1
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Schiksnis EC, Nicastro IA, Pasquinelli AE. Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599640. [PMID: 38948813 PMCID: PMC11213008 DOI: 10.1101/2024.06.18.599640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Organismal aging is marked by decline in cellular function and anatomy, ultimately resulting in death. To inform our understanding of the mechanisms underlying this degeneration, we performed standard RNA sequencing and Nanopore direct RNA sequencing over an adult time course in Caenorhabditis elegans. Long reads allowed for identification of hundreds of novel isoforms and age-associated differential isoform accumulation, resulting from alternative splicing and terminal exon choice. Genome-wide analysis reveals a decline in RNA processing fidelity and a rise in inosine and pseudouridine editing events in transcripts from older animals. In this first map of pseudouridine modifications for C. elegans, we find that they largely reside in coding sequences and that the number of genes with this modification increases with age. Collectively, this analysis discovers transcriptomic signatures associated with age and is a valuable resource to understand the many processes that dictate altered gene expression patterns and post-transcriptional regulation in aging.
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Affiliation(s)
- Erin C Schiksnis
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Ian A Nicastro
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0349, USA
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2
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Bass BL. Adenosine deaminases that act on RNA, then and now. RNA (NEW YORK, N.Y.) 2024; 30:521-529. [PMID: 38531651 PMCID: PMC11019741 DOI: 10.1261/rna.079990.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 03/28/2024]
Abstract
In this article, I recount my memories of key experiments that led to my entry into the RNA editing/modification field. I highlight initial observations made by the pioneers in the ADAR field, and how they fit into our current understanding of this family of enzymes. I discuss early mysteries that have now been solved, as well as those that still linger. Finally, I discuss important, outstanding questions and acknowledge my hope for the future of the RNA editing/modification field.
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Affiliation(s)
- Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
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3
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Cottrell KA, Andrews RJ, Bass BL. The competitive landscape of the dsRNA world. Mol Cell 2024; 84:107-119. [PMID: 38118451 PMCID: PMC10843539 DOI: 10.1016/j.molcel.2023.11.033] [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: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
The ability to sense and respond to infection is essential for life. Viral infection produces double-stranded RNAs (dsRNAs) that are sensed by proteins that recognize the structure of dsRNA. This structure-based recognition of viral dsRNA allows dsRNA sensors to recognize infection by many viruses, but it comes at a cost-the dsRNA sensors cannot always distinguish between "self" and "nonself" dsRNAs. "Self" RNAs often contain dsRNA regions, and not surprisingly, mechanisms have evolved to prevent aberrant activation of dsRNA sensors by "self" RNA. Here, we review current knowledge about the life of endogenous dsRNAs in mammals-the biosynthesis and processing of dsRNAs, the proteins they encounter, and their ultimate degradation. We highlight mechanisms that evolved to prevent aberrant dsRNA sensor activation and the importance of competition in the regulation of dsRNA sensors and other dsRNA-binding proteins.
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Affiliation(s)
- Kyle A Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
| | - Ryan J Andrews
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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4
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Zambrano-Mila MS, Witzenberger M, Rosenwasser Z, Uzonyi A, Nir R, Ben-Aroya S, Levanon EY, Schwartz S. Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2. Nat Commun 2023; 14:8212. [PMID: 38081817 PMCID: PMC10713624 DOI: 10.1038/s41467-023-43633-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: -26 nt for ADAR2 and -35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2-recruiting therapeutics, with proof-of-concept experiments demonstrating increased on-target and potentially decreased off-target editing.
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Affiliation(s)
- Marlon S Zambrano-Mila
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Zohar Rosenwasser
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Shay Ben-Aroya
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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5
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Starr LA, McKay LE, Peter KN, Seyfarth LM, Berkowitz LA, Caldwell KA, Caldwell GA. Attenuation of Dopaminergic Neurodegeneration in a C. elegans Parkinson's Model through Regulation of Xanthine Dehydrogenase (XDH-1) Expression by the RNA Editase, ADR-2. J Dev Biol 2023; 11:jdb11020020. [PMID: 37218814 DOI: 10.3390/jdb11020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023] Open
Abstract
Differential RNA editing by adenosine deaminases that act on RNA (ADARs) has been implicated in several neurological disorders, including Parkinson's disease (PD). Here, we report results of a RNAi screen of genes differentially regulated in adr-2 mutants, normally encoding the only catalytically active ADAR in Caenorhabditis elegans, ADR-2. Subsequent analysis of candidate genes that alter the misfolding of human α-synuclein (α-syn) and dopaminergic neurodegeneration, two PD pathologies, reveal that reduced expression of xdh-1, the ortholog of human xanthine dehydrogenase (XDH), is protective against α-synuclein-induced dopaminergic neurodegeneration. Further, RNAi experiments show that WHT-2, the worm ortholog of the human ABCG2 transporter and a predicted interactor of XDH-1, is the rate-limiting factor in the ADR-2, XDH-1, WHT-2 system for dopaminergic neuroprotection. In silico structural modeling of WHT-2 indicates that the editing of one nucleotide in the wht-2 mRNA leads to the substitution of threonine with alanine at residue 124 in the WHT-2 protein, changing hydrogen bonds in this region. Thus, we propose a model where wht-2 is edited by ADR-2, which promotes optimal export of uric acid, a known substrate of WHT-2 and a product of XDH-1 activity. In the absence of editing, uric acid export is limited, provoking a reduction in xdh-1 transcription to limit uric acid production and maintain cellular homeostasis. As a result, elevation of uric acid is protective against dopaminergic neuronal cell death. In turn, increased levels of uric acid are associated with a decrease in ROS production. Further, downregulation of xdh-1 is protective against PD pathologies because decreased levels of XDH-1 correlate to a concomitant reduction in xanthine oxidase (XO), the form of the protein whose by-product is superoxide anion. These data indicate that modifying specific targets of RNA editing may represent a promising therapeutic strategy for PD.
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Affiliation(s)
- Lindsey A Starr
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Luke E McKay
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kylie N Peter
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Lena M Seyfarth
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Laura A Berkowitz
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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6
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Gan WL, Ng L, Ng BYL, Chen L. Recent Advances in Adenosine-to-Inosine RNA Editing in Cancer. Cancer Treat Res 2023; 190:143-179. [PMID: 38113001 DOI: 10.1007/978-3-031-45654-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
RNA epigenetics, or epitranscriptome, is a growing group of RNA modifications historically classified into two categories: RNA editing and RNA modification. RNA editing is usually understood as post-transcriptional RNA processing (except capping, splicing and polyadenylation) that changes the RNA nucleotide sequence encoded by the genome. This processing can be achieved through the insertion or deletion of nucleotides or deamination of nucleobases, generating either standard nucleotides such as uridine (U) or the rare nucleotide inosine (I). Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent type of RNA modification in mammals and is catalyzed by adenosine deaminase acting on the RNA (ADAR) family of enzymes that recognize double-stranded RNAs (dsRNAs). Inosine mimics guanosine (G) in base pairing with cytidine (C), thereby A-to-I RNA editing alters dsRNA secondary structure. Inosine is also recognized as guanosine by the splicing and translation machineries, resulting in mRNA alternative splicing and protein recoding. Therefore, A-to-I RNA editing is an important mechanism that causes and regulates "RNA mutations" in both normal physiology and diseases including cancer. In this chapter, we reviewed current paradigms and developments in the field of A-to-I RNA editing in the context of cancer.
