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Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO. Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biol 2014; 15:R79. [PMID: 24946870 PMCID: PMC4197816 DOI: 10.1186/gb-2014-15-6-r79] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored. RESULTS Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required. CONCLUSIONS These studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
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Affiliation(s)
- Valerie Blanc
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Eddie Park
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Sabine Schaefer
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Melanie Miller
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Yiing Lin
- Departments of Surgery, Washington University St Louis, St Louis, MO 63110, USA
| | - Susan Kennedy
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Anja M Billing
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | | | - Johannes Graumann
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Ali Mortazavi
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
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Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nat Struct Mol Biol 2013; 20:1333-9. [PMID: 24077224 DOI: 10.1038/nsmb.2675] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023]
Abstract
The accurate and thorough genome-wide detection of adenosine-to-inosine editing, a biologically indispensable process, has proven challenging. Here, we present a discovery pipeline in adult Drosophila, with 3,581 high-confidence editing sites identified with an estimated accuracy of 87%. The target genes and specific sites highlight global biological properties and functions of RNA editing, including hitherto-unknown editing in well-characterized classes of noncoding RNAs and 645 sites that cause amino acid substitutions, usually at conserved positions. The spectrum of functions that these gene targets encompass suggests that editing participates in a diverse set of cellular processes. Editing sites in Drosophila exhibit sequence-motif preferences and tend to be concentrated within a small subset of total RNAs. Finally, editing regulates expression levels of target mRNAs and strongly correlates with alternative splicing.
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RNA editing and drug discovery for cancer therapy. ScientificWorldJournal 2013; 2013:804505. [PMID: 23737728 PMCID: PMC3655661 DOI: 10.1155/2013/804505] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/08/2013] [Indexed: 12/26/2022] Open
Abstract
RNA editing is vital to provide the RNA and protein complexity to regulate the gene expression. Correct RNA editing maintains the cell function and organism development. Imbalance of the RNA editing machinery may lead to diseases and cancers. Recently, RNA editing has been recognized as a target for drug discovery although few studies targeting RNA editing for disease and cancer therapy were reported in the field of natural products. Therefore, RNA editing may be a potential target for therapeutic natural products. In this review, we provide a literature overview of the biological functions of RNA editing on gene expression, diseases, cancers, and drugs. The bioinformatics resources of RNA editing were also summarized.
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Kiran AM, O'Mahony JJ, Sanjeev K, Baranov PV. Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res 2012; 41:D258-61. [PMID: 23074185 PMCID: PMC3531090 DOI: 10.1093/nar/gks961] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DARNED (DAtabase of RNa EDiting, available at http://darned.ucc.ie) is a centralized repository of reference genome coordinates corresponding to RNA nucleotides having altered templated identities in the process of RNA editing. The data in DARNED are derived from published datasets of RNA editing events. RNA editing instances have been identified with various methods, such as bioinformatics screenings, deep sequencing and/or biochemical techniques. Here we report our current progress in the development and expansion of the DARNED. In addition to novel database features the DARNED update describes inclusion of Drosophila melanogaster and Mus musculus RNA editing events and the launch of a community-based annotation in the RNA WikiProject.
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Affiliation(s)
- Anmol M Kiran
- Biochemistry Department, University College Cork, Cork, Ireland
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Yang C, Su J, Li Q, Zhang R, Rao Y. Identification and expression profiles of ADAR1 gene, responsible for RNA editing, in responses to dsRNA and GCRV challenge in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2012; 33:1042-1049. [PMID: 22796906 DOI: 10.1016/j.fsi.2012.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/25/2012] [Accepted: 07/04/2012] [Indexed: 06/01/2023]
Abstract
ADAR (adenosine deaminase acting on RNA) is an RNA editing enzyme that targets both coding and noncoding dsRNAs (double stranded RNAs) and converts adenosine to inosine, which is read by translation machinery and by polymerases during RNA-dependent RNA replication as if it is guanosine. This editing is a widespread post-transcriptional modification event in animals. In this study, we identified the full-length cDNA sequence of Ctenopharyngodon idella ADAR1 (designated as CiADAR1) and detected the mRNA expression patterns in response to dsRNA (polyinosinic-polycytidylic acid sodium salt, poly(I:C)) and grass carp reovirus (GCRV). CiADAR1 is a large gene in size, consisting of 4833 nucleotides encoding a protein of 1392 amino acids. The deduced amino acid sequence contains seven putative domains: one proline-rich region (Pro-R), two Z-DNA-binding domains (Zalpha), three dsRNA binding motifs (DSRM) and one tRNA-specific and dsRNA adenosine deaminase domain (ADEAMc). It is most homologous to Danio rerio ADAR (E-value = 0.0, identities = 80% (1110/1395)), also close homology to Homo sapiens ADAR1 (E-value = 0.0, identities = (47%) 530/1122). CiADAR1 mRNA was investigated in fifteen tissues, and was low expressed in muscle and head kidney tissues, high in blood and spleen tissues by quantitative real-time RT-PCR (qRT-PCR). mRNA expressions of CiADAR1 were significantly up-regulated and reached peak at 24 h post GCRV challenge in vivo and in vitro (P < 0.05). After poly(I:C) stimulation at different concentrations, CiADAR1 transcripts were rapidly and significantly up-regulated and recovered in dose-dependent and time-dependent manners (P < 0.05). The results indicate CiADAR1 was implicated in the antiviral immune response and laid the foundation for further studies on functions and mechanisms of RNA editing in fishes.
