Mammalian conserved ADAR targets comprise only a small fragment of the human editosome

BackgroundADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected by analyzing next generation sequencing data. Most of these novel editing sites are located in lineage-specific genomic repeats, probably a result of overactivity of editing enzymes, thus masking the functional sites. In this study we aim to identify the set of mammalian conserved ADAR targets.ResultsWe used RNA sequencing data from human, mouse, rat, cow, opossum, and platypus to define the conserved mammalian set of ADAR targets. We found that the conserved mammalian editing sites are surprisingly small in number and have unique characteristics that distinguish them from non-conserved ones. The sites that constitute the set have a distinct genomic distribution, tend to be located in genes encoding neurotransmitter receptors or other synapse related proteins, and have higher editing and expression levels. We also found a high consistency of editing levels of this set within mice strains and between human and mouse. Tight regulation of editing in these sites across strains and species implies their functional importance.ConclusionsDespite the discovery of numerous editing targets, only a small number of them are conserved within mammalian evolution. These sites are extremely highly conserved and exhibit unique features, such as tight regulation, and probably play a pivotal role in mammalian biology.

[1]  Brenda L Bass,et al.  RNA editing by adenosine deaminases that act on RNA. , 2002, Annual review of biochemistry.

[2]  Jin Billy Li,et al.  Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome” , 2012, Science.

[3]  T. Matise,et al.  Widespread RNA editing of embedded alu elements in the human transcriptome. , 2004, Genome research.

[4]  Zipora Y. Fligelman,et al.  Systematic identification of abundant A-to-I editing sites in the human transcriptome , 2004, Nature Biotechnology.

[5]  Christoph D. Rau,et al.  Limited RNA Editing in Exons of Mouse Liver and Adipose , 2013, Genetics.

[6]  B. Bass,et al.  Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[7]  P. Seeburg,et al.  RNA editing in brain controls a determinant of ion flow in glutamate-gated channels , 1991, Cell.

[8]  Victoria Arango,et al.  Altered Editing of Serotonin 2C Receptor Pre-mRNA in the Prefrontal Cortex of Depressed Suicide Victims , 2002, Neuron.

[9]  Sean P Mullen,et al.  RNA editing: a driving force for adaptive evolution? , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  Richard Durbin,et al.  High levels of RNA-editing site conservation amongst 15 laboratory mouse strains , 2012, Genome Biology.

[11]  T. Dawson,et al.  Regulation of alternative splicing by RNA editing , 1999, Nature.

[12]  B. Bass,et al.  A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. , 2000, RNA.

[13]  Ting Wang,et al.  The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..

[14]  T. Dinan,et al.  Dynamic 5-HT2C Receptor Editing in a Mouse Model of Obesity , 2012, PloS one.

[15]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[16]  S. Maas,et al.  Screening of human SNP database identifies recoding sites of A-to-I RNA editing. , 2008, RNA.

[17]  D. Feldmeyer,et al.  Neurological dysfunctions in mice expressing different levels of the Q/R site–unedited AMPAR subunit GluR–B , 1999, Nature Neuroscience.

[18]  P. Seeburg,et al.  Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[19]  J. Trojanowski,et al.  A mutation affecting the sodium/proton exchanger, SLC9A6, causes mental retardation with tau deposition. , 2010, Brain : a journal of neurology.

[20]  Eli Eisenberg,et al.  RNA-editing-mediated exon evolution , 2007, Genome Biology.

[21]  R. Reenan,et al.  Nervous System Targets of RNA Editing Identified by Comparative Genomics , 2003, Science.

[22]  Joshua J C Rosenthal,et al.  Control of human potassium channel inactivation by editing of a small mRNA hairpin , 2004, Nature Structural &Molecular Biology.

[23]  Jin Billy Li,et al.  Accurate identification of human Alu and non-Alu RNA editing sites , 2012, Nature Methods.

[24]  Yiannis A. Savva,et al.  The ADAR protein family , 2012, Genome Biology.

[25]  Richard Wooster,et al.  A survey of RNA editing in human brain. , 2004, Genome research.

[26]  A. Scadden.  The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage , 2005, Nature Structural &Molecular Biology.

[27]  Wenwei Zhang,et al.  Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome , 2012, Nature Biotechnology.

[28]  Michael D. Wilson,et al.  The Evolutionary Landscape of Alternative Splicing in Vertebrate Species , 2012, Science.

[29]  H. Fuchs,et al.  Requirement of the RNA-editing Enzyme ADAR2 for Normal Physiology in Mice* , 2011, The Journal of Biological Chemistry.

[30]  Chao-ke Tang,et al.  The magic and mystery of microRNA-27 in atherosclerosis. , 2012, Atherosclerosis.

[31]  B. Sakmann,et al.  Coincidence detection and changes of synaptic efficacy in spiny stellate neurons in rat barrel cortex , 1999, Nature Neuroscience.

