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Profiling RNA editing in human tissues: towards the inosinome Atlas 원문보기

Scientific reports, v.5, 2015년, pp.14941 -   

Picardi, Ernesto (Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari , Via Orabona 4, 70126 Bari, Italy) ,  Manzari, Caterina (Institute of Biomembranes and Bioenergetics, National Research Council , Via Amendola 165) ,  Mastropasqua, Francesca (Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari , Via Orabona 4, 70126 Bari, Italy) ,  Aiello, Italia (Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari , Via Orabona 4, 70126 Bari, Italy) ,  D’Erchia, Anna Maria (Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari , Via Orabona 4, 70126 Bari, Italy) ,  Pesole, Graziano (Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari , Via Orabona 4, 70126 Bari, Italy)

Abstract AI-Helper 아이콘AI-Helper

Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly pervasive in humans with respect to other mammals, and is implicated in a number of divers...

참고문헌 (58)

  1. Djebali S. . Landscape of transcription in human cells . Nature 489 , 101 – 108 ( 2012 ). 22955620 

  2. Bazak L. . A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes . Genome Res 24 , 365 – 376 ( 2014 ). 24347612 

  3. Gott J. M. & Emeson R. B. Functions and mechanisms of RNA editing . Annu Rev Genet 34 , 499 – 531 ( 2000 ). 11092837 

  4. Nishikura K. Functions and regulation of RNA editing by ADAR deaminases . Annu Rev Biochem 79 , 321 – 349 ( 2010 ). 20192758 

  5. Gallo A. & Locatelli F. ADARs: allies or enemies? The importance of A-to-I RNA editing in human disease: from cancer to HIV-1 . Biol Rev 87 , 95 – 110 ( 2012 ). 21682836 

  6. Silberberg G. , Lundin D. , Navon R. & Ohman M. Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders . Hum Mol Gen 21 , 311 – 321 ( 2012 ). 21984433 

  7. Wang Q. , Khillan J. , Gadue P. & Nishikura K. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis . Science 290 , 1765 – 1768 ( 2000 ). 11099415 

  8. Higuchi M. . Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2 . Nature 406 , 78 – 81 ( 2000 ). 10894545 

  9. Ramaswami G. , Lin W. , Piskol R. , Tan M. H. , Davis C. & Li J. B. Accurate identification of human Alu and non-Alu RNA editing sites . Nat methods 9 , 579 – 581 ( 2012 ). 22484847 

  10. Chen L. Characterization and comparison of human nuclear and cytosolic editomes . Proc Natl Acad Sci USA 110 , E2741 – 2747 ( 2013 ). 23818636 

  11. Ramaswami G. & Li J. B. RADAR: a rigorously annotated database of A-to-I RNA editing . Nucleic acids res 42 , D109 – 113 ( 2014 ). 24163250 

  12. Peng Z. . Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome . Nat biotechnol 30 , 253 – 260 ( 2012 ). 22327324 

  13. Chen J. Y. . RNA editome in rhesus macaque shaped by purifying selection . PLoS genet 10 , e1004274 ( 2014 ). 24722121 

  14. Consortium G. T. The Genotype-Tissue Expression (GTEx) project . Nat genet 45 , 580 – 585 ( 2013 ). 23715323 

  15. Fagerberg L. . Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics . Mol Cell Proteomics 13 , 397 – 406 ( 2014 ). 24309898 

  16. Ramaswami G. . Identifying RNA editing sites using RNA sequencing data alone . Nat methods 10 , 128 – 132 ( 2013 ). 23291724 

  17. Picardi E. , Gallo A. , Galeano F. , Tomaselli S. & Pesole G. A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue . PloS one 7 , e44184 ( 2012 ). 22957051 

  18. Porath H. T. , Carmi S. & Levanon E. Y. A genome-wide map of hyper-edited RNA reveals numerous new sites . Nat commun 5 , 4726 ( 2014 ). 25158696 

  19. Wu T. D. & Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads . Bioinformatics 26 , 873 – 881 ( 2011 ). 20147302 

  20. Picardi E. & Pesole G. REDItools: high-throughput RNA editing detection made easy . Bioinformatics 29 , 1813 – 1814 ( 2013 ). 23742983 

  21. Bass B. . The difficult calls in RNA editing. Interviewed by H Craig Mak . Nat biotechnol 30 , 1207 – 1209 ( 2012 ). 23222792 

  22. Blanc V. & Davidson N. O. APOBEC-1-mediated, R. N. A. editing . Wiley Interdiscip Rev Syst Biol Med. 2 , 594 – 602 ( 2010 ). 20836050 

  23. Kiran A. M. , O’Mahony J. J. , Sanjeev K. & Baranov P. V. Darned in 2013: inclusion of model organisms and linking with Wikipedia . Nucleic acids res 41 , D258 – 261 ( 2013 ). 23074185 

  24. St Laurent G. . Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila . Nat struct mol biol 20 , 1333 – 1339 ( 2013 ). 24077224 

  25. Rodriguez J. , Menet J. S. & Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila . Mol cell 47 , 27 – 37 ( 2012 ). 22658416 