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Affiliation(s)
- Chunrong Yang
- Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, No. 22 Xinong Rd., Yangling 712100, China
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Qureshi IA, Mehler MF. Emerging themes in epigenetics: implications for understanding and treating nervous system disorders. Epigenomics 2012; 2:345-9. [PMID: 22121894 DOI: 10.2217/epi.10.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Oguro R, Kamide K, Katsuya T, Akasaka H, Sugimoto K, Congrains A, Arai Y, Hirose N, Saitoh S, Ohishi M, Miura T, Rakugi H. A single nucleotide polymorphism of the adenosine deaminase, RNA-specific gene is associated with the serum triglyceride level, abdominal circumference, and serum adiponectin concentration. Exp Gerontol 2011; 47:183-7. [PMID: 22210125 DOI: 10.1016/j.exger.2011.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/24/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) of the adenosine deaminase, RNA-specific (ADAR) gene were reported to be associated with human longevity. There are possibilities that ADAR is associated with major risk factors of atherosclerotic cardiovascular diseases (CVD), such as hypertension, diabetes, dyslipidemia, and obesity. OBJECTIVE To investigate the association between SNPs of the ADAR gene and clinical data associated with major risk factors of atherosclerotic CVD. SUBJECTS A total of 1504 general population residents (586 males and 918 females) of two towns, Tanno-cho and Sobestu-cho, in Hokkaido, Japan. METHODS Clinical data associated with risk factors of atherosclerotic CVD were collected from these study subjects. DNA from peripheral blood and written informed consent were obtained. Three single nucleotide polymorphisms of ADARB1 and ADARB2, which were previously reported to be associated with longevity, were genotyped employing the TaqMan PCR method. The associations between SNPs in ADARB1 and ADARB2 and clinical parameters related to risk factors of atherosclerosis were analyzed. RESULTS On uni- and multivariate analyses, rs2805533 in ADARB2 was significantly associated with the abdominal circumference, body mass index, serum triglyceride level, and serum adiponectin level. The subjects with the AA genotype of rs2805533 had a greater abdominal circumference, higher body mass index, higher triglyceride level, and lower adiponectin level than those with AG and GG genotypes. CONCLUSION The SNP in ADARB2 related to longevity is associated with metabolic disorders. This finding suggests that genetic factors modulate human longevity via the regulation of metabolic factors such as abdominal obesity and lipid profiles.
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Affiliation(s)
- Ryosuke Oguro
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565, Japan
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Carmi S, Borukhov I, Levanon EY. Identification of widespread ultra-edited human RNAs. PLoS Genet 2011; 7:e1002317. [PMID: 22028664 PMCID: PMC3197674 DOI: 10.1371/journal.pgen.1002317] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 08/04/2011] [Indexed: 01/24/2023] Open
Abstract
Adenosine-to-inosine modification of RNA molecules (A-to-I RNA editing) is an important mechanism that increases transciptome diversity. It occurs when a genomically encoded adenosine (A) is converted to an inosine (I) by ADAR proteins. Sequencing reactions read inosine as guanosine (G); therefore, current methods to detect A-to-I editing sites align RNA sequences to their corresponding DNA regions and identify A-to-G mismatches. However, such methods perform poorly on RNAs that underwent extensive editing ("ultra"-editing), as the large number of mismatches obscures the genomic origin of these RNAs. Therefore, only a few anecdotal ultra-edited RNAs have been discovered so far. Here we introduce and apply a novel computational method to identify ultra-edited RNAs. We detected 760 ESTs containing 15,646 editing sites (more than 20 sites per EST, on average), of which 13,668 are novel. Ultra-edited RNAs exhibit the known sequence motif of ADARs and tend to localize in sense strand Alu elements. Compared to sites of mild editing, ultra-editing occurs primarily in Alu-rich regions, where potential base pairing with neighboring, inverted Alus creates particularly long double-stranded RNA structures. Ultra-editing sites are underrepresented in old Alu subfamilies, tend to be non-conserved, and avoid exons, suggesting that ultra-editing is usually deleterious. A possible biological function of ultra-editing could be mediated by non-canonical splicing and cleavage of the RNA near the editing sites.
