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Xing Y, Nakahama T, Wu Y, Inoue M, Kim JI, Todo H, Shibuya T, Kato Y, Kawahara Y. RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing. J Biol Chem 2023; 299:104840. [PMID: 37209819 PMCID: PMC10404624 DOI: 10.1016/j.jbc.2023.104840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by nuclear adenosine deaminase acting on RNA 1 (ADAR1) p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize dsRNAs as targets. RNA editing occurs in some coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 before splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double KO mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw 264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw 264.7 and human embryonic kidney 293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing, and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 KO mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.
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Affiliation(s)
- Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
| | - Yuke Wu
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan; Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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Zhang K, Wang S, Chen T, Tu Z, Huang X, Zang G, Wu C, Fan X, Liu J, Tian Y, Cheng Y, Lu N, Zhang G. ADAR1p110 promotes Enterovirus D68 replication through its deaminase domain and inhibition of PKR pathway. Virol J 2022; 19:222. [PMID: 36550502 PMCID: PMC9773460 DOI: 10.1186/s12985-022-01952-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Severe respiratory and neurological diseases caused by human enterovirus D68 (EV-D68) pose a serious threat to public health, and there are currently no effective drugs and vaccines. Adenosine deaminase acting on RNA1 (ADAR1) has diverse biological functions in various viral infections, but its role in EV-D68 infections remains undetermined. METHODS Rhabdomyosarcoma (RD) and human embryonic kidney 293 T (293 T) cells, and HeLa cells were used to evaluate the expression level of ADAR1 upon EV-D68 (Fermon strain) and human parainfluenza virus type 3 (HPIV3; NIH47885) infection, respectively. Knockdown through silencing RNA (siRNA) and overexpression of either ADAR1p110 or ADAR1p150 in cells were used to determine the function of the two proteins after viral infection. ADAR1p110 double-stranded RNA binding domains (dsRBDs) deletion mutation was generated using a seamless clone kit. The expression of ADAR1, EV-D68 VP1, and HPIV3 hemagglutinin-neuraminidase (HN) proteins was identified using western blotting. The median tissue culture infectious dose (TCID50) was applied to detect viral titers. The transcription level of EV-D68 mRNA was analyzed using reverse transcription-quantitative PCR (RT-qPCR) and the viral 5'-untranslated region (5'-UTR)-mediated translation was analyzed using a dual luciferase reporter system. CONCLUSION We found that the transcription and expression of ADAR1 was inhibited upon EV-D68 infection. RNA interference of endogenous ADAR1 decreased VP1 protein expression and viral titers, while overexpression of ADAR1p110, but not ADAR1p150, facilitated viral replication. Immunofluorescence assays showed that ADAR1p110 migrated from the nucleus to the cytoplasm after EV-D68 infection. Further, ADAR1p110 lost its pro-viral ability after mutations of the active sites in the deaminase domain, and 5'-UTR sequencing of the viral genome revealed that ADAR1p110 likely plays a role in EV-D68 RNA editing. In addition, after ADAR1 knockdown, the levels of both phosphorylated double-stranded RNA dependent protein kinase (p-PKR) and phosphorylated eukaryotic initiation factor 2α (p-eIF2α) increased. Attenuated translation activity of the viral genome 5'-UTR was also observed in the dual-luciferase reporter assay. Lastly, the deletion of ADAR1p110 dsRBDs increased the level of p-PKR, which correlated with a decreased VP1 expression, indicating that the promotion of EV-D68 replication by ADAR1p110 is also related to the inhibition of PKR activation by its dsRBDs. Our study illustrates that ADAR1p110 is a novel pro-viral factor of EV-D68 replication and provides a theoretical basis for EV-D68 antiviral research.
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Affiliation(s)
- Kehan Zhang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China ,grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Siyuan Wang
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Tingting Chen
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Zeng Tu
- grid.203458.80000 0000 8653 0555Department of Pathogen Biology, Basic Medical School, Chongqing Medical University, Chongqing, China
| | - Xia Huang
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Guangchao Zang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Chun Wu
- Chongqing Better Biotechnology LLC, Chongqing, China
| | - Xinyue Fan
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Jia Liu
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Yunbo Tian
- Quality Management Section, Chongqing Blood Center, Chongqing, China
| | - Yong Cheng
- Monitoring On Terrestrial Wildlife-Borne Infectious Diseases, Jinggangshan National Nature Reserve of Jiangxi Province, Ji’an, Jiangxi China
| | - Nan Lu
- grid.203458.80000 0000 8653 0555Department of Pathogen Biology, Basic Medical School, Chongqing Medical University, Chongqing, China
| | - Guangyuan Zhang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
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Mutations in the adenosine deaminase ADAR1 that prevent endogenous Z-RNA binding induce Aicardi-Goutières-syndrome-like encephalopathy. Immunity 2021; 54:1976-1988.e7. [PMID: 34525338 DOI: 10.1016/j.immuni.2021.08.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/27/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022]
Abstract
Mutations in the adenosine-to-inosine RNA-editing enzyme ADAR1 p150, including point mutations in the Z-RNA recognition domain Zα, are associated with Aicardi-Goutières syndrome (AGS). Here, we examined the in vivo relevance of ADAR1 binding of Z-RNA. Mutation of W197 in Zα, which abolished Z-RNA binding, reduced RNA editing. Adar1W197A/W197A mice displayed severe growth retardation after birth, broad expression of interferon-stimulated genes (ISGs), and abnormal development of multiple organs. Notably, malformation of the brain was accompanied by white matter vacuolation and gliosis, reminiscent of AGS-associated encephalopathy. Concurrent deletion of the double-stranded RNA sensor MDA5 ameliorated these abnormalities. ADAR1 (W197A) expression increased in a feedback manner downstream of type I interferons, resulting in increased RNA editing at a subset of, but not all, ADAR1 target sites. This increased expression did not ameliorate inflammation in Adar1W197A/W197A mice. Thus, editing of select endogenous RNAs by ADAR1 is essential for preventing inappropriate MDA5-mediated inflammation, with relevance to the pathogenesis of AGS.
