with loss of adr-2. The screen uncovered a genetic interaction between ADR-2 and SQD-1, a member of the heterogenous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins. Microscopy, reproductive assays, and high-throughput sequencing reveal that sqd-1 is essential for the onset of oogenesis and oogenic gene expression in young adult animals, and that loss of adr-2 can counteract the effects of loss of sqd-1 on gene expression and rescue the switch from spermatogenesis to oogenesis. Together, these data demonstrate that ADR-2 can contribute to the suppression of fertility and suggest novel roles for both RNA editing-dependent and independent mechanisms in regulating embryogenesis.
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Affiliation(s)
- Emily A. Erdmann
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, US 47405
| | - Melanie Forbes
- Department of Biology, Indiana University, Bloomington IN, US 47405
| | - Margaret Becker
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN, US 47405
| | - Sarina Perez
- Department of Biology, Indiana University, Bloomington IN, US 47405
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3
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Szabo B, Mandl TC, Woldrich B, Diensthuber G, Martin D, Jantsch MF, Licht K. RNA Pol II-dependent transcription efficiency fine-tunes A-to-I editing levels. Genome Res 2024; 34:231-242. [PMID: 38471738 PMCID: PMC10984384 DOI: 10.1101/gr.277686.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
A-to-I RNA editing is a widespread epitranscriptomic phenomenon leading to the conversion of adenosines to inosines, which are primarily interpreted as guanosines by cellular machines. Consequently, A-to-I editing can alter splicing or lead to recoding of transcripts. As misregulation of editing can cause a variety of human diseases, A-to-I editing requires tight regulation of the extent of deamination, particularly in protein-coding regions. The bulk of A-to-I editing occurs cotranscriptionally. Thus, we studied A-to-I editing regulation in the context of transcription and pre-mRNA processing. We show that stimulation of transcription impacts editing levels. Activation of the transcription factor MYC leads to an up-regulation of A-to-I editing, particularly in transcripts that are suppressed upon MYC activation. Moreover, low pre-mRNA synthesis rates and low pre-mRNA expression levels support high levels of editing. We also show that editing levels greatly differ between nascent pre-mRNA and mRNA in a cellular system, as well as in mouse tissues. Editing levels can increase or decrease from pre-mRNA to mRNA and can vary across editing targets and across tissues, showing that pre-mRNA processing is an important layer of editing regulation. Several lines of evidence suggest that the differences emerge during pre-mRNA splicing. Moreover, actinomycin D treatment of primary neuronal cells and editing level analysis suggests that regulation of editing levels also depends on transcription.
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Affiliation(s)
- Brigitta Szabo
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Therese C Mandl
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Bernhard Woldrich
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Gregor Diensthuber
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - David Martin
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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4
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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5
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Avram-Shperling A, Kopel E, Twersky I, Gabay O, Ben-David A, Karako-Lampert S, Rosenthal JJC, Levanon EY, Eisenberg E, Ben-Aroya S. Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms. PLoS Genet 2023; 19:e1010661. [PMID: 36877730 PMCID: PMC10019624 DOI: 10.1371/journal.pgen.1010661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/16/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
The most abundant form of RNA editing in metazoa is the deamination of adenosines into inosines (A-to-I), catalyzed by ADAR enzymes. Inosines are read as guanosines by the translation machinery, and thus A-to-I may lead to protein recoding. The ability of ADARs to recode at the mRNA level makes them attractive therapeutic tools. Several approaches for Site-Directed RNA Editing (SDRE) are currently under development. A major challenge in this field is achieving high on-target editing efficiency, and thus it is of much interest to identify highly potent ADARs. To address this, we used the baker yeast Saccharomyces cerevisiae as an editing-naïve system. We exogenously expressed a range of heterologous ADARs and identified the hummingbird and primarily mallard-duck ADARs, which evolved at 40-42°C, as two exceptionally potent editors. ADARs bind to double-stranded RNA structures (dsRNAs), which in turn are temperature sensitive. Our results indicate that species evolved to live with higher core body temperatures have developed ADAR enzymes that target weaker dsRNA structures and would therefore be more effective than other ADARs. Further studies may use this approach to isolate additional ADARs with an editing profile of choice to meet specific requirements, thus broadening the applicability of SDRE.
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Affiliation(s)
- Adi Avram-Shperling
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orshay Gabay
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Joshua J. C. Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EE); (SB-A)
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail: (EE); (SB-A)
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6
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Jimeno S, Prados-Carvajal R, Fernández-Ávila MJ, Silva S, Silvestris DA, Endara-Coll M, Rodríguez-Real G, Domingo-Prim J, Mejías-Navarro F, Romero-Franco A, Jimeno-González S, Barroso S, Cesarini V, Aguilera A, Gallo A, Visa N, Huertas P. ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair. Nat Commun 2021; 12:5512. [PMID: 34535666 PMCID: PMC8448848 DOI: 10.1038/s41467-021-25790-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
The maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution.
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Affiliation(s)
- Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
| | - Rosario Prados-Carvajal
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - María Jesús Fernández-Ávila
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Sonia Silva
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Domenico Alessandro Silvestris
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Martín Endara-Coll
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Guillermo Rodríguez-Real
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Moirai Biodesign SL, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Fernando Mejías-Navarro
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Amador Romero-Franco
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Sonia Barroso
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Valeriana Cesarini
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Andrés Aguilera
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Angela Gallo
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
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7
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Suzuki H, Matsuoka M. Proline-arginine poly-dipeptide encoded by the C9orf72 repeat expansion inhibits adenosine deaminase acting on RNA. J Neurochem 2021; 158:753-765. [PMID: 34081786 DOI: 10.1111/jnc.15445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
A GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9-ALS/FTD). Unconventional translation of the hexanucleotide repeat expansion generates five dipeptide repeat proteins (DPRs). The molecular mechanism underlying the DPR-linked neurotoxicity is under investigation. In this study, using cell-based models, we show that poly-proline-arginine DPR (poly-PR), the most neurotoxic DPR in vitro, binds to adenosine deaminase acting on RNA (ADAR)1p110 and ADAR2 and inhibits their RNA editing activity. We further show that poly-PR impairs cellular stress response that is mediated by ADAR1p110. These results together suggest that the poly-PR-mediated inhibition of the ADAR activity contributes to C9-ALS/FTD-linked neurotoxicity.
