1
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Peterson L, Coca R, Parikh S, McCarthy K, Man HY. ADAR2-mediated Q/R editing of GluA2 in homeostatic synaptic plasticity. Sci Signal 2025; 18:eadr1442. [PMID: 40359260 DOI: 10.1126/scisignal.adr1442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 06/24/2024] [Accepted: 04/22/2025] [Indexed: 05/15/2025]
Abstract
Homeostatic synaptic plasticity is a negative feedback mechanism through which neurons modify their synaptic strength to counteract chronic increases or decreases in activity. In response to activity deprivation, synaptic strength is enhanced by increasing the number of AMPA receptors (AMPARs), particularly Ca2+-permeable AMPARs, at the synapse. Here, we found that this increase in Ca2+-permeable AMPARs during homeostatic upscaling was mediated by decreased posttranscriptional editing of GRIA2 mRNA encoding the AMPAR subunit GluA2. In cultured neurons, activity deprivation resulted in increases in the amount of unedited GluA2, such that its ion channel pore contains a glutamine (Q) codon instead of arginine (R), and in the number of Ca2+-permeable AMPARs at the synapse. These effects were mediated by a splicing factor-dependent decrease in ADAR2 abundance and activity in the nucleus. Overexpression of ADAR2 or CRISPR-Cas13-directed editing of GluA2 transcripts blocked homeostatic upscaling in activity-deprived primary neurons. In mice, dark rearing resulted in decreased Q-to-R editing of GluA2-encoding transcripts in the primary visual cortex (V1), and viral overexpression of ADAR2 in the V1 blocked the induction of homeostatic synaptic plasticity. The findings indicate that activity-dependent regulation of GluA2 editing contributes to homeostatic synaptic plasticity.
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Affiliation(s)
- Lucy Peterson
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Richard Coca
- Department of Biology, Boston University, Boston, MA 02215, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA 02215, USA
| | - Shreya Parikh
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02215, USA
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2
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Wilcox XE, Zhang H, Mah JL, Cazet JF, Mozumder S, Venkatesh S, Juliano CE, Beal PA, Fisher AJ. Phylogenetic and structural analysis of Hydra ADAR. Arch Biochem Biophys 2025; 767:110353. [PMID: 39986343 DOI: 10.1016/j.abb.2025.110353] [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: 02/04/2025] [Accepted: 02/18/2025] [Indexed: 02/24/2025]
Abstract
Adenosine deaminases acting on RNAs (ADARs) perform adenosine-to-inosine (A-to-I) RNA editing for essential biological functions. While studies of editing sites in diverse animals have revealed unique biological roles of ADAR editing including temperature adaptation and reproductive maturation, rigorous biochemical and structural studies of these ADARs are lacking. Here, we present a phylogenetic sequence analysis and AlphaFold computational structure prediction to reveal that medusozoan ADAR2s contain five dsRNA binding domains (dsRBDs) with several RNA binding residues in the dsRBDs and deaminase domain conserved. Additionally, we identified evolutionary divergence between the medusozoan (e.g. Hydra) and anthozoan cnidarian subphyla. The anthozoan ADAR deaminase domains more closely resemble human ADARs with longer 5' RNA binding loops, glutamate base-flipping residues, and a conserved TWDG dimerization motif. Conversely, medusozoan ADAR deaminase domains have short 5' binding loops, glutamine flipping residues, and non-conserved helix dimerization motif. We also report the direct detection of A-to-I RNA editing by an ADAR ortholog from the freshwater cnidarian Hydra vulgaris (hyADAR). We solved the crystal structure of the monomeric deaminase domain of hyADAR (hyADARd) to 2.0 Å resolution, showing conserved active site architecture and the presence of a buried inositol hexakisphosphate known to be required for ADAR activity. In addition, these data demonstrate that medusozoans have evolved novel ADAR structural features, however the physiological consequence of this remains unknown. In addition, these results provide a framework for biochemically and structurally characterizing ADARs from evolutionarily distant organisms to understand the diverse roles of ADAR editing amongst metazoans.
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Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California, Davis, CA, USA
| | - Howard Zhang
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Jasmine L Mah
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Sukanya Mozumder
- Department of Chemistry, University of California, Davis, CA, USA
| | - Srinidhi Venkatesh
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, CA, USA
| | - Andrew J Fisher
- Department of Chemistry, University of California, Davis, CA, USA; Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
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3
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Tamizkar KH, Jantsch MF. RNA editing in disease: mechanisms and therapeutic potential. RNA (NEW YORK, N.Y.) 2025; 31:359-368. [PMID: 39746751 PMCID: PMC11874977 DOI: 10.1261/rna.080331.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 12/24/2024] [Indexed: 01/04/2025]
Abstract
Adenosine to inosine conversion by adenosine deaminases acting on RNA (ADARs) was first identified in the late 1980s of the previous century. As the conversion of adenosines to inosines can be easily detected by sequencing of cDNAs, where the presence of an inosine reads out as a guanosine, the analysis of this type of RNA editing has become widespread. Consequently, several pipelines for detecting inosines in transcriptomes have become available. Still, how to interpret the consequences and alterations of RNA-editing events in whole transciptome editomes is a matter of debate. In particular, the cause or consequence of altered editomes on disease development is poorly understood. Similarly, absolute frequencies of editing events in single molecules, their longitudinal distribution, and naturally occurring changes during development, in different tissues, or in response to physiological changes need to be explored. Lastly, while the use of site-directed RNA editing as a treatment of certain genetic diseases is rapidly evolving, the applicability of this technology still faces several technical obstacles. In this review, we describe the current state of knowledge on adenosine deamination-type RNA editing, its involvement in disease development, and its potential as a therapeutic. Lastly, we highlight open challenges and questions that need to be addressed.