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Sanchez Herrero JF, Pluvinet R, Luna de Haro A, Sumoy L. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 2021; 22:215. [PMID: 33902448 PMCID: PMC8077951 DOI: 10.1186/s12859-021-04128-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomiR variation reported so far could be due to systematic technical noise and not real. RESULTS We have developed the XICRA pipeline to analyze small RNA sequencing data at the isomiR level. We exploited its ability to use single or merged reads to compare isomiR results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomiRs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between SR and PE data which primarily affect putative internally edited isomiRs, and at a much smaller frequency terminal length changing isomiRs. This is relevant for the identification of true isomiRs in small RNA sequencing datasets. CONCLUSIONS We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomiRnome should take this into account.
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Affiliation(s)
| | | | | | - Lauro Sumoy
- Institut Germans Trias i Pujol (IGTP), Badalona, Spain.
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Marceca GP, Tomasello L, Distefano R, Acunzo M, Croce CM, Nigita G. Detecting and Characterizing A-To-I microRNA Editing in Cancer. Cancers (Basel) 2021; 13:1699. [PMID: 33916692 PMCID: PMC8038323 DOI: 10.3390/cancers13071699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.
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Affiliation(s)
- Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, 95125 Catania, Italy
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
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Kung CP, Maggi LB, Weber JD. The Role of RNA Editing in Cancer Development and Metabolic Disorders. Front Endocrinol (Lausanne) 2018; 9:762. [PMID: 30619092 PMCID: PMC6305585 DOI: 10.3389/fendo.2018.00762] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.
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Affiliation(s)
- Che-Pei Kung
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Leonard B. Maggi
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jason D. Weber
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
- Siteman Cancer Center, Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, United States
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Ishiguro S, Galipon J, Ishii R, Suzuki Y, Kondo S, Okada-Hatakeyama M, Tomita M, Ui-Tei K. Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2. RNA Biol 2018; 15:976-989. [PMID: 29950133 DOI: 10.1080/15476286.2018.1486658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) catalyze the deamination of adenosine (A) to inosine (I). A-to-I RNA editing targets double-stranded RNA (dsRNA), and increases the complexity of gene regulation by modulating base pairing-dependent processes such as splicing, translation, and microRNA (miRNA)-mediated gene silencing. This study investigates the genome-wide binding preferences of the nuclear constitutive isoforms ADAR1-p110 and ADAR2 on human miRNA species by RNA immunoprecipitation of ADAR-bound small RNAs (RIP-seq). Our results suggest that secondary structure predicted by base-pairing probability in the mainly double-stranded region of a pre-miRNA or mature miRNA duplex may determine ADAR isoform preference for binding distinct subpopulations of miRNAs. Furthermore, we identify 31 unique editing sites with statistical significance, 19 sites of which are novel editing sites. Editing sites are enriched in the seed region responsible for target recognition by miRNAs, and isoform-specific nucleotide motifs in the immediate vicinity and opposite of editing sites are consistent with previous studies, and further reveal that ADAR2 may edit A/C bulges more frequently than ADAR1-p110 in the context of miRNA.
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Affiliation(s)
- Soh Ishiguro
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan.,b Institute for Advanced Biosciences , Keio University , Tsuruoka , Japan.,c Systems Biology Program, Graduate School of Media and Governance , Keio University , Fujisawa , Japan
| | - Josephine Galipon
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan.,b Institute for Advanced Biosciences , Keio University , Tsuruoka , Japan.,c Systems Biology Program, Graduate School of Media and Governance , Keio University , Fujisawa , Japan
| | - Rintaro Ishii
- d Department of Computational Biology, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa-shi , Japan
| | - Yutaka Suzuki
- d Department of Computational Biology, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa-shi , Japan
| | - Shinji Kondo
- e Department of Multidisciplinary Center, National Institute of Polar Research , Tachikawa, Tokyo , Japan
| | - Mariko Okada-Hatakeyama
- f Laboratory for Integrated Cellular Systems , RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama , Japan.,g Laboratory of Cell Systems, Institute for Protein Research , Osaka University , Suita-shi , Japan
| | - Masaru Tomita
- b Institute for Advanced Biosciences , Keio University , Tsuruoka , Japan.,c Systems Biology Program, Graduate School of Media and Governance , Keio University , Fujisawa , Japan
| | - Kumiko Ui-Tei
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan.,d Department of Computational Biology, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa-shi , Japan
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