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Affiliation(s)
- Hiroaki Suzuki
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
| | - Masaaki Matsuoka
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
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8
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Freund EC, Sapiro AL, Li Q, Linder S, Moresco JJ, Yates JR, Li JB. Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing. Cell Rep 2021; 31:107656. [PMID: 32433965 DOI: 10.1016/j.celrep.2020.107656] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/11/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes that deaminate adenosine to inosine. Although many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data, we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a broadly influential negative regulator of editing. This work demonstrates the broad roles that RNA binding proteins play in regulating editing levels, and establishes DZF-domain-containing proteins as a group of highly influential RNA editing regulators.
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Affiliation(s)
- Emily C Freund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne L Sapiro
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Linder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James J Moresco
- Department of Molecular Medicine, 10550 North Torrey Pines Road, SR302, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, 10550 North Torrey Pines Road, SR302, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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9
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Sapiro AL, Freund EC, Restrepo L, Qiao HH, Bhate A, Li Q, Ni JQ, Mosca TJ, Li JB. Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons. Cell Rep 2021; 31:107654. [PMID: 32433963 PMCID: PMC7306179 DOI: 10.1016/j.celrep.2020.107654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/11/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, alters RNA sequences from those encoded by DNA. These editing events are dynamically regulated, but few trans regulators of ADARs are known in vivo. Here, we screen RNA-binding proteins for roles in editing regulation with knockdown experiments in the Drosophila brain. We identify zinc-finger protein at 72D (Zn72D) as a regulator of editing levels at a majority of editing sites in the brain. Zn72D both regulates ADAR protein levels and interacts with ADAR in an RNA-dependent fashion, and similar to ADAR, Zn72D is necessary to maintain proper neuromuscular junction architecture and fly mobility. Furthermore, Zn72D’s regulatory role in RNA editing is conserved because the mammalian homolog of Zn72D, Zfr, regulates editing in mouse primary neurons. The broad and conserved regulation of ADAR editing by Zn72D in neurons sustains critically important editing events. Sapiro et al. identify Drosophila Zn72D as an influential regulator of neuronal A-to-I RNA editing and synaptic morphology. Zn72D regulates ADAR levels and editing at a large subset of editing sites, providing insight into the maintenance of critical tissue-specific RNA editing events.
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Affiliation(s)
- Anne L Sapiro
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emily C Freund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lucas Restrepo
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Huan-Huan Qiao
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Timothy J Mosca
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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10
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Destefanis E, Avşar G, Groza P, Romitelli A, Torrini S, Pir P, Conticello SG, Aguilo F, Dassi E. A mark of disease: how mRNA modifications shape genetic and acquired pathologies. RNA (NEW YORK, N.Y.) 2021; 27:367-389. [PMID: 33376192 PMCID: PMC7962492 DOI: 10.1261/rna.077271.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). In mRNAs the deposition, removal, and recognition of chemical marks by writers, erasers and readers influence their structure, localization, stability, and translation. In turn, this modulates key molecular and cellular processes such as RNA metabolism, cell cycle, apoptosis, and others. Unsurprisingly, given their relevance for cellular and organismal functions, alterations of epitranscriptomic marks have been observed in a broad range of human diseases, including cancer, neurological and metabolic disorders. Here, we will review the major types of mRNA modifications and editing processes in conjunction with the enzymes involved in their metabolism and describe their impact on human diseases. We present the current knowledge in an updated catalog. We will also discuss the emerging evidence on the crosstalk of epitranscriptomic marks and what this interplay could imply for the dynamics of mRNA modifications. Understanding how this complex regulatory layer can affect the course of human pathologies will ultimately lead to its exploitation toward novel epitranscriptomic therapeutic strategies.
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Affiliation(s)
- Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
| | - Gülben Avşar
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Paula Groza
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Antonia Romitelli
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Serena Torrini
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Pınar Pir
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Silvestro G Conticello
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Francesca Aguilo
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
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11
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Abstract
RNA editing is an RNA modification that alters the RNA sequence relative to its genomic blueprint. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Editing of a protein-coding region within the RNA molecule may result in non-synonymous substitutions, leading to a modified protein product. These editing sites, also known as "recoding" sites, contribute to the complexity and diversification of the proteome. Recent computational transcriptomic studies have identified thousands of recoding sites in multiple species, many of which are conserved within (but not usually across) lineages and have functional and evolutionary importance. In this chapter we describe the recoding phenomenon across species, consider its potential utility for diversity and adaptation, and discuss its evolution.
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12
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Schaffer AA, Levanon EY. ALU A-to-I RNA Editing: Millions of Sites and Many Open Questions. Methods Mol Biol 2021; 2181:149-162. [PMID: 32729079 DOI: 10.1007/978-1-0716-0787-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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13
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Tan TY, Sedmík J, Fitzgerald MP, Halevy RS, Keegan LP, Helbig I, Basel-Salmon L, Cohen L, Straussberg R, Chung WK, Helal M, Maroofian R, Houlden H, Juusola J, Sadedin S, Pais L, Howell KB, White SM, Christodoulou J, O'Connell MA. Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures. Am J Hum Genet 2020; 106:467-483. [PMID: 32220291 DOI: 10.1016/j.ajhg.2020.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.
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Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Mark P Fitzgerald
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rivka Sukenik Halevy
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Felsenstein Medical Research Center, Petah Tikva 49100, Israel
| | - Lior Cohen
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Pediatric Neurology Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Mayada Helal
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Simon Sadedin
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katherine B Howell
- Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia; Department of Neurology, Royal Children's Hospital, Parkville 3052, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic.
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14
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Jain M, Jantsch MF, Licht K. The Editor's I on Disease Development. Trends Genet 2019; 35:903-913. [PMID: 31648814 DOI: 10.1016/j.tig.2019.09.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventing autoimmune disorders. Interestingly, A-to-I editing can be used not only to correct genomic mutations at the RNA level but also to modulate tumor antigenicity with large therapeutic potential. We highlight recent developments in the field, focusing on cancer and other human diseases.
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Affiliation(s)
- Mamta Jain
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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15
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Roth SH, Levanon EY, Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat Methods 2019; 16:1131-1138. [PMID: 31636457 DOI: 10.1038/s41592-019-0610-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing by the adenosine deaminase that acts on RNA (ADAR) enzymes is a common RNA modification, preventing false activation of the innate immune system by endogenous double-stranded RNAs. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and autoimmune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. Here, we present the Alu editing index (AEI), a robust and simple-to-use computational tool devised for this purpose. We describe its properties and demonstrate its superiority to current quantification methods of ADAR activity. The AEI is used to map global editing across a large dataset of healthy human samples and identify putative regulators of ADAR, as well as previously unknown factors affecting the observed Alu editing levels. These should be taken into account in future comparative studies of ADAR activity. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer.
