Computational approaches to discovering noncoding RNA

Wiley Interdisciplinary Reviews: RNA

Volumn 3, Issue 4, 2012, Pages 567-579

  Krzyzanowski, Paul M ^a   Muro, Enrique M ^b   Andrade Navarro, Miguel A ^b  

^a PRINCESS MARGARET HOSPITAL   (Canada)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY RNA; MICRORNA; MICRORNA 122; RIBOSOME RNA; TRANSFER RNA; UNTRANSLATED RNA; VIRUS RNA;

COMPUTER PROGRAM; DOWN REGULATION; ENDOMETRIOSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; STRUCTURE ANALYSIS; UPREGULATION;

ANIMALS; BACTERIA; COMPUTATIONAL BIOLOGY; HUMANS; MOLECULAR BIOLOGY; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; VIRUSES;

EID: 84867588334     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1121     Document Type: Review

References (104)

1. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544-548.
2. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
3. Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinform 2001, 2:8.
4. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25:1335-1337.
5. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
6. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100-3108.
7. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004, 32:11-16.
8. Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D. The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res 2004, 32:W160-W165.
9. Pantano L, Estivill X, Marti E. SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res 2010, 38:e34.
10. Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C. BlastR-fast and accurate database searches for non-coding RNAs. Nucleic Acids Res 2011, 39:6886-6895.
11. Lagana A, Forte S, Russo F, Giugno R, Pulvirenti A, Ferro A. Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints. J RNAi Gene Silencing 2010, 6:379-385.
12. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes Dev 2003, 17:991-1008.
13. Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 2005, 102:2454-2459.
14. Gruber AR, Findeiss S, Washietl S, Hofacker IL, Stadler PF. Rnaz 2.0: improved noncoding RNA detection. Pac Symp Biocomput 2010, 15:69-79.
15. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006, 2:e33.
16. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500.
17. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
18. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 2006, 126:1203-1217.
19. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284.
20. Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 2011, 39:W155-W159.
21. Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 2010, 26:2226-2234.
22. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009, 37:W68-W76.
23. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26:407-415.
24. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh Chem 1994, 125:167-188.
25. Hofacker IL, Priwitzer B, Stadler PF. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 2004, 20:186-190.
26. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 1989, 244:48-52.
27. Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinform 2005, 6:267.
28. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005, 37:766-770.
29. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107.
30. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al. The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
31. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
32. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, 37:D755-D761.
33. Krzyzanowski PM, Price FD, Muro EM, Rudnicki MA, Andrade-Navarro MA. Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLoS One 2011, 6:e20561.
34. Ott CE, Grunhagen J, Jager M, Horbelt D, Schwill S, Kallenbach K, Guo G, Manke T, Knaus P, Mundlos S, et al. MicroRNAs differentially expressed in postnatal aortic development downregulate elastin via 3′ UTR and coding-sequence binding sites. PLoS One 2011, 6:e16250.
35. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005, 33:W701-W704.
36. Spiegelman WG, Reichardt LF, Yaniv M, Heinemann SF, Kaiser AD, Eisen H. Bidirectional transcription and the regulation of Phage lambda repressor synthesis. Proc Natl Acad Sci U S A 1972, 69:3156-3160.
37. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. In search of antisense. Trends Biochem Sci 2004, 29:88-94.
38. Lehner B, Williams G, Campbell RD, Sanderson CM. Antisense transcripts in the human genome. Trends Genet 2002, 18:63-65.
39. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 2003, 21:379-386.
40. Sorber K, Dimon MT, DeRisi JL. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res 2011, 39:3820-3835.
41. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453:539-543.
42. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453:534-538.
43. Muro EM, Andrade-Navarro MA. Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol 2010, 10:338.
44. Dimon MT, Sorber K, DeRisi JL. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One 2010, 5:e13875.
45. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515.
46. Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavare S. Explaining differences in saturation levels for Affymetrix GeneChip arrays. Nucleic Acids Res 2007, 35:4154-4163.
47. Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics 2004, 20:2685-2693.
48. Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Siederdissen CH, Bort JA, Wieser M, et al. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol 2011, 153:62-75.
49. Pantano L, Estivill X, Marti E. A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Bioinformatics 2011, 27:3202-3203.
50. Washietl S, Hofacker IL. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 2004, 342:19-30.
51. Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome-sequencing data. BMC Bioinform 2011, 12:267.