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Affiliation(s)
- Kasra Honarmand Tamizkar
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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4
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Eisenberg E. Bioinformatic approaches for accurate assessment of A-to-I editing in complete transcriptomes. Methods Enzymol 2024; 710:241-265. [PMID: 39870448 DOI: 10.1016/bs.mie.2024.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2025]
Abstract
A-to-I RNA editing is an RNA modification that alters the RNA sequence relative to the its genomic blueprint. It is catalyzed by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes, and contributes to the complexity and diversification of the proteome. Advancement in the study of A-to-I RNA editing has been facilitated by computational approaches for accurate mapping and quantification of A-to-I RNA editing based on sequencing data. In this chapter we review some of the main computational approaches currently used, describe potential hurdles, challenges and pitfalls, and discuss possible ways to mitigate them.
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Affiliation(s)
- Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel.
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5
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Szabo B, Mandl TC, Woldrich B, Diensthuber G, Martin D, Jantsch MF, Licht K. RNA Pol II-dependent transcription efficiency fine-tunes A-to-I editing levels. Genome Res 2024; 34:231-242. [PMID: 38471738 PMCID: PMC10984384 DOI: 10.1101/gr.277686.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
A-to-I RNA editing is a widespread epitranscriptomic phenomenon leading to the conversion of adenosines to inosines, which are primarily interpreted as guanosines by cellular machines. Consequently, A-to-I editing can alter splicing or lead to recoding of transcripts. As misregulation of editing can cause a variety of human diseases, A-to-I editing requires tight regulation of the extent of deamination, particularly in protein-coding regions. The bulk of A-to-I editing occurs cotranscriptionally. Thus, we studied A-to-I editing regulation in the context of transcription and pre-mRNA processing. We show that stimulation of transcription impacts editing levels. Activation of the transcription factor MYC leads to an up-regulation of A-to-I editing, particularly in transcripts that are suppressed upon MYC activation. Moreover, low pre-mRNA synthesis rates and low pre-mRNA expression levels support high levels of editing. We also show that editing levels greatly differ between nascent pre-mRNA and mRNA in a cellular system, as well as in mouse tissues. Editing levels can increase or decrease from pre-mRNA to mRNA and can vary across editing targets and across tissues, showing that pre-mRNA processing is an important layer of editing regulation. Several lines of evidence suggest that the differences emerge during pre-mRNA splicing. Moreover, actinomycin D treatment of primary neuronal cells and editing level analysis suggests that regulation of editing levels also depends on transcription.
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Affiliation(s)
- Brigitta Szabo
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Therese C Mandl
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Bernhard Woldrich
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Gregor Diensthuber
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - David Martin
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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6
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Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. BMC Biol 2023; 21:160. [PMID: 37468903 PMCID: PMC10357658 DOI: 10.1186/s12915-023-01651-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys. Nonetheless, the lack of extensive independent validation in such endeavors, which is critical considering the relatively high error rate of next-generation sequencing, leads to lingering questions about the validity of the current compendiums of the editing sites and conclusions based on them. RESULTS Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA 'dark matter'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification. CONCLUSIONS Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
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Affiliation(s)
- Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
| | - Qiu Xia
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ziheng Liu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ming Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Bolin Deng
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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7
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Jain M, Weber A, Maly K, Manjaly G, Deek J, Tsvyetkova O, Stulić M, Toca‐Herrera JL, Jantsch MF. A-to-I RNA editing of Filamin A regulates cellular adhesion, migration and mechanical properties. FEBS J 2022; 289:4580-4601. [PMID: 35124883 PMCID: PMC9546289 DOI: 10.1111/febs.16391] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 12/23/2021] [Accepted: 02/04/2022] [Indexed: 02/06/2023]
Abstract
A-to-I RNA editing by ADARs is an abundant epitranscriptomic RNA-modification in metazoa. In mammals, Flna pre-mRNA harbours a single conserved A-to-I RNA editing site that introduces a Q-to-R amino acid change in Ig repeat 22 of the encoded protein. Previously, we showed that FLNA editing regulates smooth muscle contraction in the cardiovascular system and affects cardiac health. The present study investigates how ADAR2-mediated A-to-I RNA editing of Flna affects actin crosslinking, cell mechanics, cellular adhesion and cell migration. Cellular assays and AFM measurements demonstrate that the edited version of FLNA increases cellular stiffness and adhesion but impairs cell migration in both, mouse fibroblasts and human tumour cells. In vitro, edited FLNA leads to increased actin crosslinking, forming actin gels of higher stress resistance. Our study shows that Flna RNA editing is a novel regulator of cytoskeletal organisation, affecting the mechanical property and mechanotransduction of cells.