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Affiliation(s)
- Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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16
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Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M. Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries. Nucleic Acids Res 2019; 47:e22. [PMID: 30590609 PMCID: PMC6393238 DOI: 10.1093/nar/gky1228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
Adenosine to inosine editing is common in the human transcriptome and changes of this essential activity is associated with disease. Children with ADAR1 mutations develop fatal Aicardi-Goutières syndrome characterized by aberrant interferon expression. In contrast, ADAR1 overexpression is associated with increased malignancy of breast, lung and liver cancer. ADAR1 silencing in breast cancer cells leads to increased apoptosis, suggesting an anti-apoptotic function that promotes cancer progression. Yet, suitable high-throughput editing assays are needed to efficiently screen chemical libraries for modifiers of ADAR1 activity. We describe the development of a bioluminescent reporter system that facilitates rapid and accurate determination of endogenous editing activity. The system is based on the highly sensitive and quantitative Nanoluciferase that is conditionally expressed upon reporter-transcript editing. Stably introduced into cancer cell lines, the system reports on elevated endogenous ADAR1 editing activity induced by interferon as well as knockdown of ADAR1 and ADAR2. In a single-well setup we used the reporter in HeLa cells to screen a small molecule library of 33 000 compounds. This yielded a primary hit rate of 0.9% at 70% inhibition of editing. Thus, we provide a key tool for high-throughput identification of modifiers of A-to-I editing activity in cancer cells.
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Affiliation(s)
- Kajsa Fritzell
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Li-Di Xu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
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17
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Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing. Genome Res 2019; 29:1453-1463. [PMID: 31427386 PMCID: PMC6724681 DOI: 10.1101/gr.242636.118] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 07/25/2019] [Indexed: 11/25/2022]
Abstract
Pre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs). Editing-competent stems are frequently formed between exons and introns. Consistently, studies using reporter assays have shown that splicing efficiency can affect editing levels. Here, we use Nascent-seq and identify ∼90,000 novel A-to-I editing events in the mouse brain transcriptome. Most novel sites are located in intronic regions. Unlike previously assumed, we show that both ADAR (ADAR1) and ADARB1 (ADAR2) can edit repeat elements and regular transcripts to the same extent. We find that inhibition of splicing primarily increases editing levels at hundreds of sites, suggesting that reduced splicing efficiency extends the exposure of intronic and exonic sequences to ADAR enzymes. Lack of splicing factors NOVA1 or NOVA2 changes global editing levels, demonstrating that alternative splicing factors can modulate RNA editing. Finally, we show that intron retention rates correlate with editing levels across different brain tissues. We therefore demonstrate that splicing efficiency is a major factor controlling tissue-specific differences in editing levels.
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Affiliation(s)
- Konstantin Licht
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Utkarsh Kapoor
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, I-70126 Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
| | - David Martin
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Prajakta Bajad
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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18
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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19
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Piontkivska H, Plonski NM, Miyamoto MM, Wayne ML. Explaining Pathogenicity of Congenital Zika and Guillain-Barré Syndromes: Does Dysregulation of RNA Editing Play a Role? Bioessays 2019; 41:e1800239. [PMID: 31106880 PMCID: PMC6699488 DOI: 10.1002/bies.201800239] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2019] [Indexed: 12/11/2022]
Abstract
Previous studies of Zika virus (ZIKV) pathogenesis have focused primarily on virus-driven pathology and neurotoxicity, as well as host-related changes in cell proliferation, autophagy, immunity, and uterine function. It is now hypothesized that ZIKV pathogenesis arises instead as an (unintended) consequence of host innate immunity, specifically, as the side effect of an otherwise well-functioning machine. The hypothesis presented here suggests a new way of thinking about the role of host immune mechanisms in disease pathogenesis, focusing on dysregulation of post-transcriptional RNA editing as a candidate driver of a broad range of observed neurodevelopmental defects and neurodegenerative clinical symptoms in both infants and adults linked with ZIKV infections. The authors collect and synthesize existing evidence of ZIKV-mediated changes in the expression of adenosine deaminases acting on RNA (ADARs), known links between abnormal RNA editing and pathogenesis, as well as ideas for future research directions, including potential treatment strategies.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences and University, Kent, OH
44242, USA
- School of Biomedical Sciences, Kent State University, Kent,
OH 44242, USA
| | - Noel-Marie Plonski
- School of Biomedical Sciences, Kent State University, Kent,
OH 44242, USA
| | | | - Marta L. Wayne
- Department of Biology, University of Florida, Gainesville,
FL 32611, USA
- Emerging Pathogens Institute, University of Florida,
Gainesville, FL 32611, USA
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20
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Sinigaglia K, Wiatrek D, Khan A, Michalik D, Sambrani N, Sedmík J, Vukić D, O'Connell MA, Keegan LP. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:356-369. [DOI: 10.1016/j.bbagrm.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/12/2018] [Accepted: 10/27/2018] [Indexed: 01/24/2023]
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21
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Abstract
Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.
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22
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Giacopuzzi E, Gennarelli M, Sacco C, Filippini A, Mingardi J, Magri C, Barbon A. Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables. BMC Genomics 2018; 19:963. [PMID: 30587120 PMCID: PMC6307200 DOI: 10.1186/s12864-018-5364-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing contributes to generate transcriptomic diversity and it is found altered in cancer, autoimmune and neurological disorders. Emerging evidences indicate that editing process could be influenced by genetic variations, biological and environmental variables. RESULTS We analyzed RNA editing levels in human blood using RNA-seq data from 459 healthy individuals and identified 2079 sites consistently edited in this tissue. As expected, analysis of gene expression revealed that ADAR is the major contributor to editing on these sites, explaining ~ 13% of observed variability. After removing ADAR effect, we found significant associations for 1122 genes, mainly involved in RNA processing. These genes were significantly enriched in genes encoding proteins interacting with ADARs, including 276 potential ADARs interactors and 9 ADARs direct partners. In addition, our analysis revealed several factors potentially influencing RNA editing in blood, including cell composition, age, Body Mass Index, smoke and alcohol consumption. Finally, we identified genetic loci associated with editing levels, including known ADAR eQTLs and a small region on chromosome 7, containing LOC730338, a lincRNA gene that appears to modulate ADARs mRNA expression. CONCLUSIONS Our data provides a detailed picture of the most relevant RNA editing events and their variability in human blood, giving interesting insights on potential mechanisms behind this post-transcriptional modification and its regulation in this tissue.
