Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases

RNA Biology

Volumn 9, Issue 3, 2012, Pages 274-282

  Paschoal, Alexandre Rossi ^a,b   Maracaja Coutinho, Vinicius ^a   Setubal, João Carlos ^a   Simões, Zilá Luz Paulino ^a   Verjovski Almeida, Sergio ^a   Durham, Alan Mitchell ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ   (Brazil)

Author keywords

Bioinformatics; Database; ncRNA; Non coding RNA; Transcription; Web tool

Indexed keywords

SMALL CYTOPLASMIC RNA; UNTRANSLATED RNA;

GENE CLUSTER; GENOME; HUMAN; INFORMATION PROCESSING; NUCLEIC ACID DATABASE; PROTEIN ANALYSIS; RELIABILITY; REVIEW; RNA TRANSCRIPTION;

EID: 84860785771     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.19352     Document Type: Review

References (80)

1. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007; 316:1484-8; PMID:17510325; http://dx.doi.org/10. 1126/science.1138341
2. Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 2009; 10:163; PMID:19379481; http://dx.doi.org/10.1186/ 1471-2164-10-163
3. Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, et al. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 2011; 8:468-77; PMID: 21521948; http://dx.doi.org/10.4161/ rna.8.3.14421
4. Ling KH, Brautigan PJ, Hahn CN, Daish T, Rayner JR, Cheah PS, et al. Deep sequencing analysis of the developing mouse brain reveals a novel microRNA. BMC Genomics 2011; 12:176; PMID:21466694; http://dx.doi.org/10.1186/1471-2164-12- 176
5. Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, et al & Athanasius F Bompfünewerer Consortium. RNAs everywhere: genomewide annotation of structured RNAs. J Exp Zool B Mol Dev Evol 2007; 308:1-25; PMID:17171697
6. Jossinet F, Ludwig TE, Westhof E. RNA structure: bioinformatic analysis. Curr Opin Microbiol 2007; 10: 279-85; PMID:17548241; http://dx.doi.org/10.1016/ j.mib.2007.05.010
7. Machado-Lima A, del Portillo HA, Durham AM. Computational methods in noncoding RNA research. J Math Biol 2008; 56:15-49; PMID:17786447; http:// dx.doi.org/10.1007/s00285-007-0122-6
8. Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A. An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Brief Bioinform 2009; 10:475-89; PMID: 19383843; http://dx.doi.org/10.1093/bib/bbp022
9. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, et al. RNAcentral: A vision for an international database of RNA sequences. RNA 2011; 17:1941-6; PMID:21940779; http://dx.doi.org/10.1261/rna.2750811
10. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37(Database issue): D136-40; PMID:18953034; http://dx.doi.org/10.1093/nar/gkn766
11. Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007; 3:e65; PMID:17432929; http://dx.doi.org/10. 1371/journal.pcbi.0030065
12. Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 2010; 38(Database issue):D123-30; PMID:19966272; http://dx.doi.org/10.1093/nar/gkp943
13. Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V. CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic Acids Res 2007; 35(Database issue):D829-33; PMID:17169981; http://dx.doi.org/10.1093/nar/gkl991
14. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression. Nucleic Acids Res 2009; 37(Database issue):D122-6; PMID:18829717; http://dx.doi.org/10.1093/nar/gkn617
15. Wright MW, Bruford EA. Naming 'junk': human nonprotein coding RNA (ncRNA) gene nomenclature. Hum Genomics 2011; 5:90-8; PMID:21296742
16. Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, et al. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 2007; 8: R43; PMID:17386095; http://dx.doi.org/10. 1186/gb-2007-8-3-r43
17. Louro R, El-Jundi T, Nakaya HI, Reis EM, Verjovski- Almeida S. Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci. Genomics 2008; 92:18-25; PMID: 18495418; http://dx.doi.org/10. 1016/j.ygeno.2008.03.013
18. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of nonpolyadenylated RNAs. Genome Biol 2011; 12:R16; PMID:21324177; http://dx.doi.org/10.1186/gb-2011-12-2-r16
19. Szymanski M, Erdmann VA, Barciszewski J. Noncoding RNAs database (ncRNAdb). Nucleic Acids Res 2007; 35(Database issue):D162-4; PMID: 17169980; http://dx.doi.org/10.1093/nar/gkl994
20. Bu D, Yu K, Sun S, Xie C, Skogerbø G, Miao R, et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 2012; 40(Database issue):D210-5; PMID:22135294; http://dx.doi.org/10.1093/nar/gkr1175
21. Woolfe A, Goode DK, Cooke J, Callaway H, Smith S, Snell P, et al. CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Dev Biol 2007; 7:100; PMID:17760977; http://dx.doi.org/10.1186/ 1471-213X-7-100
22. Lee AP, Yang Y, Brenner S, Venkatesh B. TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. BMC Genomics 2007; 8:441; PMID:18045502; http://dx.doi.org/10.1186/ 1471-2164-8-441
23. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 2007; 17:852-64; PMID:17568003; http://dx.doi.org/10.1101/gr.5650707
