51
|
Phelps KJ, Tran K, Eifler T, Erickson AI, Fisher AJ, Beal PA. Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2. Nucleic Acids Res 2015; 43:1123-32. [PMID: 25564529 PMCID: PMC4333395 DOI: 10.1093/nar/gku1345] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) hydrolytically deaminate adenosines (A) in a wide variety of duplex RNAs and misregulation of editing is correlated with human disease. However, our understanding of reaction selectivity is limited. ADARs are modular enzymes with multiple double-stranded RNA binding domains (dsRBDs) and a catalytic domain. While dsRBD binding is understood, little is known about ADAR catalytic domain/RNA interactions. Here we use a recently discovered RNA substrate that is rapidly deaminated by the isolated human ADAR2 deaminase domain (hADAR2-D) to probe these interactions. We introduced the nucleoside analog 8-azanebularine (8-azaN) into this RNA (and derived constructs) to mechanistically trap the protein–RNA complex without catalytic turnover for EMSA and ribonuclease footprinting analyses. EMSA showed that hADAR2-D requires duplex RNA and is sensitive to 2′-deoxy substitution at nucleotides opposite the editing site, the local sequence and 8-azaN nucleotide positioning on the duplex. Ribonuclease V1 footprinting shows that hADAR2-D protects ∼23 nt on the edited strand around the editing site in an asymmetric fashion (∼18 nt on the 5′ side and ∼5 nt on the 3′ side). These studies provide a deeper understanding of the ADAR catalytic domain–RNA interaction and new tools for biophysical analysis of ADAR–RNA complexes.
Collapse
Affiliation(s)
- Kelly J Phelps
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Kiet Tran
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Tristan Eifler
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Anna I Erickson
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
52
|
Brande-Eilat N, Golumbic YN, Zaidan H, Gaisler-Salomon I. Acquisition of conditioned fear is followed by region-specific changes in RNA editing of glutamate receptors. Stress 2015; 18:309-18. [PMID: 26383032 DOI: 10.3109/10253890.2015.1073254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification process that can affect synaptic function. Transcripts encoding the kainate GRIK1 and AMPA GluA2 glutamate receptor subunits undergo editing that leads to a glycine/arginine (Q/R) exchange and reduced Ca(2+) permeability. We hypothesized that editing at these sites could be experience-dependent, temporally dynamic and region-specific. We trained C57/Bl6 mice in trace and contextual fear conditioning protocols, and examined editing levels at GRIK1 and GluA2 Q/R sites in the amygdala (CeA) and hippocampus (CA1 and CA3), at two time points after training. We also examined experience-dependent changes in the expression of RNA editing enzymes and editing targets. Animals trained in the trace fear conditioning protocol exhibited a transient increase in unedited GRIK1 RNA in the amygdala, and their learning efficiency correlated with unedited RNA levels in CA1. In line with previous reports, GluA2 RNA editing levels were nearly 100%. Additionally, we observed experience-dependent changes in mRNA expression of the RNA editing enzymes ADAR2 and ADAR1 in amygdala and hippocampus, and a learning-dependent increase in the alternatively spliced inactive form of ADAR2 in the amygdala. Since unedited transcripts code for Ca(2+)-permeable receptor subunits, these findings suggest that RNA editing at Q/R sites of glutamate receptors plays an important role in experience-dependent synaptic modification processes.
Collapse
Affiliation(s)
- Noa Brande-Eilat
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Yaela N Golumbic
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Hiba Zaidan
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Inna Gaisler-Salomon
- a Psychology Department , University of Haifa , Haifa , Israel and
- b Department of Psychiatry , Columbia University , New York , NY , USA
| |
Collapse
|
53
|
Abstract
The advent of deep sequencing technologies has greatly improved the study of complex eukaryotic genomes and transcriptomes, providing the unique opportunity to investigate posttranscriptional molecular mechanisms as alternative splicing and RNA editing at single base-pair resolution. RNA editing by adenosine deamination (A-to-I) is widespread in humans and can lead to a variety of biological effects depending on the RNA type or the RNA region involved in the editing modification. Hereafter, we describe an easy and reproducible computational protocol for the identification of candidate RNA editing sites in human using deep transcriptome (RNA-Seq) and genome (DNA-Seq) sequencing data.