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Affiliation(s)
- Edoardo Giacopuzzi
- Genetics Unit, IRCCS Istituto Centro S. Giovanni di Dio, Fatebenefratelli, 25123 Brescia, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro S. Giovanni di Dio, Fatebenefratelli, 25123 Brescia, Italy
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
| | - Chiara Sacco
- Genetics Unit, IRCCS Istituto Centro S. Giovanni di Dio, Fatebenefratelli, 25123 Brescia, Italy
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
| | - Alice Filippini
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
| | - Jessica Mingardi
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
| | - Alessandro Barbon
- Department of Molecular and Translational Medicine, Biology and Genetic Unit, University of Brescia, 25123 Brescia, Italy
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23
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Kung CP, Maggi LB, Weber JD. The Role of RNA Editing in Cancer Development and Metabolic Disorders. Front Endocrinol (Lausanne) 2018; 9:762. [PMID: 30619092 PMCID: PMC6305585 DOI: 10.3389/fendo.2018.00762] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.
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Affiliation(s)
- Che-Pei Kung
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Leonard B. Maggi
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jason D. Weber
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
- Siteman Cancer Center, Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, United States
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24
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Shallev L, Kopel E, Feiglin A, Leichner GS, Avni D, Sidi Y, Eisenberg E, Barzilai A, Levanon EY, Greenberger S. Decreased A-to-I RNA editing as a source of keratinocytes' dsRNA in psoriasis. RNA (NEW YORK, N.Y.) 2018; 24:828-840. [PMID: 29592874 PMCID: PMC5959251 DOI: 10.1261/rna.064659.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/26/2018] [Indexed: 05/30/2023]
Abstract
Recognition of dsRNA molecules activates the MDA5-MAVS pathway and plays a critical role in stimulating type-I interferon responses in psoriasis. However, the source of the dsRNA accumulation in psoriatic keratinocytes remains largely unknown. A-to-I RNA editing is a common co- or post-transcriptional modification that diversifies adenosine in dsRNA, and leads to unwinding of dsRNA structures. Thus, impaired RNA editing activity can result in an increased load of endogenous dsRNAs. Here we provide a transcriptome-wide analysis of RNA editing across dozens of psoriasis patients, and we demonstrate a global editing reduction in psoriatic lesions. In addition to the global alteration, we also detect editing changes in functional recoding sites located in the IGFBP7, COPA, and FLNA genes. Accretion of dsRNA activates autoimmune responses, and therefore the results presented here, linking for the first time an autoimmune disease to reduction in global editing level, are relevant to a wide range of autoimmune diseases.
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Affiliation(s)
- Lea Shallev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Kopel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ariel Feiglin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gil S Leichner
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dror Avni
- Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Yechezkel Sidi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Aviv Barzilai
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shoshana Greenberger
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer 52621, Israel
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25
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Schaefer M, Kapoor U, Jantsch MF. Understanding RNA modifications: the promises and technological bottlenecks of the 'epitranscriptome'. Open Biol 2018; 7:rsob.170077. [PMID: 28566301 PMCID: PMC5451548 DOI: 10.1098/rsob.170077] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023] Open
Abstract
The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the ‘epitranscriptome’. Here, we review some of the technological advances in this rapidly developing field, identify the conceptual challenges and discuss approaches that are needed to rigorously test the biological function of specific RNA modifications.
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Affiliation(s)
- Matthias Schaefer
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
| | - Utkarsh Kapoor
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
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26
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Filippini A, Bonini D, Giacopuzzi E, La Via L, Gangemi F, Colombi M, Barbon A. Differential Enzymatic Activity of Rat ADAR2 Splicing Variants Is Due to Altered Capability to Interact with RNA in the Deaminase Domain. Genes (Basel) 2018; 9:genes9020079. [PMID: 29419780 PMCID: PMC5852575 DOI: 10.3390/genes9020079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 12/17/2022] Open
Abstract
In mammals, adenosine (A) to inosine (I) RNA editing is performed by adenosine deaminases acting on RNA (ADAR), ADAR1 and ADAR2 enzymes, encoded by mRNAs that might undergo splicing process. In rat, two splicing events produce several isoforms of ADAR2, called ADAR2a, ADAR2b, ADAR2e, and ADAR2f, but only ADAR2a and ADAR2b are translated into an active protein. In particular, they differ for ten amino acids located in the catalytic domain of ADAR2b. Here, we focused on these two isoforms, analyzing the splicing pattern and their different function during rat neuronal maturation. We found an increase of editing levels in cortical neurons overexpressing ADAR2a compared to those overexpressing ADAR2b. These results indicate ADAR2a isoform as the most active one, as reported for the homologous human short variant. Furthermore, we showed that the differential editing activity is not due to a different dimerization of the two isoforms; it seems to be linked to the ten amino acids loop of ADAR2b that might interfere with RNA binding, occupying the space volume in which the RNA should be present in case of binding. These data might shed light on the complexity of ADAR2 regulations.
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Affiliation(s)
- Alice Filippini
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Daniela Bonini
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Edoardo Giacopuzzi
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Luca La Via
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Fabrizio Gangemi
- Division of Physics, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Marina Colombi
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
| | - Alessandro Barbon
- Division of Biology and Genetics-Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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27
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Abstract
One of the most prevalent forms of post-transcritpional RNA modification is the conversion of adenosine nucleosides to inosine (A-to-I), mediated by the ADAR family of enzymes. The functional requirement and regulatory landscape for the majority of A-to-I editing events are, at present, uncertain. Recent studies have identified key in vivo functions of ADAR enzymes, informing our understanding of the biological importance of A-to-I editing. Large-scale studies have revealed how editing is regulated both in cis and in trans. This review will explore these recent studies and how they broaden our understanding of the functions and regulation of ADAR-mediated RNA editing.
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Affiliation(s)
- Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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28
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Abstract
Concentration is important and not only while driving; a new study indicates how an adjacent genomic element helps to increase the efficiency of a specific adenosine to inosine RNA editing reaction, by providing a means to increase the local concentration of the RNA editing enzyme ADAR.
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Affiliation(s)
- Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
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29
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Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals. Nature 2017; 550:249-254. [PMID: 29022589 PMCID: PMC5723435 DOI: 10.1038/nature24041] [Citation(s) in RCA: 394] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 08/30/2017] [Indexed: 02/08/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.
