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Keegan LP, Hajji K, O’Connell MA. Adenosine Deaminase Acting on RNA (ADAR) Enzymes: A Journey from Weird to Wondrous. Acc Chem Res 2023; 56:3165-3174. [PMID: 37906879 PMCID: PMC10666284 DOI: 10.1021/acs.accounts.3c00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 11/02/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes that catalyze the conversion of adenosine to inosine in double-stranded (ds)RNA are evolutionarily conserved and are essential for many biological functions including nervous system function, hematopoiesis, and innate immunity. Initially it was assumed that the wide-ranging biological roles of ADARs are due to inosine in mRNA being read as guanosine by the translational machinery, allowing incomplete RNA editing in a target codon to generate two different proteins from the same primary transcript. In humans, there are approximately seventy-six positions that undergo site-specific editing in tissues at greater than 20% efficiency that result in recoding. Many of these transcripts are expressed in the central nervous system (CNS) and edited by ADAR2. Exploiting mouse genetic models revealed that transgenic mice lacking the gene encoding Adar2 die within 3 weeks of birth. Therefore, the role of ADAR2 in generating protein diversity in the nervous system is clear, but why is ADAR RNA editing activity essential in other biological processes, particularly editing mainly involving ADAR1? ADAR1 edits human transcripts having embedded Alu element inverted repeats (AluIRs), but the link from this activity to innate immunity activation was elusive. Mice lacking the gene encoding Adar1 are embryonically lethal, and a major breakthrough was the discovery that the role of Adar1 in innate immunity is due to its ability to edit such repetitive element inverted repeats which have the ability to form dsRNA in transcripts. The presence of inosine prevents activation of the dsRNA sensor melanoma differentiation-associated protein 5 (Mda5). Thus, inosine helps the cell discriminate self from non-self RNA, acting like a barcode on mRNA. As innate immunity is key to many different biological processes, the basis for this widespread biological role of the ADAR1 enzyme became evident.Our group has been studying ADARs from the outset of research on these enzymes. In this Account, we give a historical perspective, moving from the initial purification of ADAR1 and ADAR2 and cloning of their encoding genes up to the current research focus in the field and what questions still remain to be addressed. We discuss the characterizations of the proteins, their localizations, posttranslational modifications, and dimerization, and how all of these affect their biological activities. Another aspect we explore is the use of mouse and Drosophila genetic models to study ADAR functions and how these were crucial in determining the biological functions of the ADAR proteins. Finally, we describe the severe consequences of rare mutations found in the human genes encoding ADAR1 and ADAR2.
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Affiliation(s)
- Liam P. Keegan
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Khadija Hajji
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Mary A. O’Connell
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
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2
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Borovská I, Vořechovský I, Královičová J. Alu RNA fold links splicing with signal recognition particle proteins. Nucleic Acids Res 2023; 51:8199-8216. [PMID: 37309897 PMCID: PMC10450188 DOI: 10.1093/nar/gkad500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Transcriptomic diversity in primates was considerably expanded by exonizations of intronic Alu elements. To better understand their cellular mechanisms we have used structure-based mutagenesis coupled with functional and proteomic assays to study the impact of successive primate mutations and their combinations on inclusion of a sense-oriented AluJ exon in the human F8 gene. We show that the splicing outcome was better predicted by consecutive RNA conformation changes than by computationally derived splicing regulatory motifs. We also demonstrate an involvement of SRP9/14 (signal recognition particle) heterodimer in splicing regulation of Alu-derived exons. Nucleotide substitutions that accumulated during primate evolution relaxed the conserved left-arm AluJ structure including helix H1 and reduced the capacity of SRP9/14 to stabilize the closed Alu conformation. RNA secondary structure-constrained mutations that promoted open Y-shaped conformations of the Alu made the Alu exon inclusion reliant on DHX9. Finally, we identified additional SRP9/14 sensitive Alu exons and predicted their functional roles in the cell. Together, these results provide unique insights into architectural elements required for sense Alu exonization, identify conserved pre-mRNA structures involved in exon selection and point to a possible chaperone activity of SRP9/14 outside the mammalian signal recognition particle.
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Affiliation(s)
- Ivana Borovská
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
| | - Igor Vořechovský
- Faculty of Medicine, University of Southampton, HDH, MP808, Southampton SO16 6YD, United Kingdom
| | - Jana Královičová
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
- Institute of Zoology, Slovak Academy of Sciences, Bratislava 845 06, Slovak Republic
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3
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Joglekar A, Foord C, Jarroux J, Pollard S, Tilgner HU. From words to complete phrases: insight into single-cell isoforms using short and long reads. Transcription 2023; 14:92-104. [PMID: 37314295 PMCID: PMC10807471 DOI: 10.1080/21541264.2023.2213514] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/24/2023] [Accepted: 05/07/2023] [Indexed: 06/15/2023] Open
Abstract
The profiling of gene expression patterns to glean biological insights from single cells has become commonplace over the last few years. However, this approach overlooks the transcript contents that can differ between individual cells and cell populations. In this review, we describe early work in the field of single-cell short-read sequencing as well as full-length isoforms from single cells. We then describe recent work in single-cell long-read sequencing wherein some transcript elements have been observed to work in tandem. Based on earlier work in bulk tissue, we motivate the study of combination patterns of other RNA variables. Given that we are still blind to some aspects of isoform biology, we suggest possible future avenues such as CRISPR screens which can further illuminate the function of RNA variables in distinct cell populations.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Careen Foord
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Julien Jarroux
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Shaun Pollard
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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4
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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA (NEW YORK, N.Y.) 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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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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7
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Hou P, Meng S, Li M, Lin T, Chu S, Li Z, Zheng J, Gu Y, Bai J. LINC00460/DHX9/IGF2BP2 complex promotes colorectal cancer proliferation and metastasis by mediating HMGA1 mRNA stability depending on m6A modification. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:52. [PMID: 33526059 PMCID: PMC7851923 DOI: 10.1186/s13046-021-01857-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022]
Abstract
Background Increasing studies have shown that long noncoding RNAs (lncRNAs) are pivotal regulators participating in carcinogenic progression and tumor metastasis in colorectal cancer (CRC). Although lncRNA long intergenic noncoding RNA 460 (LINC00460) has been reported in CRC, the role and molecular mechanism of LINC00460 in CRC progression still requires exploration. Methods The expression levels of LINC00460 were analyzed by using a tissue microarray containing 498 CRC tissues and their corresponding non-tumor adjacent tissues. The correlations between the LINC00460 expression level and clinicopathological features were evaluated. The functional characterization of the role and molecular mechanism of LINC00460 in CRC was investigated through a series of in vitro and in vivo experiments. Results LINC00460 expression was increased in human CRC, and high LINC00460 expression was correlated with poor five-year overall survival and disease-free survival. LINC00460 overexpression sufficiently induced the epithelial–mesenchymal transition and promoted tumor cell proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. In addition, LINC00460 enhanced the protein expression of high-mobility group AT-hook 1 (HMGA1) by directly interacting with IGF2BP2 and DHX9 to bind the 3′ untranslated region (UTR) of HMGA1 mRNA and increased the stability of HMGA1 mRNA. In addition, the N6-methyladenosine (m6A) modification of HMGA1 mRNA by METTL3 enhanced HMGA1 expression in CRC. Finally, it suggested that HMGA1 was essential for LINC00460-induced cell proliferation, migration, and invasion. Conclusions LINC00460 may be a novel oncogene of CRC through interacting with IGF2BP2 and DHX9 and bind to the m6A modified HMGA1 mRNA to enhance the HMGA1 mRNA stability. LINC00460 can serve as a promising predictive biomarker for the diagnosis and prognosis among patients with CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01857-2.