Collapse
|
54
|
Li X, Teng S. RNA Sequencing in Schizophrenia. Bioinform Biol Insights 2015; 9:53-60. [PMID: 27053919 PMCID: PMC4818022 DOI: 10.4137/bbi.s28992] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/06/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SCZ) is a serious psychiatric disorder that affects 1% of general population and places a heavy burden worldwide. The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes. Next-generation sequencing, particularly of RNA sequencing (RNA-Seq), provides a powerful genome-scale technology to investigate the pathological processes of SCZ. RNA-Seq has been used to analyze the gene expressions and identify the novel splice isoforms and rare transcripts associated with SCZ. This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent stem cells and RNA-Seq in SCZ research.
Collapse
Affiliation(s)
- Xin Li
- Department of Biology, Howard University, Washington, DC, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC, USA
| |
Collapse
|
55
|
A critical analysis of codon optimization in human therapeutics. Trends Mol Med 2014; 20:604-13. [PMID: 25263172 DOI: 10.1016/j.molmed.2014.09.003] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 02/01/2023]
Abstract
Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications.
Collapse
|
56
|
Abstract
Food is a potent natural reward and food intake is a complex process. Reward and gratification associated with food consumption leads to dopamine (DA) production, which in turn activates reward and pleasure centers in the brain. An individual will repeatedly eat a particular food to experience this positive feeling of gratification. This type of repetitive behavior of food intake leads to the activation of brain reward pathways that eventually overrides other signals of satiety and hunger. Thus, a gratification habit through a favorable food leads to overeating and morbid obesity. Overeating and obesity stems from many biological factors engaging both central and peripheral systems in a bi-directional manner involving mood and emotions. Emotional eating and altered mood can also lead to altered food choice and intake leading to overeating and obesity. Research findings from human and animal studies support a two-way link between three concepts, mood, food, and obesity. The focus of this article is to provide an overview of complex nature of food intake where various biological factors link mood, food intake, and brain signaling that engages both peripheral and central nervous system signaling pathways in a bi-directional manner in obesity.
Collapse
Affiliation(s)
- Minati Singh
- Department of Pediatrics, University of Iowa Iowa City, IA, USA ; Department of Pediatrics, HHMI, University of Iowa Iowa City, IA, USA
| |
Collapse
|
57
|
Editing our way to regeneration. Cell Tissue Res 2014; 356:533-7. [PMID: 24803027 DOI: 10.1007/s00441-014-1844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
Transcription is the primary regulatory step to gene expression. However, there are numerous post-transcriptional mechanisms that are also crucial for developing the transcritptome, and the subsequent proteome, signature of any physiological setting. Organ and tissue regeneration is one such physiological setting that requires the rapid development of an environment that can supply all of the necessary molecular and cellular signalling needs necessary to attenuate infection, remove dead or necrotic cells, provide structural stability and finally replenish the compromised area with functional cells. The post-transcriptional regulatory mechanisms that have the ability to heavily influence the molecular and cellular pathways associated with regeneration are slowly being characterized. This mini-review will further clarify the possible regulation of regeneration through adenosine-to-inosine (A-I) RNA editing; a post-transcriptional mechanism that can affect the molecular and cellular pathways associated with functional restoration of damaged tissues and organs through discrete nucleotide changes in RNA transcripts. It is hoped that the intriguing links made between A-I RNA editing and regeneration in this mini-review will encourage further comparative studies into this infant field of research.
Collapse
|
58
|
Barresi S, Tomaselli S, Athanasiadis A, Galeano F, Locatelli F, Bertini E, Zanni G, Gallo A. Oligophrenin-1 (OPHN1), a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development. PLoS One 2014; 9:e91351. [PMID: 24637888 PMCID: PMC3956665 DOI: 10.1371/journal.pone.0091351] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/11/2014] [Indexed: 12/25/2022] Open
Abstract
Oligophrenin-1 (OPHN1) encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.