24. Zhang Y, Guan DG, Yang JH, Shao P, Zhou H, Qu LH. ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. RNA 2010; 16:1889-901; PMID:20801769; http://dx.doi.org/10.1261/rna.2226910
25. Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 2007; 120:2498-506; PMID: 17623775; http://dx.doi.org/10. 1242/jcs.009357
26. Yin Y, Zhao Y, Wang J, Liu C, Chen S, Chen R, et al. antiCODE: a natural sense-antisense transcripts database. BMC Bioinformatics 2007; 8:319; PMID:17760969; http://dx.doi.org/10.1186/1471-2105-8-319
27. Zhang Y, Li J, Kong L, Gao G, Liu QR, Wei L. NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res 2007; 35(Database issue):D156-61; PMID:17082204; http://dx.doi.org/10.1093/nar/gkl782
28. Li JT, Zhang Y, Kong L, Liu QR, Wei L. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res 2008; 36:4833-44; PMID:18653530; http://dx.doi.org/10.1093/nar/gkn470
29. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39(Database issue):D152- 7; PMID:21037258; http://dx.doi.org/10.1093/nar/gkq1027
30. Davis-Dusenbery BN, Hata A. Mechanisms of control of microRNA biogenesis. J Biochem 2010; 148:381- 92; PMID:20833630
31. Nicolas FE, Lopez-Martinez AF. MicroRNAs in human diseases. Recent Pat DNA Gene Seq 2010; 4:142-54; PMID:21288192; http://dx.doi.org/10.2174/ 187221510794751659
32. Silahtaroglu A, Stenvang J. MicroRNAs, epigenetics and disease. Essays Biochem 2010; 48:165-85; PMID: 20822493; http://dx.doi.org/10.1042/bse0480165
33. Plath K, Mlynarczyk-Evans S, Nusinow DA, Panning B. Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet 2002; 36:233-78; PMID:12429693; http://dx.doi.org/10.1146/annurev. genet.36.042902.092433
34. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464:1071-6; PMID:20393566; http://dx.doi.org/10.1038/nature08975
35. Ji P, Diederichs S, Wang W, Böing S, Metzger R, Schneider PM, et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003; 22:8031-41; PMID:12970751; http://dx.doi.org/10. 1038/sj.onc.1206928
36. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011; 39(Database issue):D146-51; PMID:21112873; http://dx.doi.org/10.1093/nar/gkq1138
37. Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 2011; 39(Database issue):D202-9; PMID:21037263; http://dx.doi.org/10.1093/nar/gkq1056
38. Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, et al. Update of ASRP: the Arabidopsis Small RNA Project database. Nucleic Acids Res 2008; 36(Database issue):D982-5; PMID:17999994; http://dx.doi.org/10.1093/ nar/gkm997
39. Molnár A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007; 447:1126-9; PMID:17538623; http://dx.doi.org/10.1038/ nature05903
40. Fei Z, Joung JG, Tang X, Zheng Y, Huang M, Lee JM, et al. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 2011; 39 (Database issue):D1156-63; PMID:20965973; http://dx.doi.org/10.1093/nar/gkq991
41. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7; PMID:19182780; http://dx.doi.org/10. 1038/nature07672
42. Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Hum Mol Genet 2010; 19(R2):R152-61; PMID:20729297; http://dx.doi.org/10.1093/hmg/ ddq353
43. Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011; 10:38; PMID:21489289; http://dx.doi.org/10. 1186/1476-4598-10-38
44. Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Discov 2011; 1:391-407; PMID:22096659; http://dx.doi.org/10.1158/2159- 8290.CD-11-0209
45. Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart AV, Almeida GT, et al. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene 2004; 23:6684- 92; PMID:15221013; http://dx.doi.org/10.1038/sj.onc.1207880
46. Reis EM, Ojopi EP, Alberto FL, Rahal P, Tsukumo F, Mancini UM, et al & Head and Neck Annotation Consortium. Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer. Cancer Res 2005; 65:1693-9; PMID: 15753364; http://dx.doi.org/10.1158/0008-5472.CAN-04- 3506
47. Brito GC, Fachel AA, Vettore AL, Vignal GM, Gimba ER, Campos FS, et al. Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma. Mol Carcinog 2008; 47:757-67; PMID:18348187; http://dx.doi.org/10.1002/mc.20433
48. Perez DS, Hoage TR, Pritchett JR, Ducharme-Smith AL, Halling ML, Ganapathiraju SC, et al. Long, abundantly expressed non-coding transcripts are altered in cancer. Hum Mol Genet 2008; 17:642-55; PMID: 18006640; http://dx.doi.org/10.1093/hmg/ddm336
49. Tahira AC, Kubrusly MS, Faria MF, Dazzani B, Fonseca RS, Maracaja-Coutinho V, et al. Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol Cancer 2011; 10:141; PMID:22078386; http://dx.doi.org/10.1186/1476-4598-10-141
50. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 2012; 30:99-104; PMID:22081020; http://dx.doi.org/10.1038/nbt.2024
51. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 2005; 15:987-97; PMID: 15998911; http://dx.doi.org/10.1101/gr.3455305
52. Kapranov P, St Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorensen PH, et al. The majority of total nuclearencoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol 2010; 8:149; PMID:21176148; http://dx.doi.org/10.1186/1741- 7007-8-149