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Affiliation(s)
- Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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Qureshi IA, Mehler MF. Epigenetics, nervous system tumors, and cancer stem cells. Cancers (Basel) 2011; 3:3525-56. [PMID: 24212967 PMCID: PMC3759209 DOI: 10.3390/cancers3033525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/01/2011] [Accepted: 09/08/2011] [Indexed: 12/11/2022] Open
Abstract
Recent advances have begun to elucidate how epigenetic regulatory mechanisms are responsible for establishing and maintaining cell identity during development and adult life and how the disruption of these processes is, not surprisingly, one of the hallmarks of cancer. In this review, we describe the major epigenetic mechanisms (i.e., DNA methylation, histone and chromatin modification, non-coding RNA deployment, RNA editing, and nuclear reorganization) and discuss the broad spectrum of epigenetic alterations that have been uncovered in pediatric and adult nervous system tumors. We also highlight emerging evidence that suggests epigenetic deregulation is a characteristic feature of so-called cancer stem cells (CSCs), which are thought to be present in a range of nervous system tumors and responsible for tumor maintenance, progression, treatment resistance, and recurrence. We believe that better understanding how epigenetic mechanisms operate in neural cells and identifying the etiologies and consequences of epigenetic deregulation in tumor cells and CSCs, in particular, are likely to promote the development of enhanced molecular diagnostics and more targeted and effective therapeutic agents for treating recalcitrant nervous system tumors.
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Affiliation(s)
- Irfan A. Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Mark F. Mehler
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-718-430-3543; Fax: +1-718-918-7505
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Wu D, Lamm AT, Fire AZ. Competition between ADAR and RNAi pathways for an extensive class of RNA targets. Nat Struct Mol Biol 2011; 18:1094-101. [PMID: 21909095 PMCID: PMC3190075 DOI: 10.1038/nsmb.2129] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/28/2011] [Indexed: 12/22/2022]
Abstract
Adenosine deaminases that act on RNAs (ADARs) interact with double-stranded RNAs, deaminating adenosines to inosines. Previous studies of Caenorhabditis elegans suggested an antagonistic interaction between ADAR and RNAi machineries, with ADAR defects suppressed upon additional knockout of RNAi. These results suggest a pool of common RNA substrates capable of engaging both pathways. To define and characterize such substrates, we examined small RNA and mRNA populations of ADAR mutants and identified a distinct set of loci from which RNAi-dependent short RNAs are dramatically upregulated. At these same loci, we observe populations of multiply edited transcripts, supporting a specific role for ADARs in preventing access to the RNAi pathway for an extensive population of dsRNAs. Characterization of these loci reveal an extensive overlap with non-coding and intergenic regions, suggesting that the landscape of ADAR targets may extend beyond previously annotated classes of transcripts.
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Affiliation(s)
- Diane Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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Qureshi IA, Mehler MF. Non-coding RNA networks underlying cognitive disorders across the lifespan. Trends Mol Med 2011; 17:337-46. [PMID: 21411369 DOI: 10.1016/j.molmed.2011.02.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/04/2011] [Accepted: 02/08/2011] [Indexed: 02/06/2023]
Abstract
Non-coding RNAs (ncRNAs) and their associated regulatory networks are increasingly being implicated in mediating a complex repertoire of neurobiological functions. Cognitive and behavioral processes are proving to be no exception. In this review, we discuss the emergence of many novel, diverse and rapidly expanding classes and subclasses of short and long ncRNAs. We briefly review the life cycles and molecular functions of these ncRNAs. We also examine how ncRNA circuitry mediates brain development, plasticity, stress responses and aging, and highlight its potential roles in the pathophysiology of cognitive disorders, including neural developmental and age-associated neurodegenerative diseases, as well as those that manifest throughout the lifespan.
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Affiliation(s)
- Irfan A Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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Samuel CE. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology 2011; 411:180-93. [PMID: 21211811 DOI: 10.1016/j.virol.2010.12.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 12/04/2010] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing, the deamination of adenosine (A) to inosine (I) that occurs in regions of RNA with double-stranded character, is catalyzed by a family of Adenosine Deaminases Acting on RNA (ADARs). In mammals there are three ADAR genes. Two encode proteins that possess demonstrated deaminase activity: ADAR1, which is interferon-inducible, and ADAR2 which is constitutively expressed. ADAR3, by contrast, has not yet been shown to be an active enzyme. The specificity of the ADAR1 and ADAR2 deaminases ranges from highly site-selective to non-selective, dependent on the duplex structure of the substrate RNA. A-to-I editing is a form of nucleotide substitution editing, because I is decoded as guanosine (G) instead of A by ribosomes during translation and by polymerases during RNA-dependent RNA replication. Additionally, A-to-I editing can alter RNA structure stability as I:U mismatches are less stable than A:U base pairs. Both viral and cellular RNAs are edited by ADARs. A-to-I editing is of broad physiologic significance. Among the outcomes of A-to-I editing are biochemical changes that affect how viruses interact with their hosts, changes that can lead to either enhanced or reduced virus growth and persistence depending upon the specific virus.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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