RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles

Nucleic Acids Research

Volumn 38, Issue 10, 2010, Pages

  Rederstorff, Mathieu ^a   Bernhart, Stephan H ^b   Tanzer, Andrea ^b   Zywicki, Marek ^a   Perfler, Katrin ^a   Lukasser, Melanie ^a   Hofacker, Ivo L ^b   Hüttenhofer, Alexander ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RIBONUCLEOPROTEIN; TRANSCRIPTOME; UNTRANSLATED RNA;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DENSITY GRADIENT CENTRIFUGATION; DNA LIBRARY; GENE MAPPING; GENE NUMBER; GENