Erratum: Profiling RNA editing in human tissues: Towards the inosinome Atlas (Scientific Reports (2015) 5 (14941) DOI: 10.1038/srep14941);Profiling RNA editing in human tissues: Towards the inosinome Atlas

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Picardi, Ernesto ^a,b,c   Manzari, Caterina ^b   Mastropasqua, Francesca ^a   Aiello, Italia ^a   D'Erchia, Anna Maria ^a,b   Pesole, Graziano ^a,b,c  

^a UNIVERSITY OF BARI   (Italy)

^b CNR   (Italy)

^c NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ADENOSINE DEAMINASE; INOSINE; RNA;

ANTIBODY SPECIFICITY; BINDING SITE; BRAIN; CARDIAC MUSCLE; CELL LINE; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HUMAN; HUMAN GENOME; INTERNET; KIDNEY; LIVER; LUNG; METABOLISM; MUSCLE; NUCLEOTIDE SEQUENCE; PROCEDURES; RNA EDITING;

ADENINE; ADENOSINE DEAMINASE; BASE SEQUENCE; BINDING SITES; BRAIN; CELL LINE; DATABASES, GENETIC; GENOME, HUMAN; HUMANS; INOSINE; INTERNET; KIDNEY; LIVER; LUNG; MUSCLES; MYOCARDIUM; ORGAN SPECIFICITY; RNA; RNA EDITING; SEQUENCE ANALYSIS, DNA;

EID: 84943621334     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep20755     Document Type: Erratum

References (58)

1. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
2. Bazak, L. et al. 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).
3. Gott, J. M. & Emeson, R. B. Functions and mechanisms of RNA editing. Annu Rev Genet 34, 499-531 (2000).
4. Nishikura, K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79, 321-349 (2010).
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).
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).
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).
8. Higuchi, M. et al. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406, 78-81 (2000).
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).
10. Chen, L. Characterization and comparison of human nuclear and cytosolic editomes. Proc Natl Acad Sci USA 110, E2741-2747 (2013).
11. Ramaswami, G. & Li, J. B. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic acids res 42, D109-113 (2014).
12. Peng, Z. et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat biotechnol 30, 253-260 (2012).
13. Chen, J. Y. et al. RNA editome in rhesus macaque shaped by purifying selection. PLoS genet 10, e1004274 (2014).
14. Consortium, G. T. The Genotype-Tissue Expression (GTEx) project. Nat genet 45, 580-585 (2013).
15. Fagerberg, L. et al. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibodybased proteomics. Mol Cell Proteomics 13, 397-406 (2014).
16. Ramaswami, G. et al. Identifying RNA editing sites using RNA sequencing data alone. Nat methods 10, 128-132 (2013).
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).
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).
19. Wu, T. D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2011).
20. Picardi, E. & Pesole, G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics 29, 1813-1814 (2013).
21. Bass, B. et al. The difficult calls in RNA editing. Interviewed by H Craig Mak. Nat biotechnol 30, 1207-1209 (2012).
22. Blanc, V. & Davidson, N. O. APOBEC-1-mediated, R. N. A. editing. Wiley Interdiscip Rev Syst Biol Med. 2, 594-602 (2010).
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).
24. St Laurent, G. et al. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nat struct mol biol 20, 1333-1339 (2013).
25. Rodriguez, J., Menet, J. S. & Rosbash, M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol cell 47, 27-37 (2012).
26. Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids res 38, e164 (2010).
27. Sorek, R. The birth of new exons: mechanisms and evolutionary consequences. Rna 13, 1603-1608 (2007).
28. Deininger, P. Alu elements: know the SINEs. Genome biol 12, 236 (2011).
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).
30. Kleinman, C. L., Adoue, V. & Majewski, J. RNA editing of protein sequences: a rare event in human transcriptomes. Rna 18, 1586-1596 (2012).
31. Li, J. B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210-1213 (2009).
32. Bahn, J. H. et al. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome res 22, 142-150 (2012).
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).
34. Zhao, H. Q. et al. Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. Genome res 25, 66-75 (2015).
35. Li, Q. et al. Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior. Nat commun 5, 4943 (2014).
36. Chiefari, E. et al. Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. Nat commun 1, 40 (2010).
37. Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534-538 (2008).
38. Zhang, Q. & Xiao, X. Genome sequence-independent identification of RNA editing sites. Nat methods 12, 347-350 (2015).
39. Alon, S. et al. Systematic identification of edited microRNAs in the human brain. Genome res 22, 1533-1540 (2012).
40. de Hoon, M. J. et al. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome res 20, 257-264 (2010).
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).
42. Samuel, C. E. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology 411, 180-193 (2011).
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).
44. Mele, M. et al. Human genomics. The human transcriptome across tissues and individuals. Science 348, 660-665 (2015).
45. Consortium, G. T. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648-660 (2015).
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).
47. Bahn, J. H. et al. Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. Nat commun 6, 6355 (2015).
48. Pinero, J. et al. 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).
50. Becker, K. G., Barnes, K. C., Bright, T. J. & Wang, S. A. The genetic association database. Nat genet 36, 431-432 (2004).
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).
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).
53. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
54. Roberts, A., Pimentel, H., Trapnell, C. & Pachter, L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27, 2325-2329 (2011).
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).
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. et al. Circos: an information aesthetic for comparative genomics. Genome res 19, 1639-1645 (2009).
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).