RNA editing of protein sequences: A rare event in human transcriptomes

RNA

Volumn 18, Issue 9, 2012, Pages 1586-1596

  Kleinman, Claudia L ^a   Adoue, Véronique ^a   Majewski, Jacek ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

ADAR; High throughput sequencing; RNA editing; RNA Seq; Short read mapping

Indexed keywords

ADAR1 PROTEIN; ADENOSINE DEAMINASE; PROTEIN; RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ALU SEQUENCE; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; ARTIFACT; CELL SURVIVAL; CELL TYPE; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; EXON; GENE DUPLICATION; GENE EXPRESSION; GENE MAPPING; HUMAN; HUMAN CELL; INTRON; LYMPHOBLASTOID CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; QUANTITATIVE ANALYSIS; RNA EDITING; RNA REPLICATION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; EXONS; GENOME, HUMAN; HUMANS; INTRONS; NUCLEOTIDE MOTIFS; OPEN READING FRAMES; PROTEINS; RNA EDITING; TRANSCRIPTOME;

EID: 84865149716     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.033233.112     Document Type: Article

References (51)

1. Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De La Vega FM, Donnelly P, Egholm M, et al. 2010. A map of human genome variation from populationscale sequencing. Nature 467: 1061-1073.
2. Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. 2011. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 22: 142-150.
3. Bass BL. 2002. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71: 817-846. (Pubitemid 34800236)
4. Bhat GJ, Koslowsky DJ, Feagin JE, Smiley BL, Stuart K. 1990. An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6. Cell 61: 885-894.
5. Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
6. Burns CM, Chu H, Rueter SM, Hutchinson LK, Canton H, Sanders-Bush E, Emeson RB. 1997. Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 387: 303-308. (Pubitemid 27220768)
7. Chen L-L, DeCerbo JN, Carmichael GG. 2008. Alu element-mediated gene silencing. EMBO J 27: 1694-1705.
8. Crooks GE, Hon G, Chandonia J-M, Brenner SE. 2004. WebLogo: A sequence logo generator. Genome Res 14: 1188-1190. (Pubitemid 38811555)
9. Feagin JE, Abraham JM, Stuart K. 1988. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell 53: 413-422.
10. Garber M, Grabherr MG, Guttman M, Trapnell C. 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
11. Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, Hudson TJ, Pastinen T. 2005. Survey of allelic expression using EST mining. Genome Res 15: 1584-1591. (Pubitemid 41545012)
12. George CX, Samuel CE. 1999. Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible. Proc Natl Acad Sci 96: 4621-4626. (Pubitemid 29190386)
13. Hamilton CE, Papavasiliou FN, Rosenberg BR. 2010. Diverse functions for DNA and RNA editing in the immune system. RNA Biol 7: 220-228.
14. Hartner JC, Schmittwolf C, Kispert A, Müller AM, Higuchi M, Seeburg PH. 2004. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. J Biol Chem 279: 4894-4902. (Pubitemid 38199085)
15. Higuchi M, Maas S, Single FN, Hartner J, Rozov A, Burnashev N, Feldmeyer D, Sprengel R, Seeburg PH. 2000. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406: 78-81. (Pubitemid 30460214)
16. Horsch M, Seeburg PH, Adler T, Aguilar-Pimentel JA, Becker L, Calzada-Wack J, Garrett L, Gotz A, Hans W, Higuchi M, et al. 2011. Requirement of the RNA-editing enzyme ADAR2 for normal physiology in mice. J Biol Chem 286: 18614-18622.
17. Huang H, Tan Bao Z, Shen Y, Tao J, Jiang F, Sung Ying Y, Ng Choon K, Raida M, Köhr G, Higuchi M, et al. 2012. RNA editing of the IQ domain in Cav1.3 channels modulates their Ca2+-dependent inactivation. Neuron 73: 304-316.
18. Ju YS, Kim J-I, Kim S, Hong D, Park H, Shin J-Y, Lee S, Lee W-C, Kim S, Yu S-B, et al. 2011. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 43: 745-752.
19. Kleinman CL, Majewski J. 2012. Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome". Science 335: 1302. doi: 10.1126/science.1209658.
20. Knoop V. 2010. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci 68: 567-586.
21. Lalonde E, Ha KCH, Wang Z, Bemmo A, Kleinman CL, Kwan T, Pastinen T, Majewski J. 2011. RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression. Genome Res 21: 545-554.
22. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10- 3-r25.
23. Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R, Fligelman ZY, Shoshan A, Pollock SR, Sztybel D, et al. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22: 1001-1005.
24. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. 2009a. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078- 2079.
26. Li JB, Levanon EY, Yoon JK, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM. 2009b. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324: 1210-1213.
27. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. 2011. Widespread RNA and DNA sequence differences in the human transcriptome. Science 333: 53-58.
28. Lin W, Piskol R, Tan MH, Li JB. 2012. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 335: 1302. doi: 10.1126/science.1210624.
29. Lomeli H, Mosbacher J, Melcher T, Hoger T, Geiger, Kuner T, Moner H, Higuchi M, Bach A, Seeburg P. 1994. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science 266: 1709-1713.
30. Meacham F, Boffelli D, Dhahbi J, Martin D, Singer M, Pachter L. 2011. Identification and correction of systematic error in highthroughput sequence data. BMC Bioinformatics 12: 451. doi: 10.1186/1471-2105-12-451.
31. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al. 2011. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 39: e90. doi: 10.1093/nar/gkr344.
32. Nishikura K. 2010. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79: 321-349.
33. Nishimoto Y, Yamashita T, Hideyama T, Tsuji S, Suzuki N, Kwak S. 2008. Determination of editors at the novel A-to-I editing positions. Neurosci Res 61: 201-206.
34. The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
35. Peng Z, Cheng Y, Tan BC-M, Kang L, Tian Z, Zhu Y, Zhang W, Liang Y, Hu X, Tan X, et al. 2012. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30: 253-260.
36. Pickrell JK, Gilad Y, Pritchard JK. 2012. Comment on "widespread RNA and DNA sequence differences in the human transcriptome". Science 335: 1302. doi: 10.1126/science.1210484.
37. Pullirsch D, Jantsch MF. 2010. Proteome diversification by adenosine to inosine RNA-editing. RNA Biol 7: 205-212.
38. Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
39. Ramaswami G, Lin W, Piskol R, Tan MH, Davis C, Li JB. 2012. Accurate identification of human Alu and non-Alu RNA editing sites. Nat Meth doi: 10.1038/nmeth.1982.
40. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, et al. 2010. The UCSC Genome Browser database: Update 2010. Nucleic Acids Res 38: D613-D619.
41. Riedmann EM, Schopoff S, Hartner JC, Jantsch MF. 2008. Specificity of ADAR-mediated RNA editing in newly identified targets. RNA 14: 1110-1118. (Pubitemid 351717491)
42. RIKEN Genome Exploration Research Group and Genome Science Group and the Fantom Consortium, Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
43. Rosenberg BR, Hamilton CE, Mwangi MM, Dewell S, Papavasiliou FN. 2011. Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 39 UTRs. Nat Struct Mol Biol 18: 230-236.
44. Samuel CE. 2012. Adenosine deaminases acting on RNA (ADARs) and A-to-I editing. Vol. 353 (ed. CE Samuel), pp. 163-195. Springer, Berlin, Heidelberg, Germany.
45. Schrider DR, Gout J-F, Hahn MW. 2011. Very few RNA and DNA sequence differences in the human transcriptome. PLoS ONE 6: e25842. doi: 10.1371/journal.pone.0025842.
46. Sommer B, Köhler M, Sprengel R, Seeburg PH. 1991. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 67: 11-19. (Pubitemid 121001421)
47. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
48. Treangen TJ, Salzberg SL. 2012. Repetitive DNA and next-generation sequencing: Computational challenges and solutions. Nat Rev Genet 13: 36-46.
49. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74.
50. Wang Q, Khillan J, Gadue P, Nishikura K. 2000. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis. Science 290: 1765-1768. (Pubitemid 32004807)
51. Wang K, Li M, Hakonarson H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164. doi: 10.1093/nar/gkg603.