52. Palidwor GA, Andrade-Navarro MA. MLTrends: graphing MEDLINE term usage over time. J Biomed Discov Collab 2010, 5:1-6.
53. Kan T, Sato F, Ito T, Matsumura N, David S, Cheng Y, Agarwal R, Paun BC, Jin Z, Olaru AV, et al. The miR-106b-25 polycistron, activated by genomic amplification, functions as an oncogene by suppressing p21 and Bim. Gastroenterology 2009, 136:1689-1700.
54. Richardson K, Lai CQ, Parnell LD, Lee YC, Ordovas JM. A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS. BMC Genomics 2011, 12:504.
55. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. J Pathol 2010, 220:126-139.
56. Hawkins SM, Creighton CJ, Han DY, Zariff A, Anderson ML, Gunaratne PH, Matzuk MM. Functional microRNA involved in endometriosis. Mol Endocrinol 2011, 25:821-832.
57. Pellicano M, Bramante S, Guida M, Bifulco G, Di Spiezio Sardo A, Cirillo D, Nappi C. Ovarian endometrioma: postoperative adhesions following bipolar coagulation and suture. Fertil Steril 2008, 89:796-799.
58. Boutz DR, Collins PJ, Suresh U, Lu M, Ramirez CM, Fernandez-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, et al. Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. J Biol Chem 2011, 286:18066-18078.
59. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biol 2011, 12:R16.
60. Bajak EZ, Hagedorn CH. Efficient 5′ cap-dependent RNA purification : use in identifying and studying subsets of RNA. Methods Mol Biol 2008, 419:147-160.
61. Chen Z, Duan X. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol Biol 2011, 733:93-103.
62. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010, 7:709-715.
63. Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011, 29:436-442.
64. Babitzke P, Romeo T. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 2007, 10:156-163.
65. Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. RNA 2000, 6:668-679.
66. Breaker RR. Prospects for riboswitch discovery and analysis. Mol Cell 2011, 43:867-879.
67. Altuvia S. Identification of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol 2007, 10:257-261.
68. Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009, 12:536-546.
69. Huttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006, 34:635-646.
70. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001, 11:941-950.
71. Backofen R, Hess WR. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 2010, 7:33-42.
72. Lu X, Goodrich-Blair H, Tjaden B. Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 2011, 17:1635-1647.
73. Herbig A, Nieselt K. nocoRNAc: characterization of non-coding RNAs in prokaryotes. BMC Bioinform 2011, 12:40.
74. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, et al. RNAcentral: a vision for an international database of RNA sequences. RNA 2011, 17:1941-1946.
75. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011, 39:D38-D51.
76. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2011, 40:D918-D923.
77. Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res 2010, 38:D626-D632.
78. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, et al. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2011, 39:D141-D145.
79. Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K. The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res 2009, 37:D89-D92.
80. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157.
81. Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C. RNAspace.org: an integrated environment for the prediction, annotation, and analysis of ncRNA. RNA 2011, 17:1947-1956.
82. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36:D149-D153.
83. Pang KC, Stephen S, Dinger ME, Engstrom PG, Lenhard B, Mattick JS. RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 2007, 35:D178-D182.
84. Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 2006, 34:D158-D162.
85. He S, Liu C, Skogerbo G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 2008, 36:D170-D172.
86. Sai Lakshmi S, Agrawal S. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res 2008, 36:D173-D177.
87. Lagana A, Forte S, Giudice A, Arena MR, Puglisi PL, Giugno R, Pulvirenti A, Shasha D, Ferro A. miRo: a miRNA knowledge base. Database (Oxford) 2009, 2009:bap008.
88. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37:D155-D158.
89. 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:D202-D209.
90. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011, 39:D163-D169.
91. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158.
92. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Denise CS, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. Ensembl 2012. Nucleic Acids Res 2011, 40:D84-D90.
93. Gautheret D, Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 2001, 313:1003-1011.
94. Mattick JS. The double life of RNA. Biochimie 2011, 93:viii-ix.
95. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, et al. The reality of pervasive transcription. PLoS Biol 2011, 9:e1000625; discussion e1001102.
96. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008, 18:1433-1445.
97. He H, Wang J, Liu T, Liu XS, Li T, Wang Y, Qian Z, Zheng H, Zhu X, Wu T, et al. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 2007, 17:1471-1477.
98. Mercer TR, Wilhelm D, Dinger ME, Solda G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, et al. Expression of distinct RNAs from 3′ untranslated regions. Nucleic Acids Res 2011, 39:2393-2403.
99. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
100. Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147:789-802.
101. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26:941-946.
102. Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486.
103. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 2010, 40:939-953.
104. Ameur A, Zaghlool A, Halvardson J, Wetterbom A, Gyllensten U, Cavelier L, Feuk L. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol 2011, 18:1435-1440.