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Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore.
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7
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Gabay O, Shoshan Y, Kopel E, Ben-Zvi U, Mann TD, Bressler N, Cohen-Fultheim R, Schaffer AA, Roth SH, Tzur Z, Levanon EY, Eisenberg E. Landscape of adenosine-to-inosine RNA recoding across human tissues. Nat Commun 2022; 13:1184. [PMID: 35246538 PMCID: PMC8897444 DOI: 10.1038/s41467-022-28841-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/27/2022] [Indexed: 12/18/2022] Open
Abstract
RNA editing by adenosine deaminases changes the information encoded in the mRNA from its genomic blueprint. Editing of protein-coding sequences can introduce novel, functionally distinct, protein isoforms and diversify the proteome. The functional importance of a few recoding sites has been appreciated for decades. However, systematic methods to uncover these sites perform poorly, and the full repertoire of recoding in human and other mammals is unknown. Here we present a new detection approach, and analyze 9125 GTEx RNA-seq samples, to produce a highly-accurate atlas of 1517 editing sites within the coding region and their editing levels across human tissues. Single-cell RNA-seq data shows protein recoding contributes to the variability across cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation. This comprehensive set can facilitate understanding of the role of recoding in human physiology and diseases. Gabay et al. provide a highly-accurate atlas of recoding by A-to-I RNA editing in human, profiled across tissues and cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation.
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Affiliation(s)
- Orshay Gabay
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yoav Shoshan
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Udi Ben-Zvi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Tomer D Mann
- Tel Aviv Sourasky Medical Center and Sackler school of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Bressler
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Roni Cohen-Fultheim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Amos A Schaffer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ziv Tzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel. .,The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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8
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Moldovan MA, Chervontseva ZS, Nogina DS, Gelfand MS. A hierarchy in clusters of cephalopod mRNA editing sites. Sci Rep 2022; 12:3447. [PMID: 35236910 PMCID: PMC8891338 DOI: 10.1038/s41598-022-07460-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/07/2022] [Indexed: 11/09/2022] Open
Abstract
RNA editing in the form of substituting adenine with inosine (A-to-I editing) is the most frequent type of RNA editing in many metazoan species. In most species, A-to-I editing sites tend to form clusters and editing at clustered sites depends on editing of the adjacent sites. Although functionally important in some specific cases, A-to-I editing usually is rare. The exception occurs in soft-bodied coleoid cephalopods, where tens of thousands of potentially important A-to-I editing sites have been identified, making coleoids an ideal model for studying of properties and evolution of A-to-I editing sites. Here, we apply several diverse techniques to demonstrate a strong tendency of coleoid RNA editing sites to cluster along the transcript. We show that clustering of editing sites and correlated editing substantially contribute to the transcriptome diversity that arises due to extensive RNA editing. Moreover, we identify three distinct types of editing site clusters, varying in size, and describe RNA structural features and mechanisms likely underlying formation of these clusters. In particular, these observations may explain sequence conservation at large distances around editing sites and the observed dependency of editing on mutations in the vicinity of editing sites.
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Affiliation(s)
- Mikhail A Moldovan
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, Russia, 121205.
| | - Zoe S Chervontseva
- A.A.Kharkevich Institute for Information Transmission Problems (RAS), Bolshoy Karetny Per. 19, bld.1, Moscow, Russia, 127051
| | - Daria S Nogina
- A.A.Kharkevich Institute for Information Transmission Problems (RAS), Bolshoy Karetny Per. 19, bld.1, Moscow, Russia, 127051.,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory 1, Moscow, Russia, 119991
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, Russia, 121205.,A.A.Kharkevich Institute for Information Transmission Problems (RAS), Bolshoy Karetny Per. 19, bld.1, Moscow, Russia, 127051
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9
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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10
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Salvetat N, Chimienti F, Cayzac C, Dubuc B, Checa-Robles F, Dupre P, Mereuze S, Patel V, Genty C, Lang JP, Pujol JF, Courtet P, Weissmann D. Phosphodiesterase 8A to discriminate in blood samples depressed patients and suicide attempters from healthy controls based on A-to-I RNA editing modifications. Transl Psychiatry 2021; 11:255. [PMID: 33931591 PMCID: PMC8087806 DOI: 10.1038/s41398-021-01377-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Mental health issues, including major depressive disorder, which can lead to suicidal behavior, are considered by the World Health Organization as a major threat to global health. Alterations in neurotransmitter signaling, e.g., serotonin and glutamate, or inflammatory response have been linked to both MDD and suicide. Phosphodiesterase 8A (PDE8A) gene expression is significantly decreased in the temporal cortex of major depressive disorder (MDD) patients. PDE8A specifically hydrolyzes adenosine 3',5'-cyclic monophosphate (cAMP), which is a key second messenger involved in inflammation, cognition, and chronic antidepressant treatment. Moreover, alterations of RNA editing in PDE8A mRNA has been described in the brain of depressed suicide decedents. Here, we investigated PDE8A A-to-I RNA editing-related modifications in whole blood of depressed patients and suicide attempters compared to age-matched and sex-matched healthy controls. We report significant alterations of RNA editing of PDE8A in the blood of depressed patients and suicide attempters with major depression, for which the suicide attempt took place during the last month before sample collection. The reported RNA editing modifications in whole blood were similar to the changes observed in the brain of suicide decedents. Furthermore, analysis and combinations of different edited isoforms allowed us to discriminate between suicide attempters and control groups. Altogether, our results identify PDE8A as an immune response-related marker whose RNA editing modifications translate from brain to blood, suggesting that monitoring RNA editing in PDE8A in blood samples could help to evaluate depressive state and suicide risk.
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Affiliation(s)
- Nicolas Salvetat
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Fabrice Chimienti
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Christopher Cayzac
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Benjamin Dubuc
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Francisco Checa-Robles
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Pierrick Dupre
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Sandie Mereuze
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Vipul Patel
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Catherine Genty
- Department of Emergency Psychiatry and Acute Care, University Hospital/INSERM U1061, 191 Av. du Doyen Gaston Giraud, Montpellier, 34295 France
| | - Jean-Philippe Lang
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Jean-François Pujol
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Philippe Courtet
- Department of Emergency Psychiatry and Acute Care, University Hospital/INSERM U1061, 191 Av. du Doyen Gaston Giraud, Montpellier, 34295 France
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184, France.
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11
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Uzonyi A, Nir R, Shliefer O, Stern-Ginossar N, Antebi Y, Stelzer Y, Levanon EY, Schwartz S. Deciphering the principles of the RNA editing code via large-scale systematic probing. Mol Cell 2021; 81:2374-2387.e3. [PMID: 33905683 DOI: 10.1016/j.molcel.2021.03.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/31/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Adenosine-to-inosine editing is catalyzed by ADAR1 at thousands of sites transcriptome-wide. Despite intense interest in ADAR1 from physiological, bioengineering, and therapeutic perspectives, the rules of ADAR1 substrate selection are poorly understood. Here, we used large-scale systematic probing of ∼2,000 synthetic constructs to explore the structure and sequence context determining editability. We uncover two structural layers determining the formation and propagation of A-to-I editing, independent of sequence. First, editing is robustly induced at fixed intervals of 35 bp upstream and 30 bp downstream of structural disruptions. Second, editing is symmetrically introduced on opposite sites on a double-stranded structure. Our findings suggest a recursive model for RNA editing, whereby the structural alteration induced by the editing at one site iteratively gives rise to the formation of an additional editing site at a fixed periodicity, serving as a basis for the propagation of editing along and across both strands of double-stranded RNA structures.