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Affiliation(s)
- Mamta Jain
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
| | - Andreas Weber
- Department of NanobiotechnologyInstitute for BiophysicsUniversity of Natural Resources and Life Sciences Vienna (BOKU)Austria
| | - Kathrin Maly
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
| | - Greeshma Manjaly
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
| | - Joanna Deek
- Department of Physics, Cellular Biophysics E27Technical University of MunichGarchingGermany
| | - Olena Tsvyetkova
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
| | - Maja Stulić
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
| | - José L. Toca‐Herrera
- Department of NanobiotechnologyInstitute for BiophysicsUniversity of Natural Resources and Life Sciences Vienna (BOKU)Austria
| | - Michael F. Jantsch
- Division of Cell BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaAustria
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8
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Zhai J, Koh JH, Soong TW. RNA editing of ion channels and receptors in physiology and neurological disorders. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac010. [PMID: 38596706 PMCID: PMC11003377 DOI: 10.1093/oons/kvac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/14/2022] [Accepted: 05/15/2022] [Indexed: 04/11/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification that diversifies protein functions by recoding RNA or alters protein quantity by regulating mRNA level. A-to-I editing is catalyzed by adenosine deaminases that act on RNA. Millions of editing sites have been reported, but they are mostly found in non-coding sequences. However, there are also several recoding editing sites in transcripts coding for ion channels or transporters that have been shown to play important roles in physiology and changes in editing level are associated with neurological diseases. These editing sites are not only found to be evolutionary conserved across species, but they are also dynamically regulated spatially, developmentally and by environmental factors. In this review, we discuss the current knowledge of A-to-I RNA editing of ion channels and receptors in the context of their roles in physiology and pathological disease. We also discuss the regulation of editing events and site-directed RNA editing approaches for functional study that offer a therapeutic pathway for clinical applications.
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Affiliation(s)
- Jing Zhai
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore,
Singapore 117456, Singapore
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9
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Guo X, Liu S, Yan R, Nguyen V, Zenati M, Billiar TR, Wang Q. ADAR1 RNA editing regulates endothelial cell functions via the MDA-5 RNA sensing signaling pathway. Life Sci Alliance 2022; 5:5/3/e202101191. [PMID: 34969816 PMCID: PMC8739526 DOI: 10.26508/lsa.202101191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
The RNA-sensing signaling pathway has been well studied as an essential antiviral mechanism of innate immunity. However, its role in non-infected cells is yet to be thoroughly characterized. Here, we demonstrated that the RNA sensing signaling pathway also reacts to the endogenous cellular RNAs in endothelial cells (ECs), and this reaction is regulated by the RNA-editing enzyme ADAR1. Cellular RNA sequencing analysis showed that EC RNAs endure extensive RNA editing, especially in the RNA transcripts of short interspersed nuclear elements. The EC-specific deletion of ADAR1 dramatically reduced the editing level on short interspersed nuclear element RNAs, resulting in newborn death in mice with damage evident in multiple organs. Genome-wide gene expression analysis revealed a prominent innate immune activation with a dramatically elevated expression of interferon-stimulated genes. However, blocking the RNA sensing signaling pathway by deletion of the cellular RNA receptor MDA-5 prevented interferon-stimulated gene expression and rescued the newborn mice from death. This evidence demonstrated that the RNA-editing/RNA-sensing signaling pathway dramatically modulates EC function, representing a novel molecular mechanism for the regulation of EC functions.
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Affiliation(s)
- Xinfeng Guo
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center (UPMC) and University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rose Yan
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vy Nguyen
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mazen Zenati
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA .,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center (UPMC) and University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,VA Pittsburgh Health System, Pittsburgh, PA, USA
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10
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Leptidis S, Papakonstantinou E, Diakou KI, Pierouli K, Mitsis T, Dragoumani K, Bacopoulou F, Sanoudou D, Chrousos GP, Vlachakis D. Epitranscriptomics of cardiovascular diseases (Review). Int J Mol Med 2022; 49:9. [PMID: 34791505 PMCID: PMC8651226 DOI: 10.3892/ijmm.2021.5064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.
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Affiliation(s)
- Stefanos Leptidis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Flora Bacopoulou
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Despina Sanoudou
- Fourth Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, Medical School, 'Attikon' Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - George P. Chrousos
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- School of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
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11
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Larsen K, Heide-Jørgensen MP. Conservation of A-to-I RNA editing in bowhead whale and pig. PLoS One 2021; 16:e0260081. [PMID: 34882682 PMCID: PMC8659423 DOI: 10.1371/journal.pone.0260081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 01/18/2023] Open
Abstract
RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at 'recoding' sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs-NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 -showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.
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Affiliation(s)
- Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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12
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Vesely C, Jantsch MF. An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing. Genes (Basel) 2021; 12:1026. [PMID: 34356042 PMCID: PMC8304401 DOI: 10.3390/genes12071026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as "self", therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize the known and likely mechanisms that will lead to global but also substrate-specific regulation of A to I editing.