[32]  A. Hatzigeorgiou,et al.  Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs , 2007, Science.

[33]  Angela Gallo,et al.  A-to-I RNA editing: the "ADAR" side of human cancer. , 2012, Seminars in cell & developmental biology.

[34]  D. Feldmeyer,et al.  Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2 , 2000, Nature.

[35]  Eli Eisenberg,et al.  Sequence based identification of RNA editing sites , 2010, RNA biology.

[36]  M. Rosbash,et al.  Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. , 2012, Molecular cell.

[37]  Carol Sanger,et al.  Editing , 2020, Every Day I Write the Book.

[38]  Stefanie Dimmeler,et al.  Role of Dicer and Drosha for Endothelial MicroRNA Expression and Angiogenesis , 2007, Circulation research.

[39]  Brenda L. Bass,et al.  Predicting sites of ADAR editing in double-stranded RNA , 2011, Nature communications.

[40]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[41]  Alexander Rich,et al.  Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome , 2004, PLoS biology.

[42]  G. Church,et al.  Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing , 2009, Science.

[43]  K. A. Lehmann,et al.  Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. , 2000, Biochemistry.

[44]  Charles E Samuel,et al.  RNA Editing Minireview Series* , 2003, The Journal of Biological Chemistry.

[45]  Christopher W. J. Smith,et al.  RNAi is antagonized by A→I hyper‐editing , 2001, EMBO reports.

[46]  M. Weiss,et al.  Stress-induced Apoptosis Associated with Null Mutation of ADAR1 RNA Editing Deaminase Gene* , 2004, Journal of Biological Chemistry.

[47]  Francisco Bezanilla,et al.  Extensive Editing of mRNAs for the Squid Delayed Rectifier K+ Channel Regulates Subunit Tetramerization , 2002, Neuron.

[48]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[49]  E. Levanon,et al.  Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats , 2010, BMC Genomics.

[50]  C. Burge,et al.  Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues , 2012, Science.

[51]  Pavel V. Baranov,et al.  Darned in 2013: inclusion of model organisms and linking with Wikipedia , 2012, Nucleic Acids Res..

[52]  Jin Billy Li,et al.  Edinburgh Research Explorer Identifying Rna Editing Sites Using Rna Sequencing Data Alone , 2022 .

[53]  R. Reenan.  Molecular determinants and guided evolution of species-specific RNA editing , 2005, Nature.

[54]  Mingyao Li,et al.  Widespread RNA and DNA Sequence Differences in the Human Transcriptome , 2011, Science.

[55]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[56]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[57]  Allison M. Porman,et al.  Genome-wide evaluation and discovery of vertebrate A-to-I RNA editing sites. , 2011, Biochemical and biophysical research communications.

[58]  E. Levanon,et al.  Identification of RNA editing sites in the SNP database , 2005, Nucleic acids research.

[59]  Jae-Hyung Lee,et al.  Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. , 2012, Genome research.

[60]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[61]  J. Brosius,et al.  Exonization of transposed elements: A challenge and opportunity for evolution. , 2011, Biochimie.

[62]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[63]  P. Sullivan,et al.  Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders , 2012, PloS one.

[64]  P. Seeburg,et al.  Modulation of microRNA processing and expression through RNA editing by ADAR deaminases , 2006, Nature Structural &Molecular Biology.

[65]  P. Seeburg,et al.  RNA editing of AMPA receptor subunit GluR-B: A base-paired intron-exon structure determines position and efficiency , 1993, Cell.

[66]  Kazuya Iwamoto,et al.  RNA editing of serotonin 2C receptor in human postmortem brains of major mental disorders , 2003, Neuroscience Letters.

[67]  Colleen M. Niswender,et al.  RNA Editing of the Human Serotonin 5-Hydroxytryptamine 2C Receptor Silences Constitutive Activity* , 1999, The Journal of Biological Chemistry.

[68]  K. Nishikura.  Functions and regulation of RNA editing by ADAR deaminases. , 2010, Annual review of biochemistry.

[69]  Joshua J C Rosenthal,et al.  RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses , 2012, Science.

[70]  Eli Eisenberg,et al.  RNA editing level in the mouse is determined by the genomic repeat repertoire. , 2006, RNA.

[71]  Brenda L. Bass,et al.  RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase , 1996, Nature.

[72]  B. Graveley.  The developmental transcriptome of Drosophila melanogaster , 2010, Nature.

[73]  S. Maas,et al.  IGFBP7's susceptibility to proteolysis is altered by A‐to‐I RNA editing of its transcript , 2012, FEBS letters.

[74]  Peter H. Seeburg,et al.  A-to-I RNA Editing: Effects on Proteins Key to Neural Excitability , 2012, Neuron.

[75]  Michael Q. Zhang,et al.  Regulating Gene Expression through RNA Nuclear Retention , 2005, Cell.