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Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ofir Shliefer
- Faculty of Life Sciences, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yaron Antebi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yonatan Stelzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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12
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Abstract
Following A-to-I editing of double-stranded RNA (dsRNA) molecules, sequencing reactions interpret the edited inosine (I) as guanosine (G). For this reason, current methods to detect A-to-I editing sites work to align RNA sequences to their reference DNA sequence in order to reveal A-to-G mismatches. However, areas with heavily edited reads produce dense clusters of A-to-G mismatches that hinder alignment, and complicate correct identification of the sites. The presented approach employs prudent alignment and examination of excessive mismatch events, enabling high-accuracy detection of hyper-edited reads and sites.
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13
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Mehravar M, Ghaemimanesh F, Poursani EM. An Overview on the Complexity of OCT4: at the Level of DNA, RNA and Protein. Stem Cell Rev Rep 2021; 17:1121-1136. [PMID: 33389631 DOI: 10.1007/s12015-020-10098-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
OCT4 plays critical roles in self-renewal and pluripotency maintenance of embryonic stem cells, and is considered as one of the main stemness markers. It also has pivotal roles in early stages of embryonic development. Most studies on OCT4 have focused on the expression and function of OCT4A, which is the biggest isoform of OCT4 known so far. Recently, many studies have shown that OCT4 has various transcript variants, protein isoforms, as well as pseudogenes. Distinguishing the expression and function of these variants and isoforms is a big challenge in expression profiling studies of OCT4. Understanding how OCT4 is functioning in different contexts, depends on knowing of where and when each of OCT4 transcripts, isoforms and pseudogenes are expressed. Here, we review OCT4 known transcripts, isoforms and pseudogenes, as well as its interactions with other proteins, and emphasize the importance of discriminating each of them in order to understand the exact function of OCT4 in stem cells, normal development and development of diseases.
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Affiliation(s)
- Majid Mehravar
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Fatemeh Ghaemimanesh
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ensieh M Poursani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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14
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Abstract
The type I interferonopathies comprise a heterogenous group of monogenic diseases associated with a constitutive activation of type I interferon signaling.The elucidation of the genetic causes of this group of diseases revealed an alteration of nucleic acid processing and signaling.ADAR1 is among the genes found mutated in patients with this type of disorders.This enzyme catalyzes the hydrolytic deamination of adenosines in inosines within a double-stranded RNA target (RNA editing of A to I). This RNA modification is widespread in human cells and deregulated in a variety of human diseases, ranging from cancers to neurological abnormalities.In this review, we briefly summarize the knowledge about the RNA editing alterations occurring in patients with mutations in ADAR1 gene and how these alterations might cause the inappropriate IFN activation.
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Affiliation(s)
- Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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15
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Song Y, An O, Ren X, Chan THM, Tay DJT, Tang SJ, Han J, Hong H, Ng VHE, Ke X, Shen H, Pitcheshwar P, Lin JS, Leong KW, Molias FB, Yang H, Kappei D, Chen L. RNA editing mediates the functional switch of COPA in a novel mechanism of hepatocarcinogenesis. J Hepatol 2021; 74:135-147. [PMID: 32693003 DOI: 10.1016/j.jhep.2020.07.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS RNA editing introduces nucleotide changes in RNA sequences. Recent studies have reported that aberrant adenosine-to-inosine RNA editing is implicated in cancers. Until now, very few functionally important protein-recoding editing targets have been discovered. Here, we investigated the role of a recently discovered protein-recoding editing target COPA (coatomer subunit α) in hepatocellular carcinoma (HCC). METHODS Clinical implication of COPA editing was studied in a cohort of 125 HCC patients. CRISPR/Cas9-mediated knockout of the editing site complementary sequence (ECS) was used to delete edited COPA transcripts endogenously. COPA editing-mediated change in its transcript or protein stability was investigated upon actinomycin D or cycloheximide treatment, respectively. Functional difference in tumourigenesis between wild-type and edited COPA (COPAWTvs. COPAI164V) and the exact mechanisms were also studied in cell models and mice. RESULTS ADAR2 binds to double-stranded RNA formed between edited exon 6 and the ECS at intron 6 of COPA pre-mRNA, causing an isoleucine-to-valine substitution at residue 164. Reduced editing of COPA is implicated in the pathogenesis of HCC, and more importantly, it may be involved in many cancer types. Upon editing, COPAWT switches from a tumour-promoting gene to a tumour suppressor that has a dominant-negative effect. Moreover, COPAI164V may undergo protein conformational change and therefore become less stable than COPAWT. Mechanistically, COPAI164V may deactivate the PI3K/AKT/mTOR pathway through downregulation of caveolin-1 (CAV1). CONCLUSIONS We uncover an RNA editing-associated mechanism of hepatocarcinogenesis by which downregulation of ADAR2 caused the loss of tumour suppressive COPAI164V and concurrent accumulation of tumour-promoting COPAWT in tumours; a rapid degradation of COPAI164V protein and hyper-activation of the PI3K/AKT/mTOR pathway further promote tumourigenesis. LAY SUMMARY RNA editing is a process in which RNA is changed after it is made from DNA, resulting in an altered gene product. In this study, we found that RNA editing of a gene known as coatomer subunit α (COPA) is lower in tumour samples and discovered that this editing process changes COPA protein from a tumour-promoting form to a tumour-suppressive form. Loss of the edited COPA promotes the development of liver cancer.
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Affiliation(s)
- Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore 119074, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xinyu Ke
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Priyankaa Pitcheshwar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Ka Wai Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Fernando Bellido Molias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
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16
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Moldovan M, Chervontseva Z, Bazykin G, Gelfand MS. Adaptive evolution at mRNA editing sites in soft-bodied cephalopods. PeerJ 2020; 8:e10456. [PMID: 33312772 PMCID: PMC7703385 DOI: 10.7717/peerj.10456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Background The bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein. Methods We study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site. Results Here, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.
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Affiliation(s)
- Mikhail Moldovan
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Zoe Chervontseva
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,A.A.Kharkevich Institute for Information Transmission Problems (RAS), Moscow, Russian Federation
| | - Georgii Bazykin
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,A.A.Kharkevich Institute for Information Transmission Problems (RAS), Moscow, Russian Federation
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,A.A.Kharkevich Institute for Information Transmission Problems (RAS), Moscow, Russian Federation
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17
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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18
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Schaffer AA, Kopel E, Hendel A, Picardi E, Levanon E, Eisenberg E. The cell line A-to-I RNA editing catalogue. Nucleic Acids Res 2020; 48:5849-5858. [PMID: 32383740 PMCID: PMC7293008 DOI: 10.1093/nar/gkaa305] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/30/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.