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Affiliation(s)
- Pingfu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Sen Meng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China
| | - Minle Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China
| | - Tian Lin
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China
| | - Zhongwei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
| | - Yuming Gu
- Department of Interventional Radiography, Affiliated Hospital of Xuzhou Medical University, 99 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu Province, 221002, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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8
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Míková H, Kuchtiak V, Svobodová I, Spišská V, Pačesová D, Balík A, Bendová Z. Circadian Regulation of GluA2 mRNA Processing in the Rat Suprachiasmatic Nucleus and Other Brain Structures. Mol Neurobiol 2021; 58:439-449. [PMID: 32964314 DOI: 10.1007/s12035-020-02141-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/17/2020] [Indexed: 11/30/2022]
Abstract
The mammalian circadian system consists of a major circadian pacemaker located in the suprachiasmatic nucleus (SCN) of the hypothalamus and peripheral clocks in the body, including brain structures. The SCN depends on glutamatergic neurotransmission for transmitting signals from the retina, and it exhibits spontaneous 24-h rhythmicity in neural activity. The aim of this work was to evaluate the degree and circadian rhythmicity of AMPA receptor GluA2 subunit R/G editing and alternative flip/flop splicing in the SCN and other brain structures in Wistar rats. Our data show that the circadian rhythmicity in the SCN's GluA2 mRNA level was highest at dawn, while the circadian rhythm in R/G editing peaked at CT10 and the rhythmic flip varied with the acrophase at the late subjective night. The circadian rhythmicity was confirmed for R/G editing and splicing in the CA3 hippocampal area, and rhythmic variation of the flip isoform was also measured in the olfactory bulbs and cerebellum. The correlations between the R/G editing and alternative flip/flop splicing revealed a structure-dependent direction. In the hippocampus, the edited (G)-form level was positively correlated with the flip variant abundance, in accord with published data; by contrast, in the SCN, the flip variant was in associated more with the unedited (R) form. The edited (G) form and flop isoform also predominated in the retina and cerebellum.
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Affiliation(s)
- Hana Míková
- Faculty of Science, Department of Physiology, Charles University, Viničná 7, 128 43, Prague 2, Czech Republic
| | - Viktor Kuchtiak
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Irena Svobodová
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Veronika Spišská
- Faculty of Science, Department of Physiology, Charles University, Viničná 7, 128 43, Prague 2, Czech Republic
| | - Dominika Pačesová
- Faculty of Science, Department of Physiology, Charles University, Viničná 7, 128 43, Prague 2, Czech Republic
- National Institute of Mental Health, Klecany, Czech Republic
| | - Aleš Balík
- Faculty of Science, Department of Physiology, Charles University, Viničná 7, 128 43, Prague 2, Czech Republic.
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
- Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic.
| | - Zdeňka Bendová
- Faculty of Science, Department of Physiology, Charles University, Viničná 7, 128 43, Prague 2, Czech Republic.
- National Institute of Mental Health, Klecany, Czech Republic.
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9
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Wu D, Zang YY, Shi YY, Ye C, Cai WM, Tang XH, Zhao L, Liu Y, Gan Z, Chen GQ, Xu Y, Yang JJ, Shi YS. Distant coupling between RNA editing and alternative splicing of the osmosensitive cation channel Tmem63b. J Biol Chem 2020; 295:18199-18212. [PMID: 33100268 PMCID: PMC7939439 DOI: 10.1074/jbc.ra120.016049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/17/2020] [Indexed: 11/06/2022] Open
Abstract
Post-transcriptional modifications of pre-mRNAs expand the diversity of proteomes in higher eukaryotes. In the brain, these modifications diversify the functional output of many critical neuronal signal molecules. In this study, we identified a brain-specific A-to-I RNA editing that changed glutamine to arginine (Q/R) at exon 20 and an alternative splicing of exon 4 in Tmem63b, which encodes a ubiquitously expressed osmosensitive cation channel. The channel isoforms lacking exon 4 occurred in ∼80% of Tmem63b mRNAs in the brain but were not detected in other tissues, suggesting a brain-specific splicing. We found that the Q/R editing was catalyzed by Adar2 (Adarb1) and required an editing site complementary sequence located in the proximal 5' end of intron 20. Moreover, the Q/R editing was almost exclusively identified in the splicing isoform lacking exon 4, indicating a coupling between the editing and the splicing. Elimination of the Q/R editing in brain-specific Adar2 knockout mice did not affect the splicing efficiency of exon 4. Furthermore, transfection with the splicing isoform containing exon 4 suppressed the Q/R editing in primary cultured cerebellar granule neurons. Thus, our study revealed a coupling between an RNA editing and a distant alternative splicing in the Tmem63b pre-mRNA, in which the splicing plays a dominant role. Finally, physiological analysis showed that the splicing and the editing coordinately regulate Ca2+ permeability and osmosensitivity of channel proteins, which may contribute to their functions in the brain.
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Affiliation(s)
- Dan Wu
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yan-Yu Zang
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yong-Yun Shi
- Department of Orthopaedics, Luhe People's Hospital Affiliated to Yangzhou University, Nanjing, China
| | - Chang Ye
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Wen-Min Cai
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Xiao-Hui Tang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; School of Medicine, Southeast University, Nanjing, China
| | - Liyun Zhao
- Translational Science and Clinical Biomarker, BeiGene (Shanghai) Co., Ltd., Shanghai, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Zhenji Gan
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Gui-Quan Chen
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Jian-Jun Yang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China; Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
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10
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Kapoor U, Licht K, Amman F, Jakobi T, Martin D, Dieterich C, Jantsch MF. ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Genome Res 2020; 30:1107-1118. [PMID: 32727871 PMCID: PMC7462079 DOI: 10.1101/gr.256933.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
Adenosine-to-inosine RNA editing and pre-mRNA splicing largely occur cotranscriptionally and influence each other. Here, we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA editing on splicing across different tissues. We find that ADAR has a 100× higher impact on splicing than ADARB1, although both enzymes target a similar number of substrates with a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 5′ of differentially spliced regions. Several of these ADARB1-mediated editing events change splice consensus sequences, therefore strongly influencing splicing of some mRNAs. A significant overlap between differentially edited and differentially spliced sites suggests evolutionary selection toward splicing being regulated by editing in a tissue-specific manner.