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Affiliation(s)
- Meng How Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Qin Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Robert Piskol
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jennefer Kohler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Amy N Young
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kaiwen Ivy Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Rui Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Ankita Gupte
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Liam P Keegan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Cyril X George
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Y P Sharon Goh
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Gary Peltz
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Mary A O'Connell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | | | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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30
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Filippini A, Bonini D, Lacoux C, Pacini L, Zingariello M, Sancillo L, Bosisio D, Salvi V, Mingardi J, La Via L, Zalfa F, Bagni C, Barbon A. Absence of the Fragile X Mental Retardation Protein results in defects of RNA editing of neuronal mRNAs in mouse. RNA Biol 2017. [PMID: 28640668 PMCID: PMC5785225 DOI: 10.1080/15476286.2017.1338232] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The fragile X syndrome (FXS), the most common form of inherited intellectual disability, is due to the absence of FMRP, a protein regulating RNA metabolism. Recently, an unexpected function of FMRP in modulating the activity of Adenosine Deaminase Acting on RNA (ADAR) enzymes has been reported both in Drosophila and Zebrafish. ADARs are RNA-binding proteins that increase transcriptional complexity through a post-transcriptional mechanism called RNA editing. To evaluate the ADAR2-FMRP interaction in mammals we analyzed several RNA editing re-coding sites in the fmr1 knockout (KO) mice. Ex vivo and in vitro analysis revealed that absence of FMRP leads to an increase in the editing levels of brain specific mRNAs, indicating that FMRP might act as an inhibitor of editing activity. Proximity Ligation Assay (PLA) in mouse primary cortical neurons and in non-neuronal cells revealed that ADAR2 and FMRP co-localize in the nucleus. The ADAR2-FMRP co-localization was further observed by double-immunogold Electron Microscopy (EM) in the hippocampus. Moreover, ADAR2-FMRP interaction appeared to be RNA independent. Because changes in the editing pattern are associated with neuropsychiatric and neurodevelopmental disorders, we propose that the increased editing observed in the fmr1-KO mice might contribute to the FXS molecular phenotypes.
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Affiliation(s)
- Alice Filippini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Daniela Bonini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Caroline Lacoux
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Laura Pacini
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Maria Zingariello
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Laura Sancillo
- d Department of Medicine and Aging Sciences, Section of Human Morphology , University G. D'Annunzio of Chieti-Pescara , Chieti , Italy
| | - Daniela Bosisio
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Valentina Salvi
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Jessica Mingardi
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Luca La Via
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Francesca Zalfa
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Claudia Bagni
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy.,f VIB Center for the Biology of Disease and Center for Human Genetics , Leuven , Belgium.,g Department of Fundamental Neuroscience , University of Lausanne , Lausanne , Switzerland
| | - Alessandro Barbon
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
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31
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Anantharaman A, Gholamalamdari O, Khan A, Yoon JH, Jantsch MF, Hartner JC, Gorospe M, Prasanth SG, Prasanth KV. RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA. FEBS Lett 2017; 591:2890-2904. [PMID: 28833069 DOI: 10.1002/1873-3468.12795] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/03/2017] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
Abstract
Adenosine deaminases acting on RNA (ADARs) are proteins that catalyse widespread A-to-I editing within RNA sequences. We recently reported that ADAR2 edits and stabilizes nuclear-retained Cat2 transcribed nuclear RNA (Ctn RNA). Here, we report that ADAR1 coordinates with ADAR2 to regulate editing and stability of Ctn RNA. We observe an RNA-dependent interaction between ADAR1 and ADAR2. Furthermore, ADAR1 negatively regulates interaction of Ctn RNA with RNA-destabilizing proteins. We also show that breast cancer (BC) cells display elevated ADAR1 but not ADAR2 levels, compared to nontumourigenic cells. Additionally, BC patients with elevated levels of ADAR1 show low survival. Our findings provide insights into overlapping substrate preferences of ADARs and potential involvement of ADAR1 in BC.
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Affiliation(s)
- Aparna Anantharaman
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research Program, NIH, Baltimore, MD, USA
| | - Michael F Jantsch
- Department for Medical Biochemistry, Center for Anatomy and Cell Biology, Medical University of Vienna, Austria
| | | | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute of Aging-Intramural Research Program, NIH, Baltimore, MD, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL, USA
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32
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Abstract
Inosine is one of the most common modifications found in human RNAs and the Adenosine Deaminases that act on RNA (ADARs) are the main enzymes responsible for its production. ADARs were first discovered in the 1980s and since then our understanding of ADARs has advanced tremendously. For instance, it is now known that defective ADAR function can cause human diseases. Furthermore, recently solved crystal structures of the human ADAR2 deaminase bound to RNA have provided insights regarding the catalytic and substrate recognition mechanisms. In this chapter, we describe the occurrence of inosine in human RNAs and the newest perspective on the ADAR family of enzymes, including their substrate recognition, catalytic mechanism, regulation as well as the consequences of A-to-I editing, and their relation to human diseases.
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33
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Oakes E, Anderson A, Cohen-Gadol A, Hundley HA. Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma. J Biol Chem 2017; 292:4326-4335. [PMID: 28167531 DOI: 10.1074/jbc.m117.779868] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/05/2017] [Indexed: 01/08/2023] Open
Abstract
RNA editing is a cellular process that precisely alters nucleotide sequences, thus regulating gene expression and generating protein diversity. Over 60% of human transcripts undergo adenosine to inosine RNA editing, and editing is required for normal development and proper neuronal function of animals. Editing of one adenosine in the transcript encoding the glutamate receptor subunit B, glutamate receptor ionotropic AMPA 2 (GRIA2), modifies a codon, replacing the genomically encoded glutamine (Q) with arginine (R); thus this editing site is referred to as the Q/R site. Editing at the Q/R site of GRIA2 is essential, and reduced editing of GRIA2 transcripts has been observed in patients suffering from glioblastoma. In glioblastoma, incorporation of unedited GRIA2 subunits leads to a calcium-permeable glutamate receptor, which can promote cell migration and tumor invasion. In this study, we identify adenosine deaminase that acts on RNA 3 (ADAR3) as an important regulator of Q/R site editing, investigate its mode of action, and detect elevated ADAR3 expression in glioblastoma tumors compared with adjacent brain tissue. Overexpression of ADAR3 in astrocyte and astrocytoma cell lines inhibits RNA editing at the Q/R site of GRIA2 Furthermore, the double-stranded RNA binding domains of ADAR3 are required for repression of RNA editing. As the Q/R site of GRIA2 is specifically edited by ADAR2, we suggest that ADAR3 directly competes with ADAR2 for binding to GRIA2 transcript, inhibiting RNA editing, as evidenced by the direct binding of ADAR3 to the GRIA2 pre-mRNA. Finally, we provide evidence that both ADAR2 and ADAR3 expression contributes to the relative level of GRIA2 editing in tumors from patients suffering from glioblastoma.