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Affiliation(s)
| | - Michael F. Jantsch
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria;
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13
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Sadeq S, Al-Hashimi S, Cusack CM, Werner A. Endogenous Double-Stranded RNA. Noncoding RNA 2021; 7:15. [PMID: 33669629 PMCID: PMC7930956 DOI: 10.3390/ncrna7010015] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The birth of long non-coding RNAs (lncRNAs) is closely associated with the presence and activation of repetitive elements in the genome. The transcription of endogenous retroviruses as well as long and short interspersed elements is not only essential for evolving lncRNAs but is also a significant source of double-stranded RNA (dsRNA). From an lncRNA-centric point of view, the latter is a minor source of bother in the context of the entire cell; however, dsRNA is an essential threat. A viral infection is associated with cytoplasmic dsRNA, and endogenous RNA hybrids only differ from viral dsRNA by the 5' cap structure. Hence, a multi-layered defense network is in place to protect cells from viral infections but tolerates endogenous dsRNA structures. A first line of defense is established with compartmentalization; whereas endogenous dsRNA is found predominantly confined to the nucleus and the mitochondria, exogenous dsRNA reaches the cytoplasm. Here, various sensor proteins recognize features of dsRNA including the 5' phosphate group of viral RNAs or hybrids with a particular length but not specific nucleotide sequences. The sensors trigger cellular stress pathways and innate immunity via interferon signaling but also induce apoptosis via caspase activation. Because of its central role in viral recognition and immune activation, dsRNA sensing is implicated in autoimmune diseases and used to treat cancer.
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Affiliation(s)
| | | | | | - Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.); (C.M.C.)
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14
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Increased RNA editing in maternal immune activation model of neurodevelopmental disease. Nat Commun 2020; 11:5236. [PMID: 33067431 PMCID: PMC7567798 DOI: 10.1038/s41467-020-19048-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
The etiology of major neurodevelopmental disorders such as schizophrenia and autism is unclear, with evidence supporting a combination of genetic factors and environmental insults, including viral infection during pregnancy. Here we utilized a mouse model of maternal immune activation (MIA) with the viral mimic PolyI:C infection during early gestation. We investigated the transcriptional changes in the brains of mouse fetuses following MIA during the prenatal period, and evaluated the behavioral and biochemical changes in the adult brain. The results reveal an increase in RNA editing levels and dysregulation in brain development-related gene pathways in the fetal brains of MIA mice. These MIA-induced brain editing changes are not observed in adulthood, although MIA-induced behavioral deficits are observed. Taken together, our findings suggest that MIA induces transient dysregulation of RNA editing at a critical time in brain development.
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15
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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: 32] [Impact Index Per Article: 6.4] [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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16
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Costa Cruz PH, Kato Y, Nakahama T, Shibuya T, Kawahara Y. A comparative analysis of ADAR mutant mice reveals site-specific regulation of RNA editing. RNA (NEW YORK, N.Y.) 2020; 26:454-469. [PMID: 31941663 PMCID: PMC7075269 DOI: 10.1261/rna.072728.119] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/09/2020] [Indexed: 05/03/2023]
Abstract
Adenosine-to-inosine RNA editing is an essential post-transcriptional modification catalyzed by adenosine deaminase acting on RNA (ADAR)1 and ADAR2 in mammals. For numerous sites in coding sequences (CDS) and microRNAs, editing is highly conserved and has significant biological consequences, for example, by altering amino acid residues and target recognition. However, no comprehensive and quantitative studies have been undertaken to determine how specific ADARs contribute to conserved sites in vivo. Here, we amplified each RNA region with editing site(s) separately and combined these for deep sequencing. Then, we compared the editing ratios of all sites that were conserved in CDS and microRNAs in the cerebral cortex and spleen of wild-type mice, Adar1E861A/E861AIfih-/- mice expressing inactive ADAR1 (Adar1 KI) and Adar2-/-Gria2R/R (Adar2 KO) mice. We found that most of the sites showed a preference for one ADAR. In contrast, some sites, such as miR-3099-3p, showed no ADAR preference. In addition, we found that the editing ratio for several sites, such as DACT3 R/G, was up-regulated in either Adar mutant mouse strain, whereas a coordinated interplay between ADAR1 and ADAR2 was required for the efficient editing of specific sites, such as the 5-HT2CR B site. We further created double mutant Adar1 KI Adar2 KO mice and observed viable and fertile animals with the complete absence of editing, demonstrating that ADAR1 and ADAR2 are the sole enzymes responsible for all editing sites in vivo. Collectively, these findings indicate that editing is regulated in a site-specific manner by the different interplay between ADAR1 and ADAR2.
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Affiliation(s)
- Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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17
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Jain M, Jantsch MF, Licht K. The Editor's I on Disease Development. Trends Genet 2019; 35:903-913. [PMID: 31648814 DOI: 10.1016/j.tig.2019.09.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventing autoimmune disorders. Interestingly, A-to-I editing can be used not only to correct genomic mutations at the RNA level but also to modulate tumor antigenicity with large therapeutic potential. We highlight recent developments in the field, focusing on cancer and other human diseases.