53. Cao Y, Wu J, Liu Q, Zhao Y, Ying X, Cha L, et al. sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA 2010; 16: 2051-7; PMID:20843985; http://dx.doi.org/10.1261/ rna.2193110
54. Tamura M, Hendrix DK, Klosterman PS, Schimmelman NR, Brenner SE, Holbrook SR, Sr. SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res 2004; 32(Database issue):D182-4; PMID:14681389; http://dx.doi.org/10.1093/nar/ gkh080
55. Turner DH, Mathews DH. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res 2010; 38(Database issue):D280-2; PMID:19880381; http://dx.doi.org/10.1093/nar/ gkp892
56. Tacutu R, Budovsky A, Fraifeld VE. The NetAge database: a compendium of networks for longevity, age-related diseases and associated processes. Biogerontology 2010; 11:513-22; PMID:20186480; http://dx.doi. org/10.1007/s10522-010-9265-8
57. Wu T, Wang J, Liu C, Zhang Y, Shi B, Zhu X, et al. NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Res 2006; 34(Database issue):D150-2; PMID:16381834; http://dx.doi.org/10.1093/ nar/gkj025
58. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37(Database issue):D105-10; PMID:18996891; http://dx.doi.org/10.1093/nar/gkn851
59. Piekna-Przybylska D, Decatur WA, Fournier MJ. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 2007; 13:305-12; PMID:17283215; http://dx.doi.org/10.1261/rna.373107
60. Xin Y, Olson WK. BPS: a database of RNA base-pair structures. Nucleic Acids Res 2009; 37(Database issue): D83-8; PMID:18845572; http://dx.doi.org/10. 1093/nar/gkn676
61. Nagaswamy U, Larios-Sanz M, Hury J, Collins S, Zhang Z, Zhao Q, et al. NCIR: a database of noncanonical interactions in known RNA structures. Nucleic Acids Res 2002; 30:395-7; PMID:11752347; http://dx.doi.org/10.1093/nar/30.1.395
62. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al, ENCODE Project Consortium, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute & Children's Hospital Oakland Research Institute. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816; PMID:17571346; http://dx.doi.org/10.1038/nature05874
63. Amaral PP, Mattick JS. Noncoding RNA in development. Mamm Genome 2008; 19:454-92; PMID: 18839252; http://dx.doi.org/10.1007/s00335-008-9136-7
64. Seidl CI, Stricker SH, Barlow DP. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J 2006; 25:3565-75; PMID:16874305; http://dx.doi.org/10.1038/sj.emboj.7601245
65. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39:925-38; PMID:20797886; http://dx.doi.org/10.1016/j.molcel.2010.08.011
66. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129:1311-23; PMID: 17604720; http://dx.doi.org/10. 1016/j.cell.2007.05.022
67. Tsai MC, Manor O,Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329:689-93; PMID:20616235; http://dx.doi.org/10.1126/science.1192002
68. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409-19; PMID:20673990; http://dx.doi.org/10.1016/j.cell.2010.06.040
69. Wang H, Iacoangeli A, Popp S, Muslimov IA, Imataka H, Sonenberg N, et al. Dendritic BC1 RNA: functional role in regulation of translation initiation. J Neurosci 2002; 22:10232-41; PMID:12451124
70. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43:904-14; PMID: 21925379; http://dx.doi.org/10.1016/j.molcel.2011.08.018
71. Cho S, Jun Y, Lee S, Choi HS, Jung S, Jang Y, et al. miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 2011; 39(Database issue):D158-62; PMID:21062822; http://dx.doi.org/10.1093/nar/ gkq1094
72. Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, Yang CD, et al. sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 2009; 37 (Database issue):D150-4; PMID:19015153; http://dx.doi.org/10.1093/nar/gkn852
73. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008; 14:1012-7; PMID:18426918; http://dx.doi.org/10.1261/rna.965408
74. Bandyopadhyay S, Bhattacharyya M. PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics 2010; 11:190; PMID:20398296; http://dx.doi.org/10.1186/1471-2105-11-190
75. Friard O, Re A, Taverna D, De Bortoli M, Corá D. CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics 2010; 11:435; PMID:20731828; http://dx.doi.org/10.1186/1471-2105-11-435
76. Chiromatzo AO, Oliveira TY, Pereira G, Costa AY, Montesco CA, Gras DE, et al. miRNApath: a database of miRNAs, target genes and metabolic pathways. Genet Mol Res 2007; 6:859-65; PMID:18058708
77. Schmeier S, Schaefer U, MacPherson CR, Bajic VB. dPORE-miRNA: polymorphic regulation of microRNA genes. PLoS One 2011; 6:e16657; PMID:21326606; http://dx.doi.org/10.1371/journal.pone.0016657
78. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011; 39(Database issue): D163-9; PMID:21071411; http://dx.doi.org/10. 1093/nar/gkq1107
79. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10; PMID:2231712
80. Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res 2006; 16:885-9; PMID:16751343; http://dx.doi.org/10.1101/gr.5226606