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Affiliation(s)
| | - Ashley Anderson
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
| | - Aaron Cohen-Gadol
- Department of Neurological Surgery, Goodman Campbell Brain and Spine, Indianapolis, Indiana 46202
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
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34
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Behm M, Wahlstedt H, Widmark A, Eriksson M, Öhman M. Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development. J Cell Sci 2017; 130:745-753. [PMID: 28082424 DOI: 10.1242/jcs.200055] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/30/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine to inosine (A-to-I) RNA editing is important for a functional brain, and most known sites that are subject to selective RNA editing have been found to result in diversified protein isoforms that are involved in neurotransmission. In the absence of the active editing enzymes ADAR1 or ADAR2 (also known as ADAR and ADARB1, respectively), mice fail to survive until adulthood. Nuclear A-to-I editing of neuronal transcripts is regulated during brain development, with low levels of editing in the embryo and a dramatic increase after birth. Yet, little is known about the mechanisms that regulate editing during development. Here, we demonstrate lower levels of ADAR2 in the nucleus of immature neurons than in mature neurons. We show that importin-α4 (encoded by Kpna3), which increases during neuronal maturation, interacts with ADAR2 and contributes to the editing efficiency by bringing it into the nucleus. Moreover, we detect an increased number of interactions between ADAR2 and the nuclear isomerase Pin1 as neurons mature, which contribute to ADAR2 protein stability. Together, these findings explain how the nuclear editing of substrates that are important for neuronal function can increase as the brain develops.
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Affiliation(s)
- Mikaela Behm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Helene Wahlstedt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Maria Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
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35
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Wang Y, Beal PA. Probing RNA recognition by human ADAR2 using a high-throughput mutagenesis method. Nucleic Acids Res 2016; 44:9872-9880. [PMID: 27614075 PMCID: PMC5175354 DOI: 10.1093/nar/gkw799] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 01/05/2023] Open
Abstract
Adenosine deamination is one of the most prevalent post-transcriptional modifications in mRNA. In humans, ADAR1 and ADAR2 catalyze this modification and their malfunction correlates with disease. Recently our laboratory reported crystal structures of the human ADAR2 deaminase domain bound to duplex RNA revealing a protein loop that binds the RNA on the 5′ side of the modification site. This 5′ binding loop appears to be one contributor to substrate specificity differences between ADAR family members. In this study, we endeavored to reveal detailed structure–activity relationships in this loop to advance our understanding of RNA recognition by ADAR2. To achieve this goal, we established a high-throughput mutagenesis approach which allows rapid screening of ADAR variants in single yeast cells and provides quantitative evaluation for enzymatic activity. Using this approach, we determined the importance of specific amino acids at 19 different positions in the ADAR2 5′ binding loop and revealed six residues that provide essential structural elements supporting the fold of the loop and key RNA-binding functional groups. This work provided new insight into RNA recognition by ADAR2 and established a new tool for defining structure–function relationships in ADAR reactions.
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Affiliation(s)
- Yuru Wang
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
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Dynamic regulation of RNA editing in human brain development and disease. Nat Neurosci 2016; 19:1093-9. [DOI: 10.1038/nn.4337] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/27/2016] [Indexed: 02/07/2023]
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Licht K, Kapoor U, Mayrhofer E, Jantsch MF. Adenosine to Inosine editing frequency controlled by splicing efficiency. Nucleic Acids Res 2016; 44:6398-408. [PMID: 27112566 PMCID: PMC5291252 DOI: 10.1093/nar/gkw325] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 04/14/2016] [Indexed: 11/22/2022] Open
Abstract
Alternative splicing and adenosine to inosine (A to I) RNA-editing are major factors leading to co- and post-transcriptional modification of genetic information. Both, A to I editing and splicing occur in the nucleus. As editing sites are frequently defined by exon–intron basepairing, mRNA splicing efficiency should affect editing levels. Moreover, splicing rates affect nuclear retention and will therefore also influence the exposure of pre-mRNAs to the editing-competent nuclear environment. Here, we systematically test the influence of splice rates on RNA-editing using reporter genes but also endogenous substrates. We demonstrate for the first time that the extent of editing is controlled by splicing kinetics when editing is guided by intronic elements. In contrast, editing sites that are exclusively defined by exonic structures are almost unaffected by the splicing efficiency of nearby introns. In addition, we show that editing levels in pre- and mature mRNAs do not match. This phenomenon can in part be explained by the editing state of an RNA influencing its splicing rate but also by the binding of the editing enzyme ADAR that interferes with splicing.
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Affiliation(s)
- Konstantin Licht
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Utkarsh Kapoor
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Elisa Mayrhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Michael F Jantsch
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna 1030, Austria
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Khermesh K, D'Erchia AM, Barak M, Annese A, Wachtel C, Levanon EY, Picardi E, Eisenberg E. Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease. RNA (NEW YORK, N.Y.) 2016; 22:290-302. [PMID: 26655226 PMCID: PMC4712678 DOI: 10.1261/rna.054627.115] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/18/2015] [Indexed: 05/20/2023]
Abstract
Adenosine to inosine (A-to-I) RNA editing, catalyzed by the ADAR enzyme family, acts on dsRNA structures within pre-mRNA molecules. Editing of the coding part of the mRNA may lead to recoding, amino acid substitution in the resulting protein, possibly modifying its biochemical and biophysical properties. Altered RNA editing patterns have been observed in various neurological pathologies. Here, we present a comprehensive study of recoding by RNA editing in Alzheimer's disease (AD), the most common cause of irreversible dementia. We have used a targeted resequencing approach supplemented by a microfluidic-based high-throughput PCR coupled with next-generation sequencing to accurately quantify A-to-I RNA editing levels in a preselected set of target sites, mostly located within the coding sequence of synaptic genes. Overall, editing levels decreased in AD patients' brain tissues, mainly in the hippocampus and to a lesser degree in the temporal and frontal lobes. Differential RNA editing levels were observed in 35 target sites within 22 genes. These results may shed light on a possible association between the neurodegenerative processes typical for AD and deficient RNA editing.
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Affiliation(s)
- Khen Khermesh
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Michal Barak
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anita Annese
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy
| | - Chaim Wachtel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Eli Eisenberg
- Sagol School of Neuroscience and Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, 69978, Israel
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RNA Editing: A Contributor to Neuronal Dynamics in the Mammalian Brain. Trends Genet 2016; 32:165-175. [PMID: 26803450 DOI: 10.1016/j.tig.2015.12.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 01/10/2023]
Abstract
Post-transcriptional RNA modification by adenosine to inosine (A-to-I) editing expands the functional output of many important neuronally expressed genes. The mechanism provides flexibility in the proteome by expanding the variety of isoforms, and is a requisite for neuronal function. Indeed, targets for editing include key mediators of synaptic transmission with an overall significant effect on neuronal signaling. In addition, editing influences splice-site choice and miRNA targeting capacity, and thereby regulates neuronal gene expression. Editing efficiency at most of these sites increases during neuronal differentiation and brain maturation in a spatiotemporal manner. This editing-induced dynamics in the transcriptome is essential for normal brain development, and we are only beginning to understand its role in neuronal function. In this review we discuss the impact of RNA editing in the brain, with special emphasis on the physiological consequences for neuronal development and plasticity.