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Affiliation(s)
- Mamta Jain
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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18
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Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing. Genome Res 2019; 29:1453-1463. [PMID: 31427386 PMCID: PMC6724681 DOI: 10.1101/gr.242636.118] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 07/25/2019] [Indexed: 11/25/2022]
Abstract
Pre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs). Editing-competent stems are frequently formed between exons and introns. Consistently, studies using reporter assays have shown that splicing efficiency can affect editing levels. Here, we use Nascent-seq and identify ∼90,000 novel A-to-I editing events in the mouse brain transcriptome. Most novel sites are located in intronic regions. Unlike previously assumed, we show that both ADAR (ADAR1) and ADARB1 (ADAR2) can edit repeat elements and regular transcripts to the same extent. We find that inhibition of splicing primarily increases editing levels at hundreds of sites, suggesting that reduced splicing efficiency extends the exposure of intronic and exonic sequences to ADAR enzymes. Lack of splicing factors NOVA1 or NOVA2 changes global editing levels, demonstrating that alternative splicing factors can modulate RNA editing. Finally, we show that intron retention rates correlate with editing levels across different brain tissues. We therefore demonstrate that splicing efficiency is a major factor controlling tissue-specific differences in editing levels.
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Affiliation(s)
- Konstantin Licht
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Utkarsh Kapoor
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, I-70126 Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
| | - David Martin
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Prajakta Bajad
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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19
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Huang H, Kapeli K, Jin W, Wong YP, Arumugam TV, Koh JH, Srimasorn S, Mallilankaraman K, Chua JJE, Yeo GW, Soong TW. Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9. Nucleic Acids Res 2019; 46:7323-7338. [PMID: 29733375 PMCID: PMC6101491 DOI: 10.1093/nar/gky348] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of voltage-gated calcium channel CaV1.3 are subject to brain-selective A-to-I RNA editing by ADAR2. Here, we show that editing of CaV1.3 mRNA is dependent on a 40 bp RNA duplex formed between exon 41 and an evolutionarily conserved editing site complementary sequence (ECS) located within the preceding intron. Heterologous expression of a mouse minigene that contained the ECS, intermediate intronic sequence and exon 41 with ADAR2 yielded robust editing. Interestingly, editing of CaV1.3 was potently inhibited by serine/arginine-rich splicing factor 9 (SRSF9). Mechanistically, the inhibitory effect of SRSF9 required direct RNA interaction. Selective down-regulation of SRSF9 in neurons provides a basis for the neuron-specific editing of CaV1.3 transcripts.
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Affiliation(s)
- Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Yuk Peng Wong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Thiruma Valavan Arumugam
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Sumitra Srimasorn
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Karthik Mallilankaraman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, USA.,Molecular Engineering Laboratory, A*STAR, Singapore, Singapore
| | - Tuck Wah Soong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
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20
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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21
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Rajendren S, Manning AC, Al-Awadi H, Yamada K, Takagi Y, Hundley HA. A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme. Nucleic Acids Res 2019; 46:9647-9659. [PMID: 30202880 PMCID: PMC6182170 DOI: 10.1093/nar/gky800] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/27/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) in all ADARs suggests these domains are important for substrate recognition; however, the role of dsRBDs in vivo remains largely unknown. Herein, our studies indicate the Caenorhabditis elegans ADAR enzyme, ADR-2, has low affinity for dsRNA, but interacts with ADR-1, an editing-deficient member of the ADAR family, which has a 100-fold higher affinity for dsRNA. ADR-1 uses one dsRBD to physically interact with ADR-2 and a second dsRBD to bind to dsRNAs, thereby tethering ADR-2 to substrates. ADR-2 interacts with >1200 transcripts in vivo, and ADR-1 is required for 80% of these interactions. Our results identify a novel mode of substrate recognition for ADAR enzymes and indicate that protein-protein interactions can guide substrate recognition for RNA editors.
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Affiliation(s)
- Suba Rajendren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aidan C Manning
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Haider Al-Awadi
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Kentaro Yamada
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
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22
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Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues. Genes (Basel) 2019; 10:genes10050327. [PMID: 31052161 PMCID: PMC6562383 DOI: 10.3390/genes10050327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/08/2019] [Accepted: 04/17/2019] [Indexed: 01/24/2023] Open
Abstract
Recently, the prevalence and importance of RNA editing have been illuminated in mammals. However, studies on RNA editing of pigs, a widely used biomedical model animal, are rare. Here we collected RNA sequencing data across 11 tissues and identified more than 490,000 RNA editing sites. We annotated their biological features, detected flank sequence characteristics of A-to-I editing sites and the impact of A-to-I editing on miRNA-mRNA interactions, and identified RNA editing quantitative trait loci (edQTL). Sus scrofa RNA editing sites showed high enrichment in repetitive regions with a median editing level as 15.38%. Expectedly, 96.3% of the editing sites located in non-coding regions including intron, 3' UTRs, intergenic, and gene proximal regions. There were 2233 editing sites located in the coding regions and 980 of them caused missense mutation. Our results indicated that to an A-to-I editing site, the adjacent four nucleotides, two before it and two after it, have a high impact on the editing occurrences. A commonly observed editing motif is CCAGG. We found that 4552 A-to-I RNA editing sites could disturb the original binding efficiencies of miRNAs and 4176 A-to-I RNA editing sites created new potential miRNA target sites. In addition, we performed edQTL analysis and found that 1134 edQTLs that significantly affected the editing levels of 137 RNA editing sites. Finally, we constructed PRESDB, the first pig RNA editing sites database. The site provides necessary functions associated with Sus scrofa RNA editing study.