Collapse
Affiliation(s)
- Sabina Barresi
- Molecular Medicine Laboratory, Neurosciences Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Sara Tomaselli
- RNA Editing Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | - Federica Galeano
- RNA Editing Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Franco Locatelli
- RNA Editing Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
- Università di Pavia, Pavia, Italy
| | - Enrico Bertini
- Molecular Medicine Laboratory, Neurosciences Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ginevra Zanni
- Molecular Medicine Laboratory, Neurosciences Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
- * E-mail: (GZ); (AG)
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
- * E-mail: (GZ); (AG)
| |
Collapse
|
59
|
Wang AL, Carroll RC, Nawy S. Down-regulation of the RNA editing enzyme ADAR2 contributes to RGC death in a mouse model of glaucoma. PLoS One 2014; 9:e91288. [PMID: 24608178 PMCID: PMC3946738 DOI: 10.1371/journal.pone.0091288] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 02/11/2014] [Indexed: 12/13/2022] Open
Abstract
Glaucoma is a progressive neurodegenerative disease of retinal ganglion cells (RGCs) associated with characteristic axon degeneration in the optic nerve. Excitotoxic damage due to increased Ca(2+) influx, possibly through NMDA-type glutamate receptors, has been proposed to be a cause of RGC dysfunction and death in glaucoma. Recent work has found that expression of another potentially critical receptor, the Ca(2+)-permeable AMPA receptor (CP-AMPAR), is elevated during various pathological conditions (including ALS and ischemia), resulting in increased neuronal death. Here we test the hypothesis that CP-AMPARs contribute to RGC death due to elevated Ca(2+) influx in glaucoma. AMPA receptors are impermeable to Ca(2+) if the tetrameric receptor contains a GluA2 subunit that has undergone Q/R RNA editing at a site in the pore region. The activity of ADAR2, the enzyme responsible for this RNA editing, generally ensures that the vast majority of GluA2 proteins are edited. Here, we demonstrate that ADAR2 levels decrease in a mouse model of glaucoma in which IOP is chronically elevated. Furthermore, using an in vitro model of RGCs, we find that knockdown of ADAR2 using siRNA increased the accumulation of Co(2+) in response to glutamate, and decreased the rectification index of AMPA currents detected electrophysiologically, indicating an increased Ca(2+) permeability through AMPARs. The RGCs in primary culture also exhibited increased excitotoxic cell death following knock down of ADAR2. Furthermore, cell death was reversed by NASPM, a specific blocker for CP-AMPARs. Together, our data suggest that chronically elevated IOP in adult mice reduces expression of the ADAR2 enzyme, and the loss of ADAR2 editing and subsequent disruption of GluA2 RNA editing might potentially play a role in promoting RGC neuronal death as observed in glaucoma.
Collapse
Affiliation(s)
- Ai Ling Wang
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Reed C. Carroll
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Scott Nawy
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
| |
Collapse
|
60
|
Wang IX, Core LJ, Kwak H, Brady L, Bruzel A, McDaniel L, Richards AL, Wu M, Grunseich C, Lis JT, Cheung VG. RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. Cell Rep 2014; 6:906-15. [PMID: 24561252 DOI: 10.1016/j.celrep.2014.01.037] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/27/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022] Open
Abstract
RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs) in nascent RNA. Our results show that RDDs begin to occur in RNA chains ~55 nt from the RNA polymerase II (Pol II) active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.
Collapse
Affiliation(s)
- Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lauren Brady
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lee McDaniel
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Allison L Richards
- Human Genetics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming Wu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
61
|
Kubota-Sakashita M, Iwamoto K, Bundo M, Kato T. A role of ADAR2 and RNA editing of glutamate receptors in mood disorders and schizophrenia. Mol Brain 2014; 7:5. [PMID: 24443933 PMCID: PMC3902024 DOI: 10.1186/1756-6606-7-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/09/2014] [Indexed: 01/04/2023] Open
Abstract
Background Pre-mRNAs of 2-amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)-propanoic acid (AMPA)/kainate glutamate receptors undergo post-transcriptional modification known as RNA editing that is mediated by adenosine deaminase acting on RNA type 2 (ADAR2). This modification alters the amino acid sequence and function of the receptor. Glutamatergic signaling has been suggested to have a role in mood disorders and schizophrenia, but it is unknown whether altered RNA editing of AMPA/kainate receptors has pathophysiological significance in these mental disorders. In this study, we found that ADAR2 expression tended to be decreased in the postmortem brains of patients with schizophrenia and bipolar disorder. Results Decreased ADAR2 expression was significantly correlated with decreased editing of the R/G sites of AMPA receptors. In heterozygous Adar2 knockout mice (Adar2+/− mice), editing of the R/G sites of AMPA receptors was decreased. Adar2+/− mice showed a tendency of increased activity in the open-field test and a tendency of resistance to immobility in the forced swimming test. They also showed enhanced amphetamine-induced hyperactivity. There was no significant difference in amphetamine-induced hyperactivity between Adar2+/− and wild type mice after the treatment with an AMPA/kainate receptor antagonist, 2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo[f]quinoxaline. Conclusions These findings collectively suggest that altered RNA editing efficiency of AMPA receptors due to down-regulation of ADAR2 has a possible role in the pathophysiology of mental disorders.