  26. Wang K. , Li M. & Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data . Nucleic acids res 38 , e164 ( 2010 ). 20601685 

  27. Sorek R. The birth of new exons: mechanisms and evolutionary consequences . Rna 13 , 1603 – 1608 ( 2007 ). 17709368 

  28. Deininger P. Alu elements: know the SINEs . Genome biol 12 , 236 ( 2011 ). 22204421 

  29. Pinto Y. , Cohen H. Y. & Levanon E. Y. Mammalian conserved ADAR targets comprise only a small fragment of the human editosome . Genome biol 15 , R5 ( 2014 ). 24393560 

  30. Kleinman C. L. , Adoue V. & Majewski J. RNA editing of protein sequences: a rare event in human transcriptomes . Rna 18 , 1586 – 1596 ( 2012 ). 22832026 

  31. Li J. B. . Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing . Science 324 , 1210 – 1213 ( 2009 ). 19478186 

  32. Bahn J. H. . Accurate identification of A-to-I RNA editing in human by transcriptome sequencing . Genome res 22 , 142 – 150 ( 2012 ). 21960545 

  33. Cattenoz P. B. , Taft R. J. , Westhof E. & Mattick J. S. Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage . Rna 19 , 257 – 270 ( 2013 ). 23264566 

  34. Zhao H. Q. . Profiling the RNA editomes of wild-type C. elegans and ADAR mutants . Genome res 25 , 66 – 75 ( 2015 ). 25373143 

  35. Li Q. . Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior . Nat commun 5 , 4943 ( 2014 ). 25266559 

  36. Chiefari E. . Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes . Nat commun 1 , 40 ( 2010 ). 20975707 

  37. Tam O. H. . Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes . Nature 453 , 534 – 538 ( 2008 ). 18404147 

  38. Zhang Q. & Xiao X. Genome sequence-independent identification of RNA editing sites . Nat methods 12 , 347 – 350 ( 2015 ). 25730491 

  39. Alon S. . Systematic identification of edited microRNAs in the human brain . Genome res 22 , 1533 – 1540 ( 2012 ). 22499667 

  40. de Hoon M. J. . Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries . Genome res 20 , 257 – 264 ( 2010 ). 20051556 

  41. Alon S. , Erew M. & Eisenberg E. DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data . Bioinformatics 31 , 2568 – 2570 ( 2015 ). 25840043 

  42. Samuel C. E. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral . Virology 411 , 180 – 193 ( 2011 ). 21211811 

  43. Wang I. X. , So E. , Devlin J. L. , Zhao Y. , Wu M. & Cheung V. G. ADAR regulates RNA editing, transcript stability, and gene expression . Cell rep 5 , 849 – 860 ( 2013 ). 24183664 

  44. Mele M. . Human genomics. The human transcriptome across tissues and individuals . Science 348 , 660 – 665 ( 2015 ). 25954002 

  45. Consortium G. T. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans . Science 348 , 648 – 660 ( 2015 ). 25954001 

  46. Maas S. , Kawahara Y. , Tamburro K. M. & Nishikura K. A-to-I, R. N. A. Editing and Human Disease . RNA biol 3 , 1 – 9 ( 2014 ). 17114938 

  47. Bahn J. H. . Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways . Nat commun 6 , 6355 ( 2015 ). 25751603 

  48. Pinero J. . DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes . Database (Oxford) 2015 ( 2015 ). 

  49. Huang da W. , Sherman B. T. & Lempicki R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists . Nucleic acids res 37 , 1 – 13 ( 2009 ). 19033363 

  50. Becker K. G. , Barnes K. C. , Bright T. J. & Wang S. A. The genetic association database . Nat genet 36 , 431 – 432 ( 2004 ). 15118671 

  51. Luo H. , Lin Y. , Gao F. , Zhang C. T. & Zhang R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements . Nucleic acids res 42 , D574 – 580 ( 2014 ). 24243843 

  52. Dickerson J. E. , Zhu A. , Robertson D. L. & Hentges K. E. Defining the role of essential genes in human disease . PloS one 6 , e27368 ( 2011 ). 22096564 

  53. Li H. . The Sequence Alignment/Map format and SAMtools . Bioinformatics 25 , 2078 – 2079 ( 2009 ). 19505943 

  54. Roberts A. , Pimentel H. , Trapnell C. & Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq . Bioinformatics 27 , 2325 – 2329 ( 2011 ). 21697122 

  55. Trapnell C. , Hendrickson D. G. , Sauvageau M. , Goff L. , Rinn J. L. & Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq . Nat biotechnol 31 , 46 – 53 ( 2013 ). 23222703 

  56. Picardi E. , D’Erchia A. M. , Gallo A. & Pesole G. Detection of post-transcriptional RNA editing events . Meth mol biol 1269 , 189 – 205 ( 2015 ). 

  57. Krzywinski M. . Circos: an information aesthetic for comparative genomics . Genome res 19 , 1639 – 1645 ( 2009 ). 19541911 

  58. Vacic V. , Iakoucheva L. M. & Radivojac P. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments . Bioinformatics 22 , 1536 – 1537 ( 2006 ). 16632492 

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