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23
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Modulation of ADAR mRNA expression in patients with congenital heart defects. PLoS One 2019; 14:e0200968. [PMID: 31039163 PMCID: PMC6490900 DOI: 10.1371/journal.pone.0200968] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 04/05/2019] [Indexed: 12/26/2022] Open
Abstract
Adenosine (A) to inosine (I) RNA editing is a hydrolytic deamination reaction catalyzed by the adenosine deaminase (ADAR) enzyme acting on double-stranded RNA. This posttranscriptional process diversifies a plethora of transcripts, including coding and noncoding RNAs. Interestingly, few studies have been carried out to determine the role of RNA editing in vascular disease. The aim of this study was to determine the potential role of ADARs in congenital heart disease. Strong downregulation of ADAR2 and increase in ADAR1 expression was observed in blood samples from congenital heart disease (CHD) patients. The decrease in expression of ADAR2 was in line with its downregulation in ventricular tissues of dilated cardiomyopathy patients. To further decipher the plausible regulatory pathway of ADAR2 with respect to heart physiology, miRNA profiling of ADAR2 was performed on tissues from ADAR2-/- mouse hearts. Downregulation of miRNAs (miR-29b, miR-405, and miR-19) associated with cardiomyopathy and cardiac fibrosis was observed. Moreover, the upregulation of miR-29b targets COL1A2 and IGF1, indicated that ADAR2 might be involved in cardiac myopathy. The ADAR2 target vascular development associated protein-coding gene filamin B (FLNB) was selected. The editing levels of FLNB were dramatically reduced in ADAR2-/- mice; however, no observable changes in FLNB expression were noted in ADAR2-/- mice compared to wild-type mice. This study proposes that sufficient ADAR2 enzyme activity might play a vital role in preventing cardiovascular defects.
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24
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Jain M, Mann TD, Stulić M, Rao SP, Kirsch A, Pullirsch D, Strobl X, Rath C, Reissig L, Moreth K, Klein-Rodewald T, Bekeredjian R, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Pablik E, Cimatti L, Martin D, Zinnanti J, Graier WF, Sibilia M, Frank S, Levanon EY, Jantsch MF. RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure. EMBO J 2018; 37:e94813. [PMID: 30087110 PMCID: PMC6166124 DOI: 10.15252/embj.201694813] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
Epitranscriptomic events such as adenosine-to-inosine (A-to-I) RNA editing by ADAR can recode mRNAs to translate novel proteins. Editing of the mRNA that encodes actin crosslinking protein Filamin A (FLNA) mediates a Q-to-R transition in the interactive C-terminal region. While FLNA editing is conserved among vertebrates, its physiological function remains unclear. Here, we show that cardiovascular tissues in humans and mice show massive editing and that FLNA RNA is the most prominent substrate. Patient-derived RNA-Seq data demonstrate a significant drop in FLNA editing associated with cardiovascular diseases. Using mice with only impaired FLNA editing, we observed increased vascular contraction and diastolic hypertension accompanied by increased myosin light chain phosphorylation, arterial remodeling, and left ventricular wall thickening, which eventually causes cardiac remodeling and reduced systolic output. These results demonstrate a causal relationship between RNA editing and the development of cardiovascular disease indicating that a single epitranscriptomic RNA modification can maintain cardiovascular health.
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Affiliation(s)
- Mamta Jain
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Tomer D Mann
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Maja Stulić
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Shailaja P Rao
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Andrijana Kirsch
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dieter Pullirsch
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Xué Strobl
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Claus Rath
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Lukas Reissig
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Raffi Bekeredjian
- Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Eleonore Pablik
- Section for Medical Statistics, CeMSIIS, Medical University of Vienna, Vienna, Austria
| | - Laura Cimatti
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - David Martin
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang F Graier
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Maria Sibilia
- Department of Medicine I, Comprehensive Cancer Center, Institute for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Saša Frank
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Michael F Jantsch
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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25
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Czermak P, Amman F, Jantsch MF, Cimatti L. Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system. RNA Biol 2018; 15:877-885. [PMID: 30064337 PMCID: PMC6161736 DOI: 10.1080/15476286.2018.1480252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/15/2018] [Indexed: 01/24/2023] Open
Abstract
Adenosine to inosine RNA editing in protein-coding messenger RNAs (mRNAs) potentially leads to changes in the amino acid composition of the encoded proteins. The mRNAs encoding the ubiquitously expressed actin-crosslinking proteins Filamin A and Filamin B undergo RNA editing leading to a highly conserved glutamine to arginine exchange at the identical position in either protein. Here, by targeted amplicon sequencing we analysed the RNA editing of Filamin B across several mouse tissues during post-natal development. We find highest filamin B editing levels in skeletal muscles, cartilage and bones, tissues where Filamin B function seems most important. Through the analysis of Filamin B editing in mice deficient in either ADAR1 or 2, we identified ADAR2 as the enzyme responsible for Filamin B RNA editing. We show that in neuronal tissues Filamin B editing drops in spliced transcripts indicating regulated maturation of edited transcripts. We show further that the variability of Filamin B editing across several organs correlates with its mRNA expression.