Collapse
Affiliation(s)
| | | | | | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan.
| |
Collapse
|
62
|
Li JB, Church GM. Deciphering the functions and regulation of brain-enriched A-to-I RNA editing. Nat Neurosci 2013; 16:1518-22. [PMID: 24165678 DOI: 10.1038/nn.3539] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/11/2013] [Indexed: 01/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, in which genomically encoded adenosine is changed to inosine in RNA, is catalyzed by adenosine deaminase acting on RNA (ADAR). This fine-tuning mechanism is critical during normal development and diseases, particularly in relation to brain functions. A-to-I RNA editing has also been hypothesized to be a driving force in human brain evolution. A large number of RNA editing sites have recently been identified, mostly as a result of the development of deep sequencing and bioinformatic analyses. Deciphering the functional consequences of RNA editing events is challenging, but emerging genome engineering approaches may expedite new discoveries. To understand how RNA editing is dynamically regulated, it is imperative to construct a spatiotemporal atlas at the species, tissue and cell levels. Future studies will need to identify the cis and trans regulatory factors that drive the selectivity and frequency of RNA editing. We anticipate that recent technological advancements will aid researchers in acquiring a much deeper understanding of the functions and regulation of RNA editing.
Collapse
Affiliation(s)
- Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California, USA
| | | |
Collapse
|
63
|
Stulić M, Jantsch MF. Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues. RNA Biol 2013; 10:1611-7. [PMID: 24025532 PMCID: PMC3866242 DOI: 10.4161/rna.26216] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA editing by ADARs can change the coding potential of protein-coding mRNAs. So far, this type of RNA editing has mainly been shown to affect RNAs expressed in the nervous system with much lower editing levels being observed in other tissues. The actin crosslinking proteins filamin α and filamin β are widely expressed in most tissues. The mRNAs encoding either protein are edited at the same position leading to a conserved Q to R exchange in both proteins. Using bar-coded next generation sequencing, we show that editing of filamin α is most abundant in the gastrointestinal tract and only to a lesser extent in the nervous system. Using knockout mice, we show that ADARB1 (ADAR2) is responsible for the majority of FLNA editing, while ADAR1 can edit filamin α mRNA in some tissues quite efficiently. Interestingly, editing levels of filamin α and β do not follow the same trend across tissues, suggesting a substrate-specific regulation of editing.
Collapse
Affiliation(s)
- Maja Stulić
- Department of Chromosome Biology; Max F. Perutz Laboratories; University of Vienna; A-1030 Vienna, Austria
| | - Michael F Jantsch
- Department of Chromosome Biology; Max F. Perutz Laboratories; University of Vienna; A-1030 Vienna, Austria
| |
Collapse
|
64
|
Seifuddin F, Pirooznia M, Judy JT, Goes FS, Potash JB, Zandi PP. Systematic review of genome-wide gene expression studies of bipolar disorder. BMC Psychiatry 2013; 13:213. [PMID: 23945090 PMCID: PMC3765828 DOI: 10.1186/1471-244x-13-213] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Numerous genome-wide gene expression studies of bipolar disorder (BP) have been carried out. These studies are heterogeneous, underpowered and use overlapping samples. We conducted a systematic review of these studies to synthesize the current findings. METHODS We identified all genome-wide gene expression studies on BP in humans. We then carried out a quantitative mega-analysis of studies done with post-mortem brain tissue. We obtained raw data from each study and used standardized procedures to process and analyze the data. We then combined the data and conducted three separate mega-analyses on samples from 1) any region of the brain (9 studies); 2) the prefrontal cortex (PFC) (6 studies); and 3) the hippocampus (2 studies). To minimize heterogeneity across studies, we focused primarily on the most numerous, recent and comprehensive studies. RESULTS A total of 30 genome-wide gene expression studies of BP done with blood or brain tissue were identified. We included 10 studies with data on 211 microarrays on 57 unique BP cases and 229 microarrays on 60 unique controls in the quantitative mega-analysis. A total of 382 genes were identified as significantly differentially expressed by the three analyses. Eleven genes survived correction for multiple testing with a q-value < 0.05 in the PFC. Among these were FKBP5 and WFS1, which have been previously implicated in mood disorders. Pathway analyses suggested a role for metallothionein proteins, MAP Kinase phosphotases, and neuropeptides. CONCLUSION We provided an up-to-date summary of results from gene expression studies of the brain in BP. Our analyses focused on the highest quality data available and provided results by brain region so that similarities and differences can be examined relative to disease status. The results are available for closer inspection on-line at Metamoodics [http://metamoodics.igm.jhmi.edu/], where investigators can look up any genes of interest and view the current results in their genomic context and in relation to leading findings from other genomic experiments in bipolar disorder.