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Severi F, Conticello SG. Flow-cytometric visualization of C>U mRNA editing reveals the dynamics of the process in live cells. RNA Biol 2016; 12:389-97. [PMID: 25806564 PMCID: PMC4615904 DOI: 10.1080/15476286.2015.1026033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
APOBEC1 is the catalytic subunit of the complex that edits ApolipoproteinB (ApoB) mRNA, which specifically deaminates cytidine 6666 to uracil in the human transcript. The editing leads to the generation of a stop codon, resulting in the synthesis of a truncated form of ApoB. We have developed a method to quantitatively assay ApoB RNA editing in live cells by using a double fluorescent mCherry-EGFP chimera containing a ∼300bp fragment encompassing the region of ApoB subject to RNA editing. Coexpression of APOBEC1 together with this chimera causes specific RNA editing of the ApoB fragment. The insertion of a stop codon between the mCherry and EGFP thus induces the loss of EGFP fluorescence. Using this method we analyze the dynamics of APOBEC1-dependent RNA editing under various conditions. Namely we show the interplay of APOBEC1 with known interactors (ACF, hnRNP-C1, GRY-RBP) in cells that are RNA editing-proficient (HuH-7) or -deficient (HEK-293T), and the effects of restricted cellular localization of APOBEC1 on the efficiency of the editing. Furthermore, our approach is effective in assaying the induction of RNA editing in Caco-2, a cellular model physiologically capable of ApoB RNA editing.
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Key Words
- ACF, APOBEC1 Complementation Factor
- ADAR, Adenosine Deaminase, RNA-specific
- ADAT, Adenosine Deaminase, tRNA-specific
- AID/APOBECs
- APOBEC1, Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1
- ApoB, Apolipoprotein B
- EGFP, Enhanced Green Fluorescent Protein
- FACS, Fluorescence activated cell sorting
- FBS, Fetal bovine serum
- GRY-RBP, Glycine-Arginine-Tyrosine-rich RNA-binding protein
- RBM47, RNA binding motif protein 47
- RNA editing
- cds, coding sequence
- cytosine deaminase
- hnRNP-C1, heterogeneous nuclear ribonucleoprotein C1
- lipid metabolism
- mRNA
- post-transcriptional modification
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Affiliation(s)
- Francesco Severi
- a Core Research Laboratory; Istituto Toscano Tumori ; Firenze , Italy
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41
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Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:189-213. [PMID: 27256387 DOI: 10.1007/978-3-319-29073-7_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA editing is a cellular process used to expand and diversify the RNA transcripts produced from a generally immutable genome. In animals, the most prevalent type of RNA editing is adenosine (A) to inosine (I) deamination catalyzed by the ADAR family. Throughout development, A-to-I editing levels increase while ADAR expression is constant, suggesting cellular mechanisms to regulate A-to-I editing exist. Furthermore, in several disease states, ADAR expression levels are similar to the normal state, but A-to-I editing levels are altered. Therefore, understanding how these enzymes are regulated in normal tissues and misregulated in disease states is of profound importance. This chapter will both discuss how to identify A-to-I editing sites across the transcriptome and explore the mechanisms that regulate ADAR editing activity, with particular focus on the diverse types of RNA-binding proteins implicated in regulating A-to-I editing in vivo.
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42
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Wang Y, Havel J, Beal PA. A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1. ACS Chem Biol 2015; 10:2512-9. [PMID: 26372505 DOI: 10.1021/acschembio.5b00711] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Adenosine deaminases acting on RNA (ADARs) are RNA-editing enzymes responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. ADAR1 and ADAR2 are two members of the family that have been shown to be catalytically active. Earlier, we reported a phenotypic screen for the study of human ADAR2 using budding yeast S. cerevisiae as the host system. While this screen has been successfully applied to the study of ADAR2, it failed with ADAR1. Here, we report a new reporter that uses a novel editing substrate and is suitable for the study of ADAR1. We screened plasmid libraries with randomized codons for two important residues in human ADAR1 (G1007 and E1008). The screening results combined with in vitro deamination assays led to the identification of mutants that are more active than the wild type protein. Furthermore, a screen of the ADAR1 E1008X library with a reporter construct bearing an A•G mismatch at the editing site suggests one role for the residue at position 1008 is to sense the identity of the base pairing partner for the editing site adenosine. This work has provided a starting point for future in vitro evolution studies of ADAR1 and led to new insight into ADAR's editing site selectivity.
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Affiliation(s)
- Yuru Wang
- Department of Chemistry, University of California, Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Jocelyn Havel
- Department of Chemistry, University of California, Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, 1 Shields Ave, Davis, California 95616, United States
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43
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Bonini D, Filippini A, La Via L, Fiorentini C, Fumagalli F, Colombi M, Barbon A. Chronic glutamate treatment selectively modulates AMPA RNA editing and ADAR expression and activity in primary cortical neurons. RNA Biol 2015; 12:43-53. [PMID: 25625181 DOI: 10.1080/15476286.2015.1008365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine RNA editing is a post-transcriptional process, catalyzed by ADAR enzymes, with an important role in diversifying the number of proteins derived from a single gene. In neurons, editing of ionotropic AMPA glutamate receptors has been shown to be altered under several experimental conditions, including severe pathologies, thus highlighting the potential significance of its modulation. In this study, we treated rat primary cortical cell cultures with a sub-lethal dose of glutamate (10 μM), focusing on RNA editing and ADAR activity. We found that chronic glutamate treatment down-regulates RNA editing levels at the R/G site of GluA2-4 subunits of AMPA receptors and at the K/E site of CYFIP2. These changes are site-specific since they were not observed either for the GluA2 Q/R site or for other non-glutamatergic sites. Glutamate treatment also down-regulates the protein expression levels of both ADAR1 and ADAR2 enzymes, through a pathway that is Ca(2+)- and calpain-dependent. Given that AMPA receptors containing unedited subunits show a slower recovery rate from desensitization compared to those containing edited forms, the reduced editing at the R/G site may, at least in part, compensate for glutamate over-stimulation, perhaps through the reduced activation of postsynaptic receptors. In summary, our data provide direct evidence of the involvement of ADAR1 and ADAR2 activity as a possible compensatory mechanism for neuronal protection following glutamate over-stimulation.