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Affiliation(s)
- Amos A Schaffer
- 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
| | - Ayal Hendel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, I-70126 Bari, Italy
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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19
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Ganem NS, Ben-Asher N, Manning AC, Deffit SN, Washburn MC, Wheeler EC, Yeo GW, Zgayer OBN, Mantsur E, Hundley HA, Lamm AT. Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing. Cell Rep 2020; 27:1244-1253.e4. [PMID: 31018137 PMCID: PMC8139731 DOI: 10.1016/j.celrep.2019.03.095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/25/2018] [Accepted: 03/26/2019] [Indexed: 11/25/2022] Open
Abstract
A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes on the RNA editing process. We performed comprehensive phenotypic, transcriptomics, proteomics, and RNA binding screens on worms mutated in a single ADAR gene. We found that ADR-1 mutants exhibit more-severe phenotypes than ADR-2, and some of them are a result of non-editing functions of ADR-1. We also show that ADR-1 significantly binds edited genes and regulates mRNA expression, whereas the effect on protein levels is minor. In addition, ADR-1 primarily promotes editing by ADR-2 at the L4 stage of development. Our results suggest that ADR-1 has a significant role in the RNA editing process and in altering editing levels that affect RNA expression; loss of ADR-1 results in severe phenotypes.
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Affiliation(s)
- Nabeel S Ganem
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noa Ben-Asher
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Aidan C Manning
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Sarah N Deffit
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | | | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, USA
| | - Orna Ben-Naim Zgayer
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Einav Mantsur
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Ayelet T Lamm
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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20
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Rajendren S, Manning AC, Al-Awadi H, Yamada K, Takagi Y, Hundley HA. A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme. Nucleic Acids Res 2019; 46:9647-9659. [PMID: 30202880 PMCID: PMC6182170 DOI: 10.1093/nar/gky800] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/27/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) in all ADARs suggests these domains are important for substrate recognition; however, the role of dsRBDs in vivo remains largely unknown. Herein, our studies indicate the Caenorhabditis elegans ADAR enzyme, ADR-2, has low affinity for dsRNA, but interacts with ADR-1, an editing-deficient member of the ADAR family, which has a 100-fold higher affinity for dsRNA. ADR-1 uses one dsRBD to physically interact with ADR-2 and a second dsRBD to bind to dsRNAs, thereby tethering ADR-2 to substrates. ADR-2 interacts with >1200 transcripts in vivo, and ADR-1 is required for 80% of these interactions. Our results identify a novel mode of substrate recognition for ADAR enzymes and indicate that protein-protein interactions can guide substrate recognition for RNA editors.
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Affiliation(s)
- Suba Rajendren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aidan C Manning
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Haider Al-Awadi
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Kentaro Yamada
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
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21
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RNA editing is abundant and correlates with task performance in a social bumblebee. Nat Commun 2019; 10:1605. [PMID: 30962428 PMCID: PMC6453909 DOI: 10.1038/s41467-019-09543-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/15/2019] [Indexed: 12/17/2022] Open
Abstract
Colonies of the bumblebee Bombus terrestris are characterized by wide phenotypic variability among genetically similar full-sister workers, suggesting a major role for epigenetic processes. Here, we report a high level of ADAR-mediated RNA editing in the bumblebee, despite the lack of an ADAR1-homolog. We identify 1.15 million unique genomic sites, and 164 recoding sites residing in 100 protein coding genes, including ion channels, transporters, and receptors predicted to affect brain function and behavior. Some edited sites are similarly edited in other insects, cephalopods and even mammals. The global editing level of protein coding and non-coding transcripts weakly correlates with task performance (brood care vs. foraging), but not affected by dominance rank or juvenile hormone known to influence physiology and behavior. Taken together, our findings show that brain editing levels are high in naturally behaving bees, and may be regulated by relatively short-term effects associated with brood care or foraging activities.
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22
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Abstract
Long double-stranded RNAs (dsRNAs) are abundantly expressed in animals, in which they frequently occur in introns and 3' untranslated regions of mRNAs. Functions of long, cellular dsRNAs are poorly understood, although deficiencies in adenosine deaminases that act on RNA, or ADARs, promote their recognition as viral dsRNA and an aberrant immune response. Diverse dsRNA-binding proteins bind cellular dsRNAs, hinting at additional roles. Understanding these roles is facilitated by mapping the genomic locations that express dsRNA in various tissues and organisms. ADAR editing provides a signature of dsRNA structure in cellular transcripts. In this review, we detail approaches to map ADAR editing sites and dsRNAs genome-wide, with particular focus on high-throughput sequencing methods and considerations for their successful application to the detection of editing sites and dsRNAs.
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Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
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23
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Chimienti F, Cavarec L, Vincent L, Salvetat N, Arango V, Underwood MD, Mann JJ, Pujol JF, Weissmann D. Brain region-specific alterations of RNA editing in PDE8A mRNA in suicide decedents. Transl Psychiatry 2019; 9:91. [PMID: 30770787 PMCID: PMC6377659 DOI: 10.1038/s41398-018-0331-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/26/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Phosphodiesterases (PDE) are key modulators of signal transduction and are involved in inflammatory cell activation, memory and cognition. There is a two-fold decrease in the expression of phosphodiesterase 8A (PDE8A) in the temporal cortex of major depressive disorder (MDD) patients. Here, we studied PDE8A mRNA-editing profile in two architectonically distinct neocortical regions in a clinically well-characterized cohort of age- and sex-matched non-psychiatric drug-free controls and depressed suicide decedents. By using capillary electrophoresis single-stranded conformational polymorphism (CE-SSCP), a previously validated technique to identify A-to-I RNA modifications, we report the full editing profile of PDE8A in the brain, including identification of two novel editing sites. Editing of PDE8A mRNA displayed clear regional difference when comparing dorsolateral prefrontal cortex (BA9) and anterior cingulate cortex (BA24). Furthermore, we report significant intra-regional differences between non-psychiatric control individuals and depressed suicide decedents, which could discriminate the two populations. Taken together, our results (i) highlight the importance of immune/inflammatory markers in major depressive disorder and suicide and (ii) establish a direct relationship between A-to-I RNA modifications of peripheral markers and A-to-I RNA editing-related modifications in brain. This work provides the first immune response-related brain marker for suicide and could pave the way for the identification of a blood-based biomarker that predicts suicidal behavior.
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Affiliation(s)
- Fabrice Chimienti
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
| | - Laurent Cavarec
- grid.465535.4Genomic Vision, Green Square, 80-84 rue des Meuniers, 92220 Bagneux, France
| | - Laurent Vincent
- grid.457349.8Commissariat à l’Energie Atomique, Fontenay aux Roses, France
| | - Nicolas Salvetat
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Victoria Arango
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | - Mark D. Underwood
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | - J. John Mann
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | | | - Dinah Weissmann
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
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24
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Cho CJ, Jung J, Jiang L, Lee EJ, Kim DS, Kim BS, Kim HS, Jung HY, Song HJ, Hwang SW, Park Y, Jung MK, Pack CG, Myung SJ, Chang S. Combinatory RNA-Sequencing Analyses Reveal a Dual Mode of Gene Regulation by ADAR1 in Gastric Cancer. Dig Dis Sci 2018; 63:1835-1850. [PMID: 29691780 DOI: 10.1007/s10620-018-5081-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Adenosine deaminase acting on RNA 1 (ADAR1) is known to mediate deamination of adenosine-to-inosine through binding to double-stranded RNA, the phenomenon known as RNA editing. Currently, the function of ADAR1 in gastric cancer is unclear. AIMS This study was aimed at investigating RNA editing-dependent and editing-independent functions of ADAR1 in gastric cancer, especially focusing on its influence on editing of 3' untranslated regions (UTRs) and subsequent changes in expression of messenger RNAs (mRNAs) as well as microRNAs (miRNAs). METHODS RNA-sequencing and small RNA-sequencing were performed on AGS and MKN-45 cells with a stable ADAR1 knockdown. Changed frequencies of editing and mRNA and miRNA expression were then identified by bioinformatic analyses. Targets of RNA editing were further validated in patients' samples. RESULTS In the Alu region of both gastric cell lines, editing was most commonly of the A-to-I type in 3'-UTR or intron. mRNA and protein levels of PHACTR4 increased in ADAR1 knockdown cells, because of the loss of seed sequences in 3'-UTR of PHACTR4 mRNA that are required for miRNA-196a-3p binding. Immunohistochemical analyses of tumor and paired normal samples from 16 gastric cancer patients showed that ADAR1 expression was higher in tumors than in normal tissues and inversely correlated with PHACTR4 staining. On the other hand, decreased miRNA-148a-3p expression in ADAR1 knockdown cells led to increased mRNA and protein expression of NFYA, demonstrating ADAR1's editing-independent function. CONCLUSIONS ADAR1 regulates post-transcriptional gene expression in gastric cancer through both RNA editing-dependent and editing-independent mechanisms.
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Affiliation(s)
- Charles J Cho
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Jaeeun Jung
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Lushang Jiang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Eun Ji Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Dae-Soo Kim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Byung Sik Kim
- Department of Gastric Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Hee Sung Kim
- Department of Gastric Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Hwoon-Yong Jung
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Ho-June Song
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Yangsoon Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Min Kyo Jung
- Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Chan Gi Pack
- Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Seung-Jae Myung
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea. .,Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea. .,Department of Gastroenterology and Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea.
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea.
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25
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Hsiao YHE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X. RNA editing in nascent RNA affects pre-mRNA splicing. Genome Res 2018; 28:812-823. [PMID: 29724793 PMCID: PMC5991522 DOI: 10.1101/gr.231209.117] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood. By sequencing the RNA of different subcellular fractions, we examined the timing of adenosine-to-inosine (A-to-I) RNA editing and its impact on alternative splicing. We observed that >95% A-to-I RNA editing events occurred in the chromatin-associated RNA prior to polyadenylation. We report about 500 editing sites in the 3' acceptor sequences that can alter splicing of the associated exons. These exons are highly conserved during evolution and reside in genes with important cellular function. Furthermore, we identified a second class of exons whose splicing is likely modulated by RNA secondary structures that are recognized by the RNA editing machinery. The genome-wide analyses, supported by experimental validations, revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.
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Affiliation(s)
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yun Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xianzhi Lin
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Stephen Tran
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Ei-Wen Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | | | - Xinshu Xiao
- Department of Bioengineering
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
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26
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Porath HT, Schaffer AA, Kaniewska P, Alon S, Eisenberg E, Rosenthal J, Levanon EY, Levy O. A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla. Mol Biol Evol 2018; 34:1890-1901. [PMID: 28453786 PMCID: PMC5850803 DOI: 10.1093/molbev/msx125] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
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Affiliation(s)
- Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Amos A Schaffer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Paulina Kaniewska
- Global Change Institute, The University of Queensland, St Lucia, Australia
| | - Shahar Alon
- 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
| | - 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
| | - Joshua Rosenthal
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, The Marine Biological Laboratory, Woods Hole, MA
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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27
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Andrews RJ, Baber L, Moss WN. RNAStructuromeDB: A genome-wide database for RNA structural inference. Sci Rep 2017; 7:17269. [PMID: 29222504 PMCID: PMC5722888 DOI: 10.1038/s41598-017-17510-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome. Here, we compile folding information for every base pair of the genome that may be transcribed: coding, noncoding, and intergenic regions, as well as repetitive elements, telomeres, etc. This was done by fragmenting the GRCh38 reference genome into 154,414,320 overlapping sequence fragments and, for each fragment, calculating a set of metrics based on the sequence's folding properties. These data will facilitate a wide array of investigations: e.g. discovery of structured regulatory elements in differential gene expression data or noncoding RNA discovery, as well as allow genome-scale analyses of RNA folding.
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Affiliation(s)
- Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Levi Baber
- Biology Information Technology, Iowa State University, 2310 Pammel Drive, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA.
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28
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Abstract
Adenosine-to-inosine RNA editing is a conserved process, which is performed by ADAR enzymes. By changing nucleotides in coding regions of genes and altering codons, ADARs expand the cell's protein repertoire. This function of the ADAR enzymes is essential for human brain development. However, most of the known editing sites are in non-coding repetitive regions in the transcriptome and the purpose of editing in these regions is unclear. Recent studies, which have shown that editing levels of transcripts vary between tissues and developmental stages in many organisms, suggest that the targeted RNA and ADAR editing are both regulated. We discuss the implications of these findings, and the possible role of RNA editing in innate immunity.
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Affiliation(s)
- Nabeel S Ganem
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
| | - Ayelet T Lamm
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
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29
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Liscovitch-Brauer N, Alon S, Porath HT, Elstein B, Unger R, Ziv T, Admon A, Levanon EY, Rosenthal JJC, Eisenberg E. Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. Cell 2017; 169:191-202.e11. [PMID: 28388405 DOI: 10.1016/j.cell.2017.03.025] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/02/2017] [Accepted: 03/16/2017] [Indexed: 12/29/2022]
Abstract
RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP.
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Affiliation(s)
- Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shahar Alon
- Media Lab and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hagit T Porath
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Boaz Elstein
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ron Unger
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Tamar Ziv
- Smoler Proteomics Center and Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Admon
- Smoler Proteomics Center and Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Joshua J C Rosenthal
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan 00901, Puerto Rico.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
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30
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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31
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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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32
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ADAR1 and MicroRNA; A Hidden Crosstalk in Cancer. Int J Mol Sci 2017; 18:ijms18040799. [PMID: 28398248 PMCID: PMC5412383 DOI: 10.3390/ijms18040799] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
The evolution of cancer cells is believed to be dependent on genetic or epigenetic alterations. However, this concept has recently been challenged by another mode of nucleotide alteration, RNA editing, which is frequently up-regulated in cancer. RNA editing is a biochemical process in which either Adenosine or Cytosine is deaminated by a group of RNA editing enzymes including ADAR (Adenosine deaminase; RNA specific) or APOBEC3B (Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit 3B). The result of RNA editing is usually adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) transition, which can affect protein coding, RNA stability, splicing and microRNA-target interactions. The functional impact of these alterations is largely unclear and is a subject of extensive research. In the present review, we will specifically focus on the influence of ADARs on carcinogenesis via the regulation of microRNA processing and functioning. This follows a brief review of the current knowledge of properties of ADAR enzyme, RNA editing, and microRNA processing.
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33
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Goldberg L, Abutbul-Amitai M, Paret G, Nevo-Caspi Y. Alternative Splicing of STAT3 Is Affected by RNA Editing. DNA Cell Biol 2017; 36:367-376. [PMID: 28278381 DOI: 10.1089/dna.2016.3575] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A-to-I RNA editing, carried out by adenosine deaminase acting on RNA (ADAR) enzymes, is an epigenetic phenomenon of posttranscriptional modifications on pre-mRNA. RNA editing in intronic sequences may influence alternative splicing of flanking exons. We have previously shown that conditions that induce editing result in elevated expression of signal transducer and activator of transcription 3 (STAT3), preferentially the alternatively-spliced STAT3β isoform. Mechanisms regulating alternative splicing of STAT3 have not been elucidated. STAT3 undergoes A-to-I RNA editing in an intron residing in proximity to the alternatively spliced exon. We hypothesized that RNA editing plays a role in regulating alternative splicing toward STAT3β. In this study we extend our observation connecting RNA editing to the preferential induction of STAT3β expression. We study the involvement of ADAR1 in STAT3 editing and reveal the connection between editing and alternative splicing of STAT3. Deferoaxamine treatment caused the induction in STAT3 RNA editing and STAT3β expression. Silencing ADAR1 caused a decrease in STAT3 editing and expression with a preferential decrease in STAT3β. Cells transfected with a mutated minigene showed preferential splicing toward the STAT3β transcript. Editing in the STAT3 intron is performed by ADAR1 and affects STAT3 alternative splicing. These results suggest that RNA editing is one of the molecular mechanisms regulating the expression of STAT3β.
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Affiliation(s)
- Lior Goldberg
- 1 Department of Pediatric Critical Care Medicine, Safra Children's Hospital, Sheba Medical Center , Tel Hashomer, Israel .,2 Sackler Medical School, Tel-Aviv University , Tel-Aviv, Israel
| | - Mor Abutbul-Amitai
- 1 Department of Pediatric Critical Care Medicine, Safra Children's Hospital, Sheba Medical Center , Tel Hashomer, Israel .,2 Sackler Medical School, Tel-Aviv University , Tel-Aviv, Israel
| | - Gideon Paret
- 1 Department of Pediatric Critical Care Medicine, Safra Children's Hospital, Sheba Medical Center , Tel Hashomer, Israel .,2 Sackler Medical School, Tel-Aviv University , Tel-Aviv, Israel
| | - Yael Nevo-Caspi
- 1 Department of Pediatric Critical Care Medicine, Safra Children's Hospital, Sheba Medical Center , Tel Hashomer, Israel
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34
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Mazloomian A, Meyer IM. Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. RNA Biol 2016; 12:1391-401. [PMID: 26512413 PMCID: PMC4829317 DOI: 10.1080/15476286.2015.1107703] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA editing is a widespread mechanism that plays a crucial role in diversifying gene products. Its abundance and importance in regulating cellular processes were revealed using new sequencing technologies. The majority of these editing events, however, cannot be associated with regulatory mechanisms. We use tissue-specific high-throughput libraries of D. melanogaster to study RNA editing. We introduce an analysis pipeline that utilises large input data and explicitly captures ADAR's requirement for double-stranded regions. It combines probabilistic and deterministic filters and can identify RNA editing events with a low estimated false positive rate. Analyzing ten different tissue types, we predict 2879 editing sites and provide their detailed characterization. Our analysis pipeline accurately distinguishes genuine editing sites from SNPs and sequencing and mapping artifacts. Our editing sites are 3 times more likely to occur in exons with multiple splicing acceptor/donor sites than in exons with unique splice sites (p-value < 2.10−15). Furthermore, we identify 244 edited regions where RNA editing and alternative splicing are likely to influence each other. For 96 out of these 244 regions, we find evolutionary evidence for conserved RNA secondary-structures near splice sites suggesting a potential regulatory mechanism where RNA editing may alter splicing patterns via changes in local RNA structure.
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Affiliation(s)
- Alborz Mazloomian
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
| | - Irmtraud M Meyer
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
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35
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Ramaswami G, Li JB. Identification of human RNA editing sites: A historical perspective. Methods 2016; 107:42-7. [PMID: 27208508 PMCID: PMC5014717 DOI: 10.1016/j.ymeth.2016.05.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 12/18/2022] Open
Abstract
A-to-I RNA editing is an essential gene regulatory mechanism. Once thought to be a rare phenomenon only occurring in a few transcripts, the emergence of high-throughput RNA sequencing has facilitated the identification of over 2 million RNA editing sites in the human transcriptome. In this review, we survey the current RNA-seq based methods as well as historical methods used to identify RNA editing sites.
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Affiliation(s)
- Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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36
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Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Exp Hematol 2016; 44:947-63. [PMID: 27373493 DOI: 10.1016/j.exphem.2016.06.250] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine residues to inosine in double-stranded RNA. In vivo, ADAR1 is essential for the maintenance of hematopoietic stem/progenitors. Whether other hematopoietic cell types also require ADAR1 has not been assessed. Using erythroid- and myeloid-restricted deletion of Adar1, we demonstrate that ADAR1 is dispensable for myelopoiesis but is essential for normal erythropoiesis. Adar1-deficient erythroid cells display a profound activation of innate immune signaling and high levels of cell death. No changes in microRNA levels were found in ADAR1-deficient erythroid cells. Using an editing-deficient allele, we demonstrate that RNA editing is the essential function of ADAR1 during erythropoiesis. Mapping of adenosine-to-inosine editing in purified erythroid cells identified clusters of hyperedited adenosines located in long 3'-untranslated regions of erythroid-specific transcripts and these are ADAR1-specific editing events. ADAR1-mediated RNA editing is essential for normal erythropoiesis.
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Affiliation(s)
- Brian J Liddicoat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Jochen C Hartner
- Taconic Biosciences, Cologne, Germany; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Robert Piskol
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Paul D Kingsley
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Vijay G Sankaran
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Louise E Purton
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Peter H Seeburg
- Department of Molecular Neurobiology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James Palis
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia.
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37
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Abstract
Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body's defense mechanisms.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Bronwyn A Lucas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. Center for RNA Biology, University of Rochester, Rochester, NY, USA. Department of Oncology, Wilmot Cancer Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
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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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Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. RNA Biol 2015; 12:162-74. [PMID: 25826568 DOI: 10.1080/15476286.2015.1017220] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
ADARs (Adenosine deaminases that act on RNA) "edit" RNA by converting adenosines to inosines within double-stranded regions. The primary targets of ADARs are long duplexes present within noncoding regions of mRNAs, such as introns and 3' untranslated regions (UTRs). Because adenosine and inosine have different base-pairing properties, editing within these regions can alter splicing and recognition by small RNAs. However, despite numerous studies identifying multiple editing sites in these genomic regions, little is known about the extent to which editing sites co-occur on individual transcripts or the functional output of these combinatorial editing events. To begin to address these questions, we performed an ultra-deep sequencing analysis of 4 Caenorhabditis elegans 3' UTRs that are known ADAR targets. Synchronous editing events were determined for the long duplexes in vivo. Furthermore, the validity of each editing event was confirmed by sequencing the same regions of mRNA from worms that lack A-to-I editing. This analysis identified a large number of editing sites that can occur within each 3' UTR, but interestingly, each individual transcript contained only a small fraction of these A-to-I editing events. In addition, editing patterns were not random, indicating that an editing event can affect the efficiency of editing at subsequent adenosines. Furthermore, we identified specific sites that can be both positively and negatively correlated with additional sites leading to mutually exclusive editing patterns. These results suggest that editing in noncoding regions is selective and hyper-editing of cellular RNAs is rare.
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Affiliation(s)
- Emily C Wheeler
- a Medical Sciences Program ; Indiana University ; Bloomington , IN USA
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40
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RNA rewriting, recoding, and rewiring in human disease. Trends Mol Med 2015; 21:549-59. [DOI: 10.1016/j.molmed.2015.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/18/2015] [Accepted: 07/07/2015] [Indexed: 11/15/2022]
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Lardenoije R, Iatrou A, Kenis G, Kompotis K, Steinbusch HWM, Mastroeni D, Coleman P, Lemere CA, Hof PR, van den Hove DLA, Rutten BPF. The epigenetics of aging and neurodegeneration. Prog Neurobiol 2015; 131:21-64. [PMID: 26072273 PMCID: PMC6477921 DOI: 10.1016/j.pneurobio.2015.05.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetics is a quickly growing field encompassing mechanisms regulating gene expression that do not involve changes in the genotype. Epigenetics is of increasing relevance to neuroscience, with epigenetic mechanisms being implicated in brain development and neuronal differentiation, as well as in more dynamic processes related to cognition. Epigenetic regulation covers multiple levels of gene expression; from direct modifications of the DNA and histone tails, regulating the level of transcription, to interactions with messenger RNAs, regulating the level of translation. Importantly, epigenetic dysregulation currently garners much attention as a pivotal player in aging and age-related neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, where it may mediate interactions between genetic and environmental risk factors, or directly interact with disease-specific pathological factors. We review current knowledge about the major epigenetic mechanisms, including DNA methylation and DNA demethylation, chromatin remodeling and non-coding RNAs, as well as the involvement of these mechanisms in normal aging and in the pathophysiology of the most common neurodegenerative diseases. Additionally, we examine the current state of epigenetics-based therapeutic strategies for these diseases, which either aim to restore the epigenetic homeostasis or skew it to a favorable direction to counter disease pathology. Finally, methodological challenges of epigenetic investigations and future perspectives are discussed.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Konstantinos Kompotis
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015 Lausanne-Dorigny, Switzerland
| | - Harry W M Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Paul Coleman
- L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Cynthia A Lemere
- Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080 Wuerzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.
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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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Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res 2015; 43:e109. [PMID: 26007652 PMCID: PMC4632877 DOI: 10.1093/nar/gkv537] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/10/2015] [Indexed: 12/19/2022] Open
Abstract
Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
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Affiliation(s)
- Min-Te Chou
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chiung-Po Hsiao
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
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Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL. Genome-wide profiling of the C. elegans dsRNAome. RNA (NEW YORK, N.Y.) 2015; 21:786-800. [PMID: 25805852 PMCID: PMC4408787 DOI: 10.1261/rna.048801.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 12/23/2014] [Indexed: 06/01/2023]
Abstract
Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). We compared two alignment algorithms for mapping both unique and repetitive reads and detected as many as 664 editing-enriched regions (EERs) indicative of dsRNA loci. EERs are visually enriched on the distal arms of autosomes and are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular duplexes. Most EERs were associated with protein-coding genes, with ∼1.7% of all C. elegans mRNAs containing an EER, located primarily in very long introns and in annotated, as well as unannotated, 3' UTRs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs that were distant from protein-coding genes and that had little or no coding potential. Finally, subsets of EERs are differentially expressed during development as well as during starvation and infection with bacterial or fungal pathogens. By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome.
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Affiliation(s)
- Joseph M Whipple
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA
| | - Osama A Youssef
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA
| | - P Joseph Aruscavage
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA
| | - David A Nix
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112-5775, USA
| | - Changjin Hong
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA
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New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription. J Virol 2015; 89:7120-32. [PMID: 25926645 DOI: 10.1128/jvi.00608-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/22/2015] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long noncoding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward (oriPtRs) transcripts are largely localized in the nucleus. While the oriPtLs are most likely noncoding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5' untranslated regions may partially serve noncoding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics, and their expression is inhibited by phosphonoacetic acid. RNA sequencing (RNA-seq) analysis showed that oriPtLs and oriPtRs exhibited extensive "hyperediting" at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts, suggesting that oriPts interact with the paraspeckle-based innate antiviral immune pathway. Knockdown and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade. IMPORTANCE Recent studies have revealed that the complexity of lytic herpesviral transcriptomes is significantly greater than previously appreciated with hundreds of viral long noncoding RNAs (vlncRNAs) being recently discovered. Work on cellular lncRNAs over the past several years has just begun to give us an initial appreciation for the array of functions they play in complex formation and regulatory processes in the cell. The newly identified herpesvirus lncRNAs are similarly likely to play a variety of different functions, although these functions are likely tailored to specific needs of the viral infection cycles. Here we describe novel transcripts derived from the EBV latency origin of replication. We show that they are hyperedited, that they interact with a relatively newly appreciated antiviral pathway, and that they play a role in facilitating viral lytic gene expression. These investigations are a starting point to unraveling the complex arena of vlncRNA function in herpesvirus lytic replication.
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Knisbacher BA, Levanon EY. DNA and RNA editing of retrotransposons accelerate mammalian genome evolution. Ann N Y Acad Sci 2015; 1341:115-25. [PMID: 25722083 DOI: 10.1111/nyas.12713] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome evolution is commonly viewed as a gradual process that is driven by random mutations that accumulate over time. However, DNA- and RNA-editing enzymes have been identified that can accelerate evolution by actively modifying the genomically encoded information. The apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBECs) are potent restriction factors that can inhibit retroelements by cytosine-to-uridine editing of retroelement DNA after reverse transcription. In some cases, a retroelement may successfully integrate into the genome despite being hypermutated. Such events introduce unique sequences into the genome and are thus a source of genomic innovation. adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine editing in double-stranded RNA, commonly formed by oppositely oriented retroelements. The RNA editing confers plasticity to the transcriptome by generating many transcript variants from a single genomic locus. If the editing produces a beneficial variant, the genome may maintain the locus that produces the RNA-edited transcript for its novel function. Here, we discuss how these two powerful editing mechanisms, which both target inserted retroelements, facilitate expedited genome evolution.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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47
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Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJC, Eisenberg E. The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. eLife 2015; 4. [PMID: 25569156 PMCID: PMC4384741 DOI: 10.7554/elife.05198] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/08/2015] [Indexed: 12/29/2022] Open
Abstract
RNA editing by adenosine deamination alters genetic information from the genomic
blueprint. When it recodes mRNAs, it gives organisms the option to express diverse,
functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans,
express RNA editing enzymes. However, transcriptome-wide screens have only uncovered
about 25 transcripts harboring conserved recoding RNA editing sites in mammals and
several hundred recoding sites in Drosophila. These studies on few
established models have led to the general assumption that recoding by RNA editing is
extremely rare. Here we employ a novel bioinformatic approach with extensive
validation to show that the squid Doryteuthis pealeii recodes
proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites
in the nervous system, affecting the majority of the proteins studied. Recoding is
tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions,
suggesting it plays an important role in brain physiology. DOI:http://dx.doi.org/10.7554/eLife.05198.001 For living cells to create a protein, a genetic code found in its DNA must first be
‘transcribed’ to create a corresponding molecule of messenger RNA
(mRNA). DNA and RNA are both made from smaller molecules called nucleotides that are
linked together into long chains; the information in both DNA and RNA is contained in
the sequence of these molecules. The mRNA nucleotides coding for proteins are
‘translated’ in groups of three, and most of these nucleotide triplets
instruct for a specific amino acid to be added to the newly forming protein. DNA sequences were thought to exactly correspond with the sequence of amino acids in
the resulting protein. However, it is now known that processes called RNA editing can
change the nucleotide sequence of the mRNA molecules after they have been transcribed
from the DNA. One such editing process, called A-to-I editing, alters the
‘A’ nucleotide so that the translation machinery reads it as a
‘G’ nucleotide instead. In some—but not all—cases, this
event will change, or ‘recode’, the amino acid encoded by this stretch
of mRNA, which may change how the protein behaves. This ability to create a range of
proteins from a single DNA sequence could help organisms to evolve new traits. Evidence of amino acid recoding has only been found to a very limited extent in the
few species investigated so far. There has been some evidence that suggests that
recoding might occur more often, and alter more proteins, in squids and octopuses.
However, this could not be confirmed as the genomes of these species have not been
sequenced, and these sequences were required to investigate RNA recoding using
existing techniques. Alon et al. have now developed a new approach that allows the recoding sites to be
identified in organisms whose genomes have not been sequenced. Using this
technique—which compares mRNA sequences with the DNA sequence they have been
transcribed from—to examine the squid nervous system revealed over 57,000
recoding sites where an ‘A’ nucleotide had been modified to
‘G’ and thereby changed the coded amino acid. Many of the identified
mRNA molecules had been recoded in more than one place, and many more of these than
expected changed the amino acid sequence of the protein translated from them. Alon et
al. therefore suggest that RNA editing may have been crucial in the evolution of the
squid's nervous system, and suggest that recoding should be considered a normal part
of the process used by squids to make proteins. DOI:http://dx.doi.org/10.7554/eLife.05198.002
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Affiliation(s)
- Shahar Alon
- George S Wise Faculty of Life Sciences, Department of Neurobiology, Tel Aviv University, Tel Aviv, Israel
| | - Sandra C Garrett
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, United States
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Sara Olson
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, United States
| | - Brenton R Graveley
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, United States
| | - Joshua J C Rosenthal
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Eli Eisenberg
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Zhao HQ, Zhang P, Gao H, He X, Dou Y, Huang AY, Liu XM, Ye AY, Dong MQ, Wei L. Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. Genome Res 2015; 25:66-75. [PMID: 25373143 PMCID: PMC4317174 DOI: 10.1101/gr.176107.114] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
RNA editing increases transcriptome diversity through post-transcriptional modifications of RNA. Adenosine deaminases that act on RNA (ADARs) catalyze the adenosine-to-inosine (A-to-I) conversion, the most common type of RNA editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a "bisulfite-seq-mapping-like" step and achieved a threefold increase in identification sensitivity. A total of 99.5% of the 47,660 A-to-I editing sites were found in clusters. Of the 3080 editing clusters, 65.7% overlapped with DNA transposons in noncoding regions and 73.7% could form hairpin structures. The numbers of editing sites and clusters were highest at the L1 and embryonic stages. The editing frequency of a cluster positively correlated with the number of editing sites within it. Intriguingly, for 80% of the clusters with 10 or more editing sites, almost all expressed transcripts were edited. Deletion of adr-1 reduced the editing frequency but not the number of editing clusters, whereas deletion of adr-2 nearly abolished RNA editing, indicating a modulating role of ADR-1 and an essential role of ADR-2 in A-to-I editing. Quantitative proteomics analysis showed that adr-2 mutant worms altered the abundance of proteins involved in aging and lifespan regulation. Consistent with this finding, we observed that worms lacking RNA editing were short-lived. Taken together, our results reveal a sophisticated landscape of RNA editing and distinct modes of action of different ADARs.
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Affiliation(s)
- Han-Qing Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Pan Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Hua Gao
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiandong He
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - August Y Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Ming Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Adam Y Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China;
| | - Liping Wei
- National Institute of Biological Sciences, Beijing 102206, China; Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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49
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Drake M, Furuta T, Man KS, Gonzalez G, Liu B, Kalia A, Ladbury J, Fire AZ, Skeath JB, Arur S. A requirement for ERK-dependent Dicer phosphorylation in coordinating oocyte-to-embryo transition in C. elegans. Dev Cell 2014; 31:614-28. [PMID: 25490268 PMCID: PMC4261158 DOI: 10.1016/j.devcel.2014.11.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 08/12/2014] [Accepted: 11/04/2014] [Indexed: 02/03/2023]
Abstract
Signaling pathways and small RNAs direct diverse cellular events, but few examples are known of defined signaling pathways directly regulating small RNA biogenesis. We show that ERK phosphorylates Dicer on two conserved residues in its RNase IIIb and double-stranded RNA (dsRNA)-binding domains and that phosphorylation of these residues is necessary and sufficient to trigger Dicer's nuclear translocation in worms, mice, and human cells. Phosphorylation of Dicer on either site inhibits Dicer function in the female germline and dampens small RNA repertoire. Our data demonstrate that ERK phosphorylates and inhibits Dicer during meiosis I for oogenesis to proceed normally in Caenorhabditis elegans and that this inhibition is released before fertilization for embryogenesis to proceed normally. The conserved Dicer residues, their phosphorylation by ERK, and the consequences of the resulting modifications implicate an ERK-Dicer nexus as a fundamental component of the oocyte-to-embryo transition and an underlying mechanism coupling extracellular cues to small RNA production.
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Affiliation(s)
- Melanie Drake
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tokiko Furuta
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kin Suen Man
- Department of Biochemistry and Molecular Biology, UT MD Anderson Cancer Center, Houston, TX, 77030, USA,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Gabriel Gonzalez
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Bin Liu
- Center for Genetics and Genomics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John Ladbury
- Department of Biochemistry and Molecular Biology, UT MD Anderson Cancer Center, Houston, TX, 77030, USA,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Andrew Z. Fire
- Department of Pathology and Genetics, Stanford University, Stanford, CA, 94305, USA
| | - James B Skeath
- Department of Genetics, Washington University School of Medicine, Scott Avenue, Saint Louis, MO, 63110, USA
| | - Swathi Arur
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA,Center for Genetics and Genomics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA,Address correspondence to: Swathi Arur, Ph.D, Department of Genetics, Unit 1010, UT MD Anderson Cancer Center, Houston, 77030, Phone: 713-745-8424,
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Saldi TK, Ash PE, Wilson G, Gonzales P, Garrido-Lecca A, Roberts CM, Dostal V, Gendron TF, Stein LD, Blumenthal T, Petrucelli L, Link CD. TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA. EMBO J 2014; 33:2947-66. [PMID: 25391662 PMCID: PMC4282642 DOI: 10.15252/embj.201488740] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans mutants deleted for TDP-1, an ortholog of the neurodegeneration-associated RNA-binding protein TDP-43, display only mild phenotypes. Nevertheless, transcriptome sequencing revealed that many RNAs were altered in accumulation and/or processing in the mutant. Analysis of these transcriptional abnormalities demonstrates that a primary function of TDP-1 is to limit formation or stability of double-stranded RNA. Specifically, we found that deletion of tdp-1: (1) preferentially alters the accumulation of RNAs with inherent double-stranded structure (dsRNA); (2) increases the accumulation of nuclear dsRNA foci; (3) enhances the frequency of adenosine-to-inosine RNA editing; and (4) dramatically increases the amount of transcripts immunoprecipitable with a dsRNA-specific antibody, including intronic sequences, RNAs with antisense overlap to another transcript, and transposons. We also show that TDP-43 knockdown in human cells results in accumulation of dsRNA, indicating that suppression of dsRNA is a conserved function of TDP-43 in mammals. Altered accumulation of structured RNA may account for some of the previously described molecular phenotypes (e.g., altered splicing) resulting from reduction of TDP-43 function.
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Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Peter Ea Ash
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gavin Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Patrick Gonzales
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Vishantie Dostal
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Thomas Blumenthal
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Christopher D Link
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA Integrative Physiology, University of Colorado, Boulder, CO, USA
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