Collapse
Affiliation(s)
- Fayaz Seifuddin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer T Judy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| |
Collapse
|
65
|
Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. ACTA ACUST UNITED AC 2013; 29:1813-4. [PMID: 23742983 DOI: 10.1093/bioinformatics/btt287] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY The reliable detection of RNA editing sites from massive sequencing data remains challenging and, although several methodologies have been proposed, no computational tools have been released to date. Here, we introduce REDItools a suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. AVAILABILITY AND IMPLEMENTATION REDItools are in python programming language and freely available at http://code.google.com/p/reditools/. CONTACT ernesto.picardi@uniba.it or graziano.pesole@uniba.it SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy.
| | | |
Collapse
|
66
|
Lee JH, Ang JK, Xiao X. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. RNA (NEW YORK, N.Y.) 2013; 19:725-32. [PMID: 23598527 PMCID: PMC3683905 DOI: 10.1261/rna.037903.112] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA-sequencing (RNA-Seq) technologies hold enormous promise for novel discoveries in genomics and transcriptomics. In the past year, a surge of reports has analyzed RNA-Seq data to gain a global view of the RNA editome. Opposing results have been presented, giving rise to extensive debate surrounding one of the first such studies in which a daunting list of all 12 types of RNA-DNA differences (RDDs) were identified. Although a consensus is forming that some of the initial "paradigm-shifting" results of this study may be questionable, recent reports on this topic differed in terms of the number and relative abundance of each type of RDD. Many outstanding issues exist, most importantly, the choice of bioinformatic approaches. Here we discuss the critical data analysis and experimental design issues of such studies to enable improved systematic investigation of the largely unexplored frontier of single-nucleotide variants in RNA.
Collapse
|
67
|
Wright C, Turner JA, Calhoun VD, Perrone-Bizzozero N. Potential Impact of miR-137 and Its Targets in Schizophrenia. Front Genet 2013; 4:58. [PMID: 23637704 PMCID: PMC3636510 DOI: 10.3389/fgene.2013.00058] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 04/02/2013] [Indexed: 12/16/2022] Open
Abstract
The significant impact of microRNAs (miRNAs) on disease pathology is becoming increasingly evident. These small non-coding RNAs have the ability to post-transcriptionally silence the expression of thousands of genes. Therefore, dysregulation of even a single miRNA could confer a large polygenic effect. Schizophrenia is a genetically complex illness thought to involve multiple genes each contributing a small risk. Large genome-wide association studies identified miR-137, a miRNA shown to be involved in neuronal maturation, as one of the top risk genes. To assess the potential mechanism of impact of miR-137 in this disorder and identify its targets, we used a combination of literature searches, ingenuity pathway analysis (IPA), and freely accessible bioinformatics resources. Using TargetScan and the schizophrenia gene resource (SZGR) database, we found that in addition to CSMD1, C10orf26, CACNA1C, TCF4, and ZNF804A, five schizophrenia risk genes whose transcripts are also validated miR-137 targets, there are other schizophrenia-associated genes that may be targets of miR-137, including ERBB4, GABRA1, GRIN2A, GRM5, GSK3B, NRG2, and HTR2C. IPA analyses of all the potential targets identified several nervous system (NS) functions as the top canonical pathways including synaptic long-term potentiation, a process implicated in learning and memory mechanisms and recently shown to be altered in patients with schizophrenia. Among the subset of targets involved in NS development and function, the top scoring pathways were ephrin receptor signaling and axonal guidance, processes that are critical for proper circuitry formation and were shown to be disrupted in schizophrenia. These results suggest that miR-137 may indeed play a substantial role in the genetic etiology of schizophrenia by regulating networks involved in neural development and brain function.