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Affiliation(s)
- Philipp Czermak
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute of Theoretical Biochemistry, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria
| | - Michael F. Jantsch
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Laura Cimatti
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria
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26
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Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals. Nature 2017; 550:249-254. [PMID: 29022589 PMCID: PMC5723435 DOI: 10.1038/nature24041] [Citation(s) in RCA: 433] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 08/30/2017] [Indexed: 02/08/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.
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Affiliation(s)
- Meng How Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Qin Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Robert Piskol
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jennefer Kohler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Amy N Young
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kaiwen Ivy Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Rui Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Ankita Gupte
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Liam P Keegan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Cyril X George
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Y P Sharon Goh
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Gary Peltz
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Mary A O'Connell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | | | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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27
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Chen YB, Liao XY, Zhang JB, Wang F, Qin HD, Zhang L, Shugart YY, Zeng YX, Jia WH. ADAR2 functions as a tumor suppressor via editing IGFBP7 in esophageal squamous cell carcinoma. Int J Oncol 2016; 50:622-630. [PMID: 28035363 DOI: 10.3892/ijo.2016.3823] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 11/28/2016] [Indexed: 01/07/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), one of the most aggressive cancers, is characterized by heterogeneous genetic and epigenetic changes. Recently, A-to-I RNA editing, catalyzed by adenosine deaminases acting on RNA (ADARs), was found to be aberrantly regulated during tumorigenesis. We previously reported that ADAR2 was downregulated in ESCC but its role was unclear. Thus, we report here that overexpression of ADAR2 can induce apoptosis in ESCC cell lines and inhibit tumor growth in vitro and in vivo. ADAR2 knockdown inhibited apoptosis in ADAR2 highly expressing tumor cells. RNA-seq assay showed that ADAR2, not ADAR1 or active-site-mutated ADAR2, could edit insulin-like growth factor binding protein 7 (IGFBP7) mRNA in ESCC. IGFBP7 knockdown or ADAR2 catalytic activity destruction abolished the pro-apoptotic function of ADAR2. Mechanistically, RNA editing may stabilize IGFBP7 protein by changing the protease recognition site of matriptase and this is essential for IGFBP7 to induce apoptosis. Western blotting revealed that ADAR2 overexpression could induce IGFBP7-dependent inhibition of Akt signaling. Thus, our data indicate that ADAR2 suppresses tumor growth and induces apoptosis by editing and stabilizing IGFBP7 in ESCC, and this may represent a novel therapeutic target for treating ESCC.
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Affiliation(s)
- Yuan-Bin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Xiao-Yu Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Fang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Hai-De Qin
- Unit on Statistical Genomics, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Yin Yao Shugart
- Unit on Statistical Genomics, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
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28
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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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29
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Washburn MC, Hundley HA. Trans and cis factors affecting A-to-I RNA editing efficiency of a noncoding editing target in C. elegans. RNA (NEW YORK, N.Y.) 2016; 22:722-728. [PMID: 26917557 PMCID: PMC4836646 DOI: 10.1261/rna.055079.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 05/30/2023]
Abstract
Adenosine-to-inosine RNA editing by ADARs affects thousands of adenosines in an organism's transcriptome. However, adenosines are not edited at equal levels nor do these editing levels correlate well with ADAR expression levels. Therefore, additional mechanisms are utilized by the cell to dictate the editing efficiency at a given adenosine. To examine cis-and trans-acting factors that regulate A-to-I editing levels specifically in neural cells, we utilized the model organism Caenorhabditis elegans We demonstrate that a double-stranded RNA (dsRNA) binding protein, ADR-1, inhibits editing in neurons, which is largely masked when examining editing levels from whole animals. Furthermore, expression of ADR-1 and mRNA expression of the editing target can act synergistically to regulate editing efficiency. In addition, we identify a dsRNA region within the Y75B8A.83' UTR that acts as acis-regulatory element by enhancing ADR-2 editing efficiency. Together, this work identifies mechanisms that regulate editing efficiency of noncoding A-to-I editing sites, which comprise the largest class of ADAR targets.
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Affiliation(s)
- Michael C Washburn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405, USA
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30
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Licht K, Kapoor U, Mayrhofer E, Jantsch MF. Adenosine to Inosine editing frequency controlled by splicing efficiency. Nucleic Acids Res 2016; 44:6398-408. [PMID: 27112566 PMCID: PMC5291252 DOI: 10.1093/nar/gkw325] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 04/14/2016] [Indexed: 11/22/2022] Open
Abstract
Alternative splicing and adenosine to inosine (A to I) RNA-editing are major factors leading to co- and post-transcriptional modification of genetic information. Both, A to I editing and splicing occur in the nucleus. As editing sites are frequently defined by exon–intron basepairing, mRNA splicing efficiency should affect editing levels. Moreover, splicing rates affect nuclear retention and will therefore also influence the exposure of pre-mRNAs to the editing-competent nuclear environment. Here, we systematically test the influence of splice rates on RNA-editing using reporter genes but also endogenous substrates. We demonstrate for the first time that the extent of editing is controlled by splicing kinetics when editing is guided by intronic elements. In contrast, editing sites that are exclusively defined by exonic structures are almost unaffected by the splicing efficiency of nearby introns. In addition, we show that editing levels in pre- and mature mRNAs do not match. This phenomenon can in part be explained by the editing state of an RNA influencing its splicing rate but also by the binding of the editing enzyme ADAR that interferes with splicing.