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Affiliation(s)
- Daniela Bonini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; National Institute of Neuroscience; University of Brescia ; Brescia , Italy
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44
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Liscovitch N, Bazak L, Levanon EY, Chechik G. Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain. RNA Biol 2015; 11:1447-56. [PMID: 25692240 DOI: 10.4161/15476286.2014.992286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.
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Affiliation(s)
- Noa Liscovitch
- a Gonda Multidisiplinary Brain Research Center ; Bar-Ilan University ; Ramat Gan , Israel
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45
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Zhao W, Vaithiyalingam S, San Filippo J, Maranon DG, Jimenez-Sainz J, Fontenay GV, Kwon Y, Leung SG, Lu L, Jensen RB, Chazin WJ, Wiese C, Sung P. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry. Mol Cell 2015; 59:176-87. [PMID: 26145171 PMCID: PMC4506714 DOI: 10.1016/j.molcel.2015.05.032] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/21/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes.
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Affiliation(s)
- Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sivaraja Vaithiyalingam
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Joseph San Filippo
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gerald V Fontenay
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stanley G Leung
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
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46
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Tajaddod M, Jantsch MF, Licht K. The dynamic epitranscriptome: A to I editing modulates genetic information. Chromosoma 2015; 125:51-63. [PMID: 26148686 PMCID: PMC4761006 DOI: 10.1007/s00412-015-0526-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023]
Abstract
Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the nervous system. Here, A to I editing leads to recoding and changes of single amino acids since inosine is normally interpreted as guanosine by cellular machines. However, more recently, new roles for A to I editing have emerged: Editing was shown to influence splicing and is found massively in Alu elements. Moreover, A to I editing is required to modulate innate immunity. We summarize the multiple ways in which A to I editing generates transcriptome variability and highlight recent findings in the field.
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Affiliation(s)
- Mansoureh Tajaddod
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria
| | - Michael F Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria. .,Department of Cell Biology, Center of Cell Biology and Anatomy, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
| | - Konstantin Licht
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria.
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47
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Frésard L, Leroux S, Roux PF, Klopp C, Fabre S, Esquerré D, Dehais P, Djari A, Gourichon D, Lagarrigue S, Pitel F. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates. PLoS One 2015; 10:e0126776. [PMID: 26024316 PMCID: PMC4449034 DOI: 10.1371/journal.pone.0126776] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/07/2015] [Indexed: 12/15/2022] Open
Abstract
RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.
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Affiliation(s)
- Laure Frésard
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Sophie Leroux
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Pierre-François Roux
- Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
- INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
| | - Christophe Klopp
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Stéphane Fabre
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Diane Esquerré
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, GeT-PlaGe Genotoul, Castanet-Tolosan, France
| | - Patrice Dehais
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Anis Djari
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - David Gourichon
- INRA, Pôle d'Expérimentation Avicole de Tours, Nouzilly, France
| | - Sandrine Lagarrigue
- Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
- INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
| | - Frédérique Pitel
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
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48
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Sapiro AL, Deng P, Zhang R, Li JB. Cis regulatory effects on A-to-I RNA editing in related Drosophila species. Cell Rep 2015; 11:697-703. [PMID: 25921533 DOI: 10.1016/j.celrep.2015.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/25/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023] Open
Abstract
Adenosine-to-inosine RNA editing modifies maturing mRNAs through the binding of adenosine deaminase acting on RNA (Adar) proteins to double-stranded RNA structures in a process critical for neuronal function. Editing levels at individual editing sites span a broad range and are mediated by both cis-acting elements (surrounding RNA sequence and secondary structure) and trans-acting factors. Here, we aim to determine the roles that cis-acting elements and trans-acting factors play in regulating editing levels. Using two closely related Drosophila species, D. melanogaster and D. sechellia, and their F1 hybrids, we dissect the effects of cis sequences from trans regulators on editing levels by comparing species-specific editing in parents and their hybrids. We report that cis sequence differences are largely responsible for editing level differences between these two Drosophila species. This study presents evidence for cis sequence and structure changes as the dominant evolutionary force that modulates RNA editing levels between these Drosophila species.
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Affiliation(s)
- Anne L Sapiro
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patricia Deng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Nussbacher JK, Batra R, Lagier-Tourenne C, Yeo GW. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci 2015; 38:226-36. [PMID: 25765321 PMCID: PMC4403644 DOI: 10.1016/j.tins.2015.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 12/13/2022]
Abstract
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, genome-wide manner. Development of high-throughput sequencing (Seq) methodologies provides unparalleled potential to discover new mechanisms of disease-associated perturbations of RNA homeostasis. Complementary to candidate single-gene studies, these innovative technologies may elicit the discovery of unexpected mechanisms, and enable us to determine the widespread influence of the multifunctional RBPs on their targets. Given that the disruption of RNA processing is increasingly implicated in neurological diseases, these approaches will continue to provide insights into the roles of RBPs in disease pathogenesis.
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Affiliation(s)
- Julia K Nussbacher
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Ranjan Batra
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
| | - Gene W Yeo
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Department of Physiology, National University of Singapore, Singapore.
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George CX, John L, Samuel CE. An RNA editor, adenosine deaminase acting on double-stranded RNA (ADAR1). J Interferon Cytokine Res 2015; 34:437-46. [PMID: 24905200 DOI: 10.1089/jir.2014.0001] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Adenosine deaminase acting on RNA1 (ADAR1) catalyzes the C6 deamination of adenosine (A) to produce inosine (I) in regions of RNA with double-stranded (ds) character. This process is known as A-to-I RNA editing. Alternative promoters drive the expression of the Adar1 gene and alternative splicing gives rise to transcripts that encode 2 ADAR1 protein size isoforms. ADAR1 p150 is an interferon (IFN)-inducible dsRNA adenosine deaminase found in the cytoplasm and nucleus, whereas ADAR1 p110 is constitutively expressed and nuclear in localization. Dependent on the duplex structure of the dsRNA substrate, deamination of adenosine by ADAR can be either highly site-selective or nonspecific. A-to-I editing can alter the stability of RNA structures and the coding of RNA as I is read as G instead of A by ribosomes during mRNA translation and by polymerases during RNA replication. A-to-I editing is of broad physiologic significance. Both the production and the action of IFNs, and hence the subsequent interaction of viruses with their hosts, are among the processes affected by A-to-I editing.
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Affiliation(s)
- Cyril X George
- Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California
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