Collapse
Affiliation(s)
- Carrie Wright
- Department of Neurosciences, Health Sciences Center, University of New MexicoAlbuquerque, NM, USA
| | - Jessica A. Turner
- The Mind Research NetworkAlbuquerque, NM, USA
- Psychology Department, University of New MexicoAlbuquerque, NM, USA
| | - Vince D. Calhoun
- The Mind Research NetworkAlbuquerque, NM, USA
- Psychology Department, University of New MexicoAlbuquerque, NM, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, Health Sciences Center, University of New MexicoAlbuquerque, NM, USA
| |
Collapse
|
68
|
Dahabieh MS, Samanta D, Brodovitch JC, Frech C, O'Neill MA, Pinto BM. Sequence-dependent structural dynamics of primate adenosine-to-inosine editing substrates. Chembiochem 2012. [PMID: 23193088 DOI: 10.1002/cbic.201200526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Humans have the highest level of adenosine-to-inosine (A-to-I) editing amongst primates, yet the reasons for this difference remain unclear. Sequence analysis of the Alu Sg elements (A-to-I RNA substrates) corresponding to the Nup50 gene in human, chimp, and rhesus reveals subtle sequence variations surrounding the edit sites. We have developed three constructs that represent human (HuAp5), chimp (ChAp5), and rhesus (RhAp5) Nup50 Alu Sg A-to-I editing substrates. Here, 2-aminopurine (2-Ap) was substituted for edited adenosine (A5) so as to monitor the fluorescence intensity with respect to temperature. UV and steady-state fluorescence (SSF) T(M) plots indicate that local and global unfolding are coincident, with the human construct displaying a T(M) of approximately 70°C, compared to 60°C for chimp and 54°C for rhesus. However, time-resolved fluorescence (TRF) resolves three different fluorescence lifetimes that we assign to folded, intermediate(s), and unfolded states. The TRF data fit well to a two-intermediate model, whereby both intermediates (M, J) are in equilibrium with each other, and the folded/unfolded states. Our model suggests that, at 37°C, human state J and the folded state will be the most heavily populated in comparison to the other primate constructs. In order for adenosine deaminase acting on RNA (ADAR) to efficiently dock, a stable duplex must be present that corresponds to the human construct, globally. Next, the enzyme must "flip out" the base of interest to facilitate the A-to-I conversion; a nucleotide in an intermediate-like position would enhance this conformational change. Our experiments demonstrate that subtle variations in RNA sequence might contribute to the high A-to-I editing levels found in humans.
Collapse
|
69
|
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.
Collapse
Affiliation(s)
- Chunrong Yang
- Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, No. 22 Xinong Rd., Yangling 712100, China
| | | | | | | | | |
Collapse
|
70
|
Dependencies among editing sites in serotonin 2C receptor mRNA. PLoS Comput Biol 2012; 8:e1002663. [PMID: 22969417 PMCID: PMC3435259 DOI: 10.1371/journal.pcbi.1002663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 07/15/2012] [Indexed: 12/14/2022] Open
Abstract
The serotonin 2C receptor (5-HT2CR)–a key regulator of diverse neurological processes–exhibits functional variability derived from editing of its pre-mRNA by site-specific adenosine deamination (A-to-I pre-mRNA editing) in five distinct sites. Here we describe a statistical technique that was developed for analysis of the dependencies among the editing states of the five sites. The statistical significance of the observed correlations was estimated by comparing editing patterns in multiple individuals. For both human and rat 5-HT2CR, the editing states of the physically proximal sites A and B were found to be strongly dependent. In contrast, the editing states of sites C and D, which are also physically close, seem not to be directly dependent but instead are linked through the dependencies on sites A and B, respectively. We observed pronounced differences between the editing patterns in humans and rats: in humans site A is the key determinant of the editing state of the other sites, whereas in rats this role belongs to site B. The structure of the dependencies among the editing sites is notably simpler in rats than it is in humans implying more complex regulation of 5-HT2CR editing and, by inference, function in the human brain. Thus, exhaustive statistical analysis of the 5-HT2CR editing patterns indicates that the editing state of sites A and B is the primary determinant of the editing states of the other three sites, and hence the overall editing pattern. Taken together, these findings allow us to propose a mechanistic model of concerted action of ADAR1 and ADAR2 in 5-HT2CR editing. Statistical approach developed here can be applied to other cases of interdependencies among modification sites in RNA and proteins. The serotonin receptor 2C is a key regulator of diverse neurological processes that affect feeding behavior, sleep, sexual behavior, anxiety and depression. The function of the receptor itself is regulated via so-called pre-mRNA editing, i.e. site-specific adenosine deamination in five distinct sites. The greater the number of edited sites in the serotonin receptor mRNA, the lower the activity of the receptor it encodes. Here we used the results of extensive massively parallel sequencing from human and rat brains to elucidate the dependencies among the editing states of the five sites. Despite the apparent simplicity of the problem, disambiguation of these dependencies is a difficult task that required development of a new statistical technique. We employed this method to analyse the dependencies among editing in the 5 susceptible sites of the receptor mRNA and found that the proximal, juxtaposed sites A and B are strongly interdependent, and that the editing state of these two sites is a major determinant of the editing states of the other three sites, and hence the overall editing pattern. The statistical approach we developed for the analysis of mRNA editing can be applied to other cases of multiple site modification in RNA and proteins.