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Affiliation(s)
- Konstantin Licht
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Utkarsh Kapoor
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Elisa Mayrhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Michael F Jantsch
- Department of Cell- and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna 1030, Austria
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31
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Licht K, Jantsch MF. Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications. J Cell Biol 2016; 213:15-22. [PMID: 27044895 PMCID: PMC4828693 DOI: 10.1083/jcb.201511041] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/14/2022] Open
Abstract
Advances in next-generation sequencing and mass spectrometry have revealed widespread messenger RNA modifications and RNA editing, with dramatic effects on mammalian transcriptomes. Factors introducing, deleting, or interpreting specific modifications have been identified, and analogous with epigenetic terminology, have been designated "writers," "erasers," and "readers." Such modifications in the transcriptome are referred to as epitranscriptomic changes and represent a fascinating new layer of gene expression regulation that has only recently been appreciated. Here, we outline how RNA editing and RNA modification can rapidly affect gene expression, making both processes as well suited to respond to cellular stress and to regulate the transcriptome during development or circadian periods.
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Affiliation(s)
- Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, A-1030 Vienna, Austria
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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 2016; 125:51-63. [PMID: 26148686 PMCID: PMC4761006 DOI: 10.1007/s00412-015-0526-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3. G3-GENES GENOMES GENETICS 2015; 6:321-35. [PMID: 26637431 PMCID: PMC4751552 DOI: 10.1534/g3.115.022251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RNA editing is a posttranscriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, yielding contradictory conclusions regarding the extent of this phenomenon. We show, by detailed description of the 25 studies focusing so far on mRNA editing at the whole-transcriptome scale, that systematic sequencing artifacts are considered in most studies whereas biological replication is often neglected and multi-alignment not properly evaluated, which ultimately impairs the legitimacy of results. We recently developed a rigorous strategy to identify mRNA editing using mRNA and genomic DNA sequencing, taking into account sequencing and mapping artifacts, and biological replicates. We applied this method to screen for mRNA editing in liver and white adipose tissue from eight chickens and confirm the small extent of mRNA recoding in this species. Among the 25 unique edited sites identified, three events were previously described in mammals, attesting that this phenomenon is conserved throughout evolution. Deeper investigations on five sites revealed the impact of tissular context, genotype, age, feeding conditions, and sex on mRNA editing levels. More specifically, this analysis highlighted that the editing level at the site located on COG3 was strongly regulated by four of these factors. By comprehensively characterizing the mRNA editing landscape in chickens, our results highlight how this phenomenon is limited and suggest regulation of editing levels by various genetic and environmental factors.
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34
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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: 67] [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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35
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Stilling RM, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF. Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala. Brain Behav Immun 2015; 50:209-220. [PMID: 26184083 DOI: 10.1016/j.bbi.2015.07.009] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/09/2015] [Accepted: 07/11/2015] [Indexed: 12/14/2022] Open
Abstract
The mammalian amygdala is a key emotional brain region for eliciting social behaviour, critically involved in anxiety and fear-related behaviours, and hence a focus of research on neurodevelopmental and stress-related disorders such as autism and anxiety. Recently, increasing evidence implicates host-microbe interactions in the aetiology of these conditions. Germ-free (GF) mice, devoid of any microbiota throughout organismal maturation, are a well-established tool to study the effects of absence of the microbiota on host physiology. A growing body of independently replicated findings confirm that GF animals demonstrate altered anxiety-related behaviour and impaired social behaviour. However, the underlying mechanisms of this interaction and the nature of the pathways involved are only insufficiently understood. To further elucidate the molecular underpinnings of microbe-brain interaction, we therefore exploited unbiased genome-wide transcriptional profiling to determine gene expression in the amygdala of GF and GF mice that have been colonised after weaning. Using RNA-sequencing and a comprehensive downstream analysis pipeline we studied the amygdala transcriptome and found significant differences at the levels of differential gene expression, exon usage and RNA-editing. Most surprisingly, we noticed upregulation of several immediate early response genes such as Fos, Fosb, Egr2 or Nr4a1 in association with increased CREB signalling in GF mice. In addition, we found differential expression and recoding of several genes implicated in brain physiology processes such as neurotransmission, neuronal plasticity, metabolism and morphology. In conclusion, our data suggest altered baseline neuronal activity in the amygdala of germ-free animals, which is established during early life and may have implications for understanding development and treatment of neurodevelopmental disorders.
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Affiliation(s)
- Roman M Stilling
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Microbiology, University College Cork, Cork, Ireland
| | - Alan E Hoban
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Microbiology, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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