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Affiliation(s)
- Utkarsh Kapoor
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Konstantin Licht
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Tobias Jakobi
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - David Martin
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christoph Dieterich
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - Michael F Jantsch
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
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11
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Tan TY, Sedmík J, Fitzgerald MP, Halevy RS, Keegan LP, Helbig I, Basel-Salmon L, Cohen L, Straussberg R, Chung WK, Helal M, Maroofian R, Houlden H, Juusola J, Sadedin S, Pais L, Howell KB, White SM, Christodoulou J, O'Connell MA. Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures. Am J Hum Genet 2020; 106:467-483. [PMID: 32220291 DOI: 10.1016/j.ajhg.2020.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.
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Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Mark P Fitzgerald
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rivka Sukenik Halevy
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Felsenstein Medical Research Center, Petah Tikva 49100, Israel
| | - Lior Cohen
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Pediatric Neurology Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Mayada Helal
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Simon Sadedin
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katherine B Howell
- Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia; Department of Neurology, Royal Children's Hospital, Parkville 3052, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic.
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12
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Levitsky LI, Kliuchnikova AA, Kuznetsova KG, Karpov DS, Ivanov MV, Pyatnitskiy MA, Kalinina OV, Gorshkov MV, Moshkovskii SA. Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes. Proteomics 2019; 19:e1900195. [PMID: 31576663 DOI: 10.1002/pmic.201900195] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/25/2019] [Indexed: 12/30/2022]
Abstract
Proteogenomics is based on the use of customized genome or RNA sequencing databases for interrogation of shotgun proteomics data in search for proteome-level evidence of genome variations or RNA editing. In this work, the products of adenosine-to-inosine RNA editing in human and murine brain proteomes are identified using publicly available brain proteome LC-MS/MS datasets and an RNA editome database compiled from several sources. After filtering of false-positive results, 20 and 37 sites of editing in proteins belonging to 14 and 32 genes are identified for murine and human brain proteomes, respectively. Eight sites of editing identified with high spectral counts overlapped between human and mouse brain samples. Some of these sites have been previously reported using orthogonal methods, such as α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptors, CYFIP2, coatomer alpha. Also, differential editing between neurons and microglia is demonstrated in this work for some of the proteins from primary murine brain cell cultures. Because many edited sites are still not characterized functionally at the protein level, the results provide a necessary background for their further analysis in normal and diseased cells and tissues using targeted proteomic approaches.
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Affiliation(s)
- Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna A Kliuchnikova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
| | - Ksenia G Kuznetsova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia
| | - Dmitry S Karpov
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail A Pyatnitskiy
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Onco Genotest LLC, Moscow, 125047, Russia.,Department of Technologies for Complex System Modelling, National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, 66123, Germany.,Medical Faculty, Saarland University, Kirrberger Straße, Homburg, 66421, Germany
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141700, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
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13
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Hong H, An O, Chan THM, Ng VHE, Kwok HS, Lin JS, Qi L, Han J, Tay DJT, Tang SJ, Yang H, Song Y, Bellido Molias F, Tenen DG, Chen L. Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer. Nucleic Acids Res 2019; 46:7953-7969. [PMID: 29796672 PMCID: PMC6125626 DOI: 10.1093/nar/gky396] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/30/2018] [Indexed: 12/25/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing entails the enzymatic deamination of adenosines to inosines by adenosine deaminases acting on RNA (ADARs). Dysregulated A-to-I editing has been implicated in various diseases, including cancers. However, the precise factors governing the A-to-I editing and their physiopathological implications remain as a long-standing question. Herein, we unravel that DEAH box helicase 9 (DHX9), at least partially dependent of its helicase activity, functions as a bidirectional regulator of A-to-I editing in cancer cells. Intriguingly, the ADAR substrate specificity determines the opposing effects of DHX9 on editing as DHX9 silencing preferentially represses editing of ADAR1-specific substrates, whereas augments ADAR2-specific substrate editing. Analysis of 11 cancer types from The Cancer Genome Atlas (TCGA) reveals a striking overexpression of DHX9 in tumors. Further, tumorigenicity studies demonstrate a helicase-dependent oncogenic role of DHX9 in cancer development. In sum, DHX9 constitutes a bidirectional regulatory mode in A-to-I editing, which is in part responsible for the dysregulated editome profile in cancer.
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Affiliation(s)
- HuiQi Hong
- 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
| | - Tim H M Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Vanessa H E Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hui Si Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jaymie S Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Daryl J T 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
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yangyang Song
- 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
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - 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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14
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Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M. Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries. Nucleic Acids Res 2019; 47:e22. [PMID: 30590609 PMCID: PMC6393238 DOI: 10.1093/nar/gky1228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
Adenosine to inosine editing is common in the human transcriptome and changes of this essential activity is associated with disease. Children with ADAR1 mutations develop fatal Aicardi-Goutières syndrome characterized by aberrant interferon expression. In contrast, ADAR1 overexpression is associated with increased malignancy of breast, lung and liver cancer. ADAR1 silencing in breast cancer cells leads to increased apoptosis, suggesting an anti-apoptotic function that promotes cancer progression. Yet, suitable high-throughput editing assays are needed to efficiently screen chemical libraries for modifiers of ADAR1 activity. We describe the development of a bioluminescent reporter system that facilitates rapid and accurate determination of endogenous editing activity. The system is based on the highly sensitive and quantitative Nanoluciferase that is conditionally expressed upon reporter-transcript editing. Stably introduced into cancer cell lines, the system reports on elevated endogenous ADAR1 editing activity induced by interferon as well as knockdown of ADAR1 and ADAR2. In a single-well setup we used the reporter in HeLa cells to screen a small molecule library of 33 000 compounds. This yielded a primary hit rate of 0.9% at 70% inhibition of editing. Thus, we provide a key tool for high-throughput identification of modifiers of A-to-I editing activity in cancer cells.
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Affiliation(s)
- Kajsa Fritzell
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Li-Di Xu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
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15
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Yan X, Chang J, Sun R, Meng X, Wang W, Zeng L, Liu B, Li W, Yan X, Huang C, Zhao Y, Li Z, Yang S. DHX9 inhibits epithelial-mesenchymal transition in human lung adenocarcinoma cells by regulating STAT3. Am J Transl Res 2019; 11:4881-4894. [PMID: 31497206 PMCID: PMC6731401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
DHX9 has numerous functions regulating transcription, translation, RNA processing and transport, and DNA replication and maintenance of genomic stability. It is involved in human cancers as either an oncogene or tumor suppressor. However, its role in the progression of lung cancer and underlying mechanisms remains unclear. In this study, we demonstrated that DHX9 is overexpressed in human lung cancer tissues and serum. Also, a favorable prognosis of lung adenocarcinoma is predicted when DHX9 is at a high level. DHX9 knockdown promoted cell proliferation, migration, and invasion and inhibited apoptosis progression in A549 cells. Moreover, DHX9 knockdown led to a significant decrease of E-cadherin expression, an increase of vimentin and snail, and a significant increase in the phosphorylation of STAT3 in A549 cells. In summary, our studies identified a novel role of DHX9 in driving tumor growth and epithelial-mesenchymal transition progress of A549 cells. We propose that the STAT3 pathway may be implicated in the DHX9-related epithelial-mesenchymal transition of lung adenocarcinoma. Therefore, DHX9 may be a prognostic marker or potential therapeutic target for lung adenocarcinoma.
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Affiliation(s)
- Xueli Yan
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Jing Chang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Ruiying Sun
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Xia Meng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Wei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Lizhong Zeng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Boxuan Liu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Wei Li
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Xuehua Yan
- Department of Assisted Reproductive Centre, Northwest Women’s and Children’s HospitalXi’an, Shaanxi, China
| | - Chen Huang
- Department of Genetics and Molecular Biology, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Yongxi Zhao
- School of Life Science and Technology, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Zongfang Li
- Department of General Surgery, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Shuanying Yang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
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16
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Shanmugam R, Zhang F, Srinivasan H, Charles Richard JL, Liu KI, Zhang X, Woo CWA, Chua ZHM, Buschdorf JP, Meaney MJ, Tan MH. SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Res 2019; 46:7379-7395. [PMID: 29992293 PMCID: PMC6101530 DOI: 10.1093/nar/gky615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/26/2018] [Indexed: 02/05/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing displays diverse spatial patterns across different tissues. However, the human genome encodes only two catalytically active editing enzymes (ADAR1 and ADAR2), suggesting that other regulatory factors help shape the editing landscape. Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in primates. SRSF9 is more lowly expressed in the brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain. This interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Transcriptome-wide location analysis and RNA sequencing revealed 1328 editing sites that are controlled directly by SRSF9. This regulon is significantly enriched for brain-specific sites. We further uncovered a novel motif in the ADAR2-dependent SRSF9 binding sites and provided evidence that the splicing factor prevents loss of cell viability by inhibiting ADAR2-mediated editing of genes involved in proteostasis, energy metabolism, the cell cycle and DNA repair. Collectively, our results highlight the importance of SRSF9 as an editing regulator and suggest potential roles for other splicing factors.
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Affiliation(s)
- Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Fan Zhang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Harini Srinivasan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | | | - Kaiwen I Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Xiujun Zhang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Cheok Wei A Woo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Zi Hao M Chua
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore.,School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore 599489, Singapore
| | - Jan Paul Buschdorf
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore 117609, Singapore
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore 117609, Singapore.,Douglas Mental Health University Institute, McGill University, Montreal (Quebec) H4H 1R3, Canada
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
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17
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Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol 2019; 2:19. [PMID: 30652130 PMCID: PMC6331435 DOI: 10.1038/s42003-018-0271-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythematosus. Additionally, most key editing regulators act in a cell type-specific manner. Together, our work provides insights for the regulatory mechanisms of RNA editing.
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Affiliation(s)
| | - Stephen S. Tran
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Hyun-Ik Jun
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Ei-Wen Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Anneke Brümmer
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Gabriel A. Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Xinshu Xiao
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095 USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
- Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
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18
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Chakraborty P, Huang JTJ, Hiom K. DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing. Nat Commun 2018; 9:4346. [PMID: 30341290 PMCID: PMC6195550 DOI: 10.1038/s41467-018-06677-1] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/06/2018] [Indexed: 01/05/2023] Open
Abstract
R-loops are stable nucleic acid structures that have important physiological functions, but which also pose a significant threat to genomic stability. Increased R-loops cause replication stress and chromosome fragility and have been associated with diseases such as neurodegeneration and cancer. Although excessive R-loops are a feature of cells that are defective in RNA processing, what causes them to form is unclear. Here, we demonstrate that DHX9 (RNA helicase A) promotes the formation of pathological and non-pathological R-loops. In the absence of splicing factors, formation of R-loops correlates with the prolonged association of DHX9 with RNA Polymerase II (RNA Pol II). This leads to the production of DNA–RNA hybrid, which traps RNA Pol II on chromatin with the potential to block DNA replication. Our data provide a molecular mechanism for the formation of R-loops that is relevant to neurodegenerative diseases and cancers in which deregulated RNA processing is a feature. Unresolved R-loops can represent a threat to genome stability. Here the authors reveal that DHX9 helicase can promote R-loop formation in the absence of splicing factors SFPQ and SF3B3.
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Affiliation(s)
- Prasun Chakraborty
- Division of Cellular Medicine, School of Medicine, University of Dundee, Scotland, UK
| | - Jeffrey T J Huang
- Biomarker and Drug Analysis Core Facility, School of Medicine, University of Dundee, Scotland, UK
| | - Kevin Hiom
- Division of Cellular Medicine, School of Medicine, University of Dundee, Scotland, UK.
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19
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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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20
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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21
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Daniel C, Widmark A, Rigardt D, Öhman M. Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome. Genome Biol 2017; 18:195. [PMID: 29061182 PMCID: PMC5654063 DOI: 10.1186/s13059-017-1324-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo. We have previously shown that some editing sites require adjacent long stem loop structures acting as editing inducer elements (EIEs) for efficient editing. RESULTS The glutamate receptor subunit A2 is edited at the Q/R site in almost 100% of all transcripts. We show that efficient editing at the Q/R site requires an EIE in the downstream intron, separated by an internal loop. Also, other efficiently edited sites are flanked by conserved, highly structured EIEs and we propose that this is a general requisite for efficient editing, while sites with low levels of editing lack EIEs. This phenomenon is not limited to mRNA, as non-coding primary miRNAs also use EIEs to recruit ADAR to specific sites. CONCLUSIONS We propose a model where two regions of dsRNA are required for efficient editing: first, an RNA stem that recruits ADAR and increases the local concentration of the enzyme, then a shorter, less stable duplex that is ideal for efficient and specific catalysis. This discovery changes the way we define and determine a substrate for A-to-I editing. This will be important in the discovery of novel editing sites, as well as explaining cases of altered editing in relation to disease.
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Affiliation(s)
- Chammiran Daniel
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Ditte Rigardt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
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22
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Wen W, Lin CY, Niu L. R/G editing in GluA2R flop modulates the functional difference between GluA1 flip and flop variants in GluA1/2R heteromeric channels. Sci Rep 2017; 7:13654. [PMID: 29057893 PMCID: PMC5651858 DOI: 10.1038/s41598-017-13233-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022] Open
Abstract
In α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate (AMPA) receptors, RNA editing and alternative splicing generate sequence variants, and those variants, as in GluA2-4 AMPA receptor subunits, generally show different properties. Yet, earlier studies have shown that the alternatively spliced, flip and flop variants of GluA1 AMPA receptor subunit exhibit no functional difference in homomeric channel form. Using a laser-pulse photolysis technique, combined with whole-cell recording, we measured the rate of channel opening, among other kinetic properties, for a series of AMPA channels with different arginine/glycine (R/G) editing and flip/flop status. We find that R/G editing in the GluA2 subunit modulates the channel properties in both homomeric (GluA2Q) and complex (GluA2Q/2R and GluA1/2R) channel forms. However, R/G editing is only effective in flop channels. Specifically, editing at the R/G site on the GluA2R flop isoform accelerates the rate of channel opening and desensitization for GluA1/2R channels more pronouncedly with the GluA1 being in the flop form than in the flip form; yet R/G editing has no effect on either channel-closing rate or EC50. Our results suggest R/G editing via GluA2R serve as a regulatory mechanism to modulate the function of GluA2R-containing, native receptors involved in fast excitatory synaptic transmission.
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Affiliation(s)
- Wei Wen
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York, 12222, United States
| | - Chi-Yen Lin
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York, 12222, United States
| | - Li Niu
- Department of Chemistry, and Center for Neuroscience Research, University at Albany, SUNY, Albany, New York, 12222, United States.
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23
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Capitanio JS, Montpetit B, Wozniak RW. Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein. Nucleus 2017; 9:1-8. [PMID: 28934014 PMCID: PMC5973140 DOI: 10.1080/19491034.2017.1364826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, 1-3 but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. 4-6 Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity. 7 Furthermore, these proteins were dependent on one another for their proper association with a subset of gene loci to control transcription and modulate mRNA splicing. 7 On the basis of these observations, we proposed that Nup98 functions to regulate DHX9 activity within the nucleoplasm. 7 Since Nup98 is associated with several DBPs, regulation of DHX9 by Nup98 may represent a paradigm for understanding how Nup98, and possibly other FG-Nup proteins, could direct the diverse cellular activities of multiple DBPs.
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Affiliation(s)
| | - Ben Montpetit
- a Department of Cell Biology , University of Alberta , Edmonton , Canada.,b Department of Viticulture and Enology , University of California at Davis , Davis , CA , USA
| | - Richard W Wozniak
- a Department of Cell Biology , University of Alberta , Edmonton , Canada
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24
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Herzel L, Ottoz DSM, Alpert T, Neugebauer KM. Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. Nat Rev Mol Cell Biol 2017; 18:637-650. [PMID: 28792005 DOI: 10.1038/nrm.2017.63] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Diana S M Ottoz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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25
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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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26
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Capitanio JS, Montpetit B, Wozniak RW. Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. eLife 2017; 6. [PMID: 28221134 PMCID: PMC5338925 DOI: 10.7554/elife.18825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022] Open
Abstract
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, our analysis revealed that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on our results, we propose that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases.
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Affiliation(s)
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, United states
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27
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Behm M, Wahlstedt H, Widmark A, Eriksson M, Öhman M. Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development. J Cell Sci 2017; 130:745-753. [PMID: 28082424 DOI: 10.1242/jcs.200055] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/30/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine to inosine (A-to-I) RNA editing is important for a functional brain, and most known sites that are subject to selective RNA editing have been found to result in diversified protein isoforms that are involved in neurotransmission. In the absence of the active editing enzymes ADAR1 or ADAR2 (also known as ADAR and ADARB1, respectively), mice fail to survive until adulthood. Nuclear A-to-I editing of neuronal transcripts is regulated during brain development, with low levels of editing in the embryo and a dramatic increase after birth. Yet, little is known about the mechanisms that regulate editing during development. Here, we demonstrate lower levels of ADAR2 in the nucleus of immature neurons than in mature neurons. We show that importin-α4 (encoded by Kpna3), which increases during neuronal maturation, interacts with ADAR2 and contributes to the editing efficiency by bringing it into the nucleus. Moreover, we detect an increased number of interactions between ADAR2 and the nuclear isomerase Pin1 as neurons mature, which contribute to ADAR2 protein stability. Together, these findings explain how the nuclear editing of substrates that are important for neuronal function can increase as the brain develops.
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Affiliation(s)
- Mikaela Behm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Helene Wahlstedt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Maria Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
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28
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Dillman AA, Cookson MR, Galter D. ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo. RNA Biol 2016; 13:15-24. [PMID: 26669816 DOI: 10.1080/15476286.2015.1110675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Adenosine deaminases bind double stranded RNA and convert adenosine to inosine. Editing creates multiple isoforms of neurotransmitter receptors, such as with Gria2. Adar2 KO mice die of seizures shortly after birth, but if the Gria2 Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on frontal cortices of Adar2(-/-) Gria2(R/R) mice and littermates. We found 56 editing sites with significantly diminished editing levels in Adar2 deficient animals with the majority in coding regions. Only two genes and 3 exons showed statistically significant differences in expression levels. This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has relatively modest effects on gene expression and splicing in the adult mouse frontal cortex.
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Affiliation(s)
- Allissa A Dillman
- a Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health , Bethesda , MD , USA.,b Department of Neuroscience , Karolinska Institute , 171 77 Stockholm , Sweden.,c Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute , Bethesda , MD , USA
| | - Mark R Cookson
- a Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health , Bethesda , MD , USA
| | - Dagmar Galter
- b Department of Neuroscience , Karolinska Institute , 171 77 Stockholm , Sweden
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29
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Abstract
All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.
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Affiliation(s)
- Joshua J C Rosenthal
- Universidad de Puerto Rico, Recinto de Ciencias Medicas, Instituto de Neurobiologia, 201 Blvd. del Valle, San Juan, PR 00901, USA
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30
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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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31
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Deffit SN, Hundley HA. To edit or not to edit: regulation of ADAR editing specificity and efficiency. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:113-27. [PMID: 26612708 DOI: 10.1002/wrna.1319] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 11/08/2022]
Abstract
Hundreds to millions of adenosine (A)-to-inosine (I) modifications are present in eukaryotic transcriptomes and play an essential role in the creation of proteomic and phenotypic diversity. As adenosine and inosine have different base-pairing properties, the functional consequences of these modifications or 'edits' include altering coding potential, splicing, and miRNA-mediated gene silencing of transcripts. However, rather than serving as a static control of gene expression, A-to-I editing provides a means to dynamically rewire the genetic code during development and in a cell-type specific manner. Interestingly, during normal development, in specific cells, and in both neuropathological diseases and cancers, the extent of RNA editing does not directly correlate with levels of the substrate mRNA or the adenosine deaminase that act on RNA (ADAR) editing enzymes, implying that cellular factors are required for spatiotemporal regulation of A-to-I editing. The factors that affect the specificity and extent of ADAR activity have been thoroughly dissected in vitro. Yet, we still lack a complete understanding of how specific ADAR family members can selectively deaminate certain adenosines while others cannot. Additionally, in the cellular environment, ADAR specificity and editing efficiency is likely to be influenced by cellular factors, which is currently an area of intense investigation. Data from many groups have suggested two main mechanisms for controlling A-to-I editing in the cell: (1) regulating ADAR accessibility to target RNAs and (2) protein-protein interactions that directly alter ADAR enzymatic activity. Recent studies suggest cis- and trans-acting RNA elements, heterodimerization and RNA-binding proteins play important roles in regulating RNA editing levels in vivo. WIREs RNA 2016, 7:113-127. doi: 10.1002/wrna.1319.
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Affiliation(s)
- Sarah N Deffit
- Medical Sciences Program, Indiana University, Bloomington, IN, USA
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32
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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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33
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Hood JL, Morabito MV, Martinez CR, Gilbert JA, Ferrick EA, Ayers GD, Chappell JD, Dermody TS, Emeson RB. Reovirus-mediated induction of ADAR1 (p150) minimally alters RNA editing patterns in discrete brain regions. Mol Cell Neurosci 2014; 61:97-109. [PMID: 24906008 PMCID: PMC4134954 DOI: 10.1016/j.mcn.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 05/22/2014] [Accepted: 06/02/2014] [Indexed: 12/11/2022] Open
Abstract
Transcripts encoding ADAR1, a double-stranded, RNA-specific adenosine deaminase involved in the adenosine-to-inosine (A-to-I) editing of mammalian RNAs, can be alternatively spliced to produce an interferon-inducible protein isoform (p150) that is up-regulated in both cell culture and in vivo model systems in response to pathogen or interferon stimulation. In contrast to other tissues, p150 is expressed at extremely low levels in the brain and it is unclear what role, if any, this isoform may play in the innate immune response of the central nervous system (CNS) or whether the extent of editing for RNA substrates critical for CNS function is affected by its induction. To investigate the expression of ADAR1 isoforms in response to viral infection and subsequent alterations in A-to-I editing profiles for endogenous ADAR targets, we used a neurotropic strain of reovirus to infect neonatal mice and quantify A-to-I editing in discrete brain regions using a multiplexed, high-throughput sequencing strategy. While intracranial injection of reovirus resulted in a widespread increase in the expression of ADAR1 (p150) in multiple brain regions and peripheral organs, significant changes in site-specific A-to-I conversion were quite limited, suggesting that steady-state levels of p150 expression are not a primary determinant for modulating the extent of editing for numerous ADAR targets in vivo.
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Affiliation(s)
- Jennifer L Hood
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Michael V Morabito
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Charles R Martinez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - James A Gilbert
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Elizabeth A Ferrick
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Gregory D Ayers
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James D Chappell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Terence S Dermody
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Ronald B Emeson
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States.
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34
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Fukuda M, Kurihara K, Yamaguchi S, Oyama Y, Deshimaru M. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing. RNA (NEW YORK, N.Y.) 2014; 20:392-405. [PMID: 24448449 PMCID: PMC3923133 DOI: 10.1261/rna.041202.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.
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Daniel C, Silberberg G, Behm M, Öhman M. Alu elements shape the primate transcriptome by cis-regulation of RNA editing. Genome Biol 2014; 15:R28. [PMID: 24485196 PMCID: PMC4053975 DOI: 10.1186/gb-2014-15-2-r28] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/03/2014] [Indexed: 11/25/2022] Open
Abstract
Background RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought.
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Differences between RNA and DNA due to RNA editing in temporal lobe epilepsy. Neurobiol Dis 2013; 56:66-73. [PMID: 23607937 DOI: 10.1016/j.nbd.2013.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/02/2013] [Indexed: 01/21/2023] Open
Abstract
To investigate whether alterations in RNA editing (an enzymatic base-specific change to the RNA sequence during primary transcript formation from DNA) of neurotransmitter receptor genes and of transmembrane ion channel genes play a role in human temporal lobe epilepsy (TLE), this exploratory study analyzed 14 known cerebral editing sites in RNA extracted from the brain tissue of 41 patients who underwent surgery for mesial TLE, 23 with hippocampal sclerosis (MTLE+HS). Because intraoperatively sampled RNA cannot be obtained from healthy controls and the best feasible control is identically sampled RNA from patients with a clinically shorter history of epilepsy, the primary aim of the study was to assess the correlation between epilepsy duration and RNA editing in the homogenous group of MTLE+HS. At the functionally relevant I/V site of the voltage-gated potassium channel Kv1.1, an inverse correlation of RNA editing was found with epilepsy duration (r=-0.52, p=0.01) but not with patient age at surgery, suggesting a specific association with either the epileptic process itself or its antiepileptic medication history. No significant correlations were found between RNA editing and clinical parameters at other sites within glutamate receptor or serotonin 2C receptor gene transcripts. An "all-or-none" (≥95% or ≤5%) editing pattern at most or all sites was discovered in 2 patients. As a secondary part of the study, RNA editing was also analyzed as in the previous literature where up to now, few single editing sites were compared with differently obtained RNA from inhomogenous patient groups and autopsies, and by measuring editing changes in our mouse model. The present screening study is first to identify an editing site correlating with a clinical parameter, and to also provide an estimate of the possible effect size at other sites, which is a prerequisite for power analysis needed in planning future studies.
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Tariq A, Garncarz W, Handl C, Balik A, Pusch O, Jantsch MF. RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation. Nucleic Acids Res 2012; 41:2581-93. [PMID: 23275536 PMCID: PMC3575830 DOI: 10.1093/nar/gks1353] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA editing by adenosine deaminases that act on RNA (ADARs) diversifies the transcriptome by changing adenosines to inosines. In mammals, editing levels vary in different tissues, during development, and also in pathogenic conditions. From a screen for repressors of editing we have isolated three proteins that repress ADAR2-mediated RNA editing. The three proteins RPS14, SFRS9 and DDX15 interact with RNA. Overexpression or depletion of these proteins can decrease or increase editing levels by 15%, thus allowing a modulation of RNA editing up to 30%. Interestingly, the three proteins alter RNA editing in a substrate-specific manner that correlates with their RNA binding preferences. In mammalian cells, SFRS9 significantly affects editing of the two substrates CFLAR and cyFIP2, while the ribosomal protein RPS14 mostly inhibits editing of cyFIP2 messenger RNA. The helicase DDX15, in turn, has a strong effect on editing in Caenorhabditis elegans. Expression of the three factors decreases during mouse brain development. Moreover, expression levels of SFRS9 and DDX15 respond strongly to neuronal stimulation or repression, showing an inverse correlation with editing levels. Colocalization and immunoprecipitation studies demonstrate a direct interaction of SFRS9 and RPS14 with ADAR2, while DDX15 associates with other helicases and splicing factors. Our data show that different editing sites can be specifically altered in their editing pattern by changing the local RNP landscape.
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Affiliation(s)
- Aamira Tariq
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 1, A-1030 Vienna, Austria
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Decher N, Netter MF, Streit AK. Putative Impact of RNA Editing on Drug Discovery. Chem Biol Drug Des 2012; 81:13-21. [DOI: 10.1111/cbdd.12045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Balik A, Penn AC, Nemoda Z, Greger IH. Activity-regulated RNA editing in select neuronal subfields in hippocampus. Nucleic Acids Res 2012; 41:1124-34. [PMID: 23172290 PMCID: PMC3553983 DOI: 10.1093/nar/gks1045] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, facilitating fine tuning and homeostasis of cellular functions, a similar regulation has not been described for RNA editing. Here, we show that the AMPA receptor R/G editing site is dynamically regulated in the hippocampus in response to activity. These changes are bi-directional, reversible and correlate with levels of the editase Adar2. This regulation is observed in the CA1 hippocampal subfield but not in CA3 and is thus subfield/celltype-specific. Moreover, alternative splicing of the flip/flop cassette downstream of the R/G site is closely linked to the editing state, which is regulated by Ca2+. Our data show that A-to-I RNA editing has the capacity to tune protein function in response to external stimuli.
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Affiliation(s)
- Ales Balik
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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Daniel C, Venø MT, Ekdahl Y, Kjems J, Öhman M. A distant cis acting intronic element induces site-selective RNA editing. Nucleic Acids Res 2012; 40:9876-86. [PMID: 22848101 PMCID: PMC3479170 DOI: 10.1093/nar/gks691] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated the requirements for editing at the I/M site in the Gabra-3 transcript of the GABAA receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce editing of coding regions throughout the transcriptome.
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Affiliation(s)
- Chammiran Daniel
- Department of Molecular Biology and Functional Genomics, Stockholm University, Svante Arrheniusväg 20C, SE-10691, Stockholm, Sweden
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Rodriguez J, Menet JS, Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell 2012; 47:27-37. [PMID: 22658416 DOI: 10.1016/j.molcel.2012.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 03/08/2012] [Accepted: 04/16/2012] [Indexed: 01/31/2023]
Abstract
The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila by isolating nascent RNA from adult fly heads and subjecting samples to high throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR-null strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally.
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Affiliation(s)
- Joseph Rodriguez
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, and Department of Biology, Brandeis University, Waltham, MA 02451, USA
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Barraud P, Heale BSE, O'Connell MA, Allain FHT. Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA. Biochimie 2011; 94:1499-509. [PMID: 22210494 DOI: 10.1016/j.biochi.2011.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
Abstract
Adenosine deaminases that act on RNA (ADAR) catalyze adenosine to inosine (A-to-I) editing in double-stranded RNA (dsRNA) substrates. Inosine is read as guanosine by the translation machinery; therefore A-to-I editing events in coding sequences may result in recoding genetic information. Whereas vertebrates have two catalytically active enzymes, namely ADAR1 and ADAR2, Drosophila has a single ADAR protein (dADAR) related to ADAR2. The structural determinants controlling substrate recognition and editing of a specific adenosine within dsRNA substrates are only partially understood. Here, we report the solution structure of the N-terminal dsRNA binding domain (dsRBD) of dADAR and use NMR chemical shift perturbations to identify the protein surface involved in RNA binding. Additionally, we show that Drosophila ADAR edits the R/G site in the mammalian GluR-2 pre-mRNA which is naturally modified by both ADAR1 and ADAR2. We then constructed a model showing how dADAR dsRBD1 binds to the GluR-2 R/G stem-loop. This model revealed that most side chains interacting with the RNA sugar-phosphate backbone need only small displacement to adapt for dsRNA binding and are thus ready to bind to their dsRNA target. It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, CH-8093 Zürich, Switzerland
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The intricate relationship between RNA structure, editing, and splicing. Semin Cell Dev Biol 2011; 23:281-8. [PMID: 22178616 DOI: 10.1016/j.semcdb.2011.11.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 11/23/2022]
Abstract
Post-transcriptional modifications such as RNA editing and splicing diversify the proteome while limiting the necessary size of the genome. Although splicing globally rearranges existing information within the transcript, the conserved process of adenosine-to-inosine RNA editing recodes the message through single nucleotide changes, often at very specific locations. Because inosine is interpreted as guanosine by the cellular machineries, editing effectively results in the substitution of a guanosine for an adenosine in the primary RNA sequence. Precise control of editing is dictated by duplex structures in the transcript, formed between the exonic region surrounding the editing site and cis regulatory elements often localized in a nearby intron, suggesting that editing must precede splicing. However, the precise relationship between these post-transcriptional processes remains unclear. Here we present general commonalities of RNA editing substrates and consequential predictions regarding the interaction between editing and splicing. We also discuss anomalies and interesting cases of RNA editing that confound our understanding of the relationship between these post-transcriptional processes.
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Abstract
The main type of RNA editing in mammals is the conversion of adenosine to inosine which is translated as if it were guanosine. The enzymes that catalyze this reaction are ADARs (adenosine deaminases that act on RNA), of which there are four in mammals, two of which are catalytically inactive. ADARs edit transcripts that encode proteins expressed mainly in the CNS and editing is crucial to maintain a correctly functioning nervous system. However, the majority of editing has been found in transcripts encoding Alu repeat elements and the biological role of this editing remains a mystery. This chapter describes in detail the different ADAR enzymes and the phenotype of animals that are deficient in their activity. Besides being enzymes, ADARs are also double-stranded RNA-binding proteins, so by binding alone they can interfere with other processes such as RNA interference. Lack of editing by ADARs has been implicated in disorders such as forebrain ischemia and Amyotrophic Lateral Sclerosis (ALS) and this will also be discussed.
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Affiliation(s)
- Marion Hogg
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
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Zychlinski D, Erkelenz S, Melhorn V, Baum C, Schaal H, Bohne J. Limited complementarity between U1 snRNA and a retroviral 5' splice site permits its attenuation via RNA secondary structure. Nucleic Acids Res 2010; 37:7429-40. [PMID: 19854941 PMCID: PMC2794156 DOI: 10.1093/nar/gkp694] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Multiple types of regulation are used by cells and viruses to control alternative splicing. In murine leukemia virus, accessibility of the 5′ splice site (ss) is regulated by an upstream region, which can fold into a complex RNA stem–loop structure. The underlying sequence of the structure itself is negligible, since most of it could be functionally replaced by a simple heterologous RNA stem–loop preserving the wild-type splicing pattern. Increasing the RNA duplex formation between U1 snRNA and the 5′ss by a compensatory mutation in position +6 led to enhanced splicing. Interestingly, this mutation affects splicing only in the context of the secondary structure, arguing for a dynamic interplay between structure and primary 5′ss sequence. The reduced 5′ss accessibility could also be counteracted by recruiting a splicing enhancer domain via a modified MS2 phage coat protein to a single binding site at the tip of the simple RNA stem–loop. The mechanism of 5′ss attenuation was revealed using hyperstable U1 snRNA mutants, showing that restricted U1 snRNP access is the cause of retroviral alternative splicing.
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Affiliation(s)
- Daniela Zychlinski
- Institute for Virology, Hannover Medical School, 30625 Hannover, Germany
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Kobiyama K, Takeshita F, Ishii KJ, Koyama S, Aoshi T, Akira S, Sakaue-Sawano A, Miyawaki A, Yamanaka Y, Hirano H, Suzuki K, Okuda K. A signaling polypeptide derived from an innate immune adaptor molecule can be harnessed as a new class of vaccine adjuvant. THE JOURNAL OF IMMUNOLOGY 2009; 182:1593-601. [PMID: 19155508 DOI: 10.4049/jimmunol.182.3.1593] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Modulation of intracellular signaling using cell-permeable polypeptides is a promising technology for future clinical applications. To develop a novel approach to activate innate immune signaling by synthetic polypeptides, we characterized several different polypeptides derived from the caspase recruitment domain (CARD) of IFN-beta promoter stimulator 1, each of which localizes to a different subcellular compartment. Of particular interest was, N'-CARD, which consisted of the nuclear localization signal of histone H2B and the IFN-beta promoter stimulator 1CARD and which localized to the nucleus. This polypeptide led to a strong production of type I IFNs and molecular and genetic analyses showed that nuclear DNA helicase II is critically involved in this response. N'-CARD polypeptide fused to a protein transduction domain (N'-CARD-PTD) readily transmigrated from the outside to the inside of the cell and triggered innate immune signaling. Administration of N'-CARD-PTD polypeptide elicited production of type I IFNs, maturation of bone marrow-derived dendritic cells, and promotion of vaccine immunogenicity by enhancing Ag-specific Th1-type immune responses, thereby protecting mice from lethal influenza infection and from outgrowth of transplanted tumors in vivo. Thus, our results indicate that the N'-CARD-PTD polypeptide belongs to a new class of vaccine adjuvant that directly triggers intracellular signal transduction by a distinct mechanism from those engaged by conventional vaccine adjuvants, such as TLR ligands.
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Affiliation(s)
- Kouji Kobiyama
- Department of Molecular Biodefense Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Yang Y, Lv J, Gui B, Yin H, Wu X, Zhang Y, Jin Y. A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: implications for dual functions in evolution. RNA (NEW YORK, N.Y.) 2008; 14:1516-25. [PMID: 18567816 PMCID: PMC2491475 DOI: 10.1261/rna.1063708] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The molecular mechanism and physiological function of recoding by A-to-I RNA editing is well known, but its evolutionary significance remains a mystery. We analyzed the RNA editing of the Kv2 K(+) channel from different insects spanning more than 300 million years of evolution: Drosophila melanogaster, Culex pipiens (Diptera), Pulex irritans (Siphonaptera), Bombyx mori (Lepidoptera), Tribolium castaneum (Coleoptera), Apis mellifera (Hymenoptera), Pediculus humanus (Phthiraptera), and Myzus persicae (Homoptera). RNA editing was detected across all Kv2 orthologs, representing the most highly conserved RNA editing event yet reported in invertebrates. Surprisingly, five of these editing sites were conserved in squid (Mollusca) and were possibly of independent origin, suggesting phylogenetic conservation of editing between mollusks and insects. Based on this result, we predicted and experimentally verified two novel A-to-I editing sites in squid synaptotagmin I transcript. In addition, comparative analysis indicated that RNA editing usually occurred within highly conserved coding regions, but mostly altered less-conserved coding positions of these regions. Moreover, more than half of these edited amino acids are genomically encoded in the orthologs of other species; an example of a conversion model of the nonconservative edited site is addressed. Therefore, these data imply that RNA editing might play dual roles in evolution by extending protein diversity and maintaining phylogenetic conservation.
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Affiliation(s)
- Yun Yang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China
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Abstract
In an earlier study, we showed increases in serotonin 2C receptor (5-HT2CR) pre-mRNA editing in prefrontal cortex that were specific to suicide victims irrespective of associated psychiatric diagnoses. Here we demonstrate that the ratio between the two 5-HT2CR splice variants is increased in people who committed suicide, but does not vary among the diagnostic groups. This provides further evidence for suicide-specific neurobiology and suggests that, as it was previously shown in vitro, 5-HT2CR editing modulates its splicing in human brain. The association analysis indicates, however, that the efficiency of 5-HT2CR editing is an imperfect predictor of the splicing outcome, and that splice site selection is only partially controlled by the level of editing in vivo.
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Affiliation(s)
- Olena Maydanovych
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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Ryman K, Fong N, Bratt E, Bentley DL, Ohman M. The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA (NEW YORK, N.Y.) 2007; 13:1071-8. [PMID: 17525170 PMCID: PMC1894935 DOI: 10.1261/rna.404407] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The C-terminal domain (CTD) of the large subunit of RNA polymerase II (Pol II) influences many steps in the synthesis of an mRNA and helps control the final destiny of the mature transcript. ADAR2 edits RNA by converting adenosine to inosine within double-stranded or structured RNA. Site-selective A-to-I editing often occurs at sites near exon/intron borders, where it depends on intronic sequences for substrate recognition. It is therefore essential that editing precedes splicing. We have investigated whether there is coordination between ADAR2 editing and splicing of the GluR-B pre-mRNA. We show that the CTD is required for efficient editing at the R/G site one base upstream of a 5'-splice site. The results suggest that the CTD enhances editing at the R/G site by preventing premature splicing that would remove the intronic recognition sites for ADAR2. Editing at the GluR-B Q/R site, 24 bases upstream of the intron 11 5'-splice site, stimulates splicing at this intron. Furthermore, unlike previously studied introns, the CTD actually inhibits excision of intron 11, which includes the complementary recognition sequences for the Q/R editing site. In summary, these results show that the CTD and ADAR2 function together to enforce the order of events that allows editing to precede splicing, and they furthermore suggest a new role for the CTD as a coordinator of two interdependent pre-mRNA processing events.
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Affiliation(s)
- Kicki Ryman
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
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