Collapse
|
71
|
Sanjana NE, Levanon EY, Hueske EA, Ambrose JM, Li JB. Activity-dependent A-to-I RNA editing in rat cortical neurons. Genetics 2012; 192:281-7. [PMID: 22714409 PMCID: PMC3430542 DOI: 10.1534/genetics.112.141200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 06/05/2012] [Indexed: 12/31/2022] Open
Abstract
Changes in neural activity influence synaptic plasticity/scaling, gene expression, and epigenetic modifications. We present the first evidence that short-term and persistent changes in neural activity can alter adenosine-to-inosine (A-to-I) RNA editing, a post-transcriptional site-specific modification found in several neuron-specific transcripts. In rat cortical neuron cultures, activity-dependent changes in A-to-I RNA editing in coding exons are present after 6 hr of high potassium depolarization but not after 1 hr and require calcium entry into neurons. When treatments are extended from hours to days, we observe a negative feedback phenomenon: Chronic depolarization increases editing at many sites and chronic silencing decreases editing. We present several different modulations of neural activity that change the expression of different mRNA isoforms through editing.
Collapse
Affiliation(s)
- Neville E. Sanjana
- Broad Institute, Cambridge, Massachusetts 02142
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Erez Y. Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel, and
| | - Emily A. Hueske
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jessica M. Ambrose
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305
| |
Collapse
|
72
|
Barry G, Mattick JS. The role of regulatory RNA in cognitive evolution. Trends Cogn Sci 2012; 16:497-503. [PMID: 22940578 DOI: 10.1016/j.tics.2012.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/12/2012] [Accepted: 08/13/2012] [Indexed: 12/18/2022]
Abstract
The evolution of the human brain has resulted in the emergence of higher-order cognitive abilities, such as reasoning, planning and social awareness. Although there has been a concomitant increase in brain size and complexity, and component diversification, we argue that RNA regulation of epigenetic processes, RNA editing, and the controlled mobilization of transposable elements have provided the major substrates for cognitive advance. We also suggest that these expanded capacities and flexibilities have led to the collateral emergence of psychiatric fragilities and conditions.
Collapse
Affiliation(s)
- Guy Barry
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland, 4072, Australia.
| | | |
Collapse
|
73
|
Zhu H, Urban DJ, Blashka J, McPheeters MT, Kroeze WK, Mieczkowski P, Overholser JC, Jurjus GJ, Dieter L, Mahajan GJ, Rajkowska G, Wang Z, Sullivan PF, Stockmeier CA, Roth BL. Quantitative analysis of focused a-to-I RNA editing sites by ultra-high-throughput sequencing in psychiatric disorders. PLoS One 2012; 7:e43227. [PMID: 22912834 PMCID: PMC3422315 DOI: 10.1371/journal.pone.0043227] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/18/2012] [Indexed: 12/01/2022] Open
Abstract
A-to-I RNA editing is a post-transcriptional modification of single nucleotides in RNA by adenosine deamination, which thereby diversifies the gene products encoded in the genome. Thousands of potential RNA editing sites have been identified by recent studies (e.g. see Li et al, Science 2009); however, only a handful of these sites have been independently confirmed. Here, we systematically and quantitatively examined 109 putative coding region A-to-I RNA editing sites in three sets of normal human brain samples by ultra-high-throughput sequencing (uHTS). Forty of 109 putative sites, including 25 previously confirmed sites, were validated as truly edited in our brain samples, suggesting an overestimation of A-to-I RNA editing in these putative sites by Li et al (2009). To evaluate RNA editing in human disease, we analyzed 29 of the confirmed sites in subjects with major depressive disorder and schizophrenia using uHTS. In striking contrast to many prior studies, we did not find significant alterations in the frequency of RNA editing at any of the editing sites in samples from these patients, including within the 5HT2C serotonin receptor (HTR2C). Our results indicate that uHTS is a fast, quantitative and high-throughput method to assess RNA editing in human physiology and disease and that many prior studies of RNA editing may overestimate both the extent and disease-related variability of RNA editing at the sites we examined in the human brain.
Collapse
Affiliation(s)
- Hu Zhu
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Daniel J. Urban
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Jared Blashka
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Matthew T. McPheeters
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Wesley K. Kroeze
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, Chapel Hill, North Carolina, United States of America
| | - James C. Overholser
- Department of Psychology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - George J. Jurjus
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Psychiatry, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
| | - Lesa Dieter
- Department of Psychology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gouri J. Mahajan
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Grazyna Rajkowska
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Craig A. Stockmeier
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
74
|
Mizrahi RA, Phelps KJ, Ching AY, Beal PA. Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases. Nucleic Acids Res 2012; 40:9825-35. [PMID: 22885375 PMCID: PMC3479202 DOI: 10.1093/nar/gks752] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Adenosine deaminases acting on RNA (ADAR1 and ADAR2) are human RNA-editing adenosine deaminases responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. Since inosine is recognized during translation as guanosine, this often results in the expression of protein sequences different from those encoded in the genome. While our knowledge of the ADAR2 structure and catalytic mechanism has grown over the years, our knowledge of ADAR1 has lagged. This is due, at least in part, to the lack of well defined, small RNA substrates useful for mechanistic studies of ADAR1. Here, we describe an ADAR1 substrate RNA that can be prepared by a combination of chemical synthesis and enzymatic ligation. Incorporation of adenosine analogs into this RNA and analysis of the rate of ADAR1 catalyzed deamination revealed similarities and differences in the way the ADARs recognize the edited nucleotide. Importantly, ADAR1 is more dependent than ADAR2 on the presence of N7 in the edited base. This difference between ADAR1 and ADAR2 appears to be dependent on the identity of a single amino acid residue near the active site. Thus, this work provides an important starting point in defining mechanistic differences between two functionally distinct human RNA editing ADARs.
Collapse
Affiliation(s)
- Rena A Mizrahi
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | | | | |
Collapse
|
75
|
Venø MT, Bramsen JB, Bendixen C, Panitz F, Holm IE, Öhman M, Kjems J. Spatio-temporal regulation of ADAR editing during development in porcine neural tissues. RNA Biol 2012; 9:1054-65. [PMID: 22858680 DOI: 10.4161/rna.21082] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Editing by ADAR enzymes is essential for mammalian life. Still, knowledge of the spatio-temporal editing patterns in mammals is limited. By use of 454 amplicon sequencing we examined the editing status of 12 regionally extracted mRNAs from porcine developing brain encompassing a total of 64 putative ADAR editing sites. In total 24 brain tissues, dissected from up to five regions from embryonic gestation day 23, 42, 60, 80, 100 and 115, were examined for editing. Generally, editing increased during embryonic development concomitantly with an increase in ADAR2 mRNA level. Notably, the Gria2 (GluR-B) Q/R site, reported to be ~100% edited in previous studies, is only 54% edited at embryonic day 23. Transcripts with multiple editing sites in close proximity to each other exhibit coupled editing and an extraordinary incidence of long-range coupling of editing events more than 32 kb apart is observed for the kainate glutamate receptor 2 transcript, Grik2. Our study reveals complex spatio-temporal ADAR editing patterns of coordinated editing events that may play important roles in the development of the mammalian brain.
Collapse
Affiliation(s)
- Morten T Venø
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | | |
Collapse
|
76
|
Tariq A, Jantsch MF. Transcript diversification in the nervous system: a to I RNA editing in CNS function and disease development. Front Neurosci 2012; 6:99. [PMID: 22787438 PMCID: PMC3391646 DOI: 10.3389/fnins.2012.00099] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/14/2012] [Indexed: 12/16/2022] Open
Abstract
RNA editing by adenosine deaminases that act on RNA converts adenosines to inosines in coding and non-coding regions of mRNAs. Inosines are interpreted as guanosines and hence, this type of editing can change codons, alter splice patterns, or influence the fate of an RNA. A to I editing is most abundant in the central nervous system (CNS). Here, targets for this type of nucleotide modification frequently encode receptors and channels. In many cases, the editing-induced amino acid exchanges alter the properties of the receptors and channels. Consistently, changes in editing patterns are frequently found associated with diseases of the CNS. In this review we describe the mechanisms of RNA editing and focus on target mRNAs of editing that are functionally relevant to normal and aberrant CNS activity.
Collapse
Affiliation(s)
- Aamira Tariq
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna Vienna, Austria
| | | |
Collapse
|
77
|
Lin W, Piskol R, Tan MH, Li JB. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 2012; 335:1302; author reply 1302. [PMID: 22422964 DOI: 10.1126/science.1210419] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported widespread differences between the RNA and DNA sequences of the same human cells, including all 12 possible mismatch types. Before accepting such a fundamental claim, a deeper analysis of the sequencing data is required to discern true differences between RNA and DNA from potential artifacts.
Collapse
Affiliation(s)
- Wei Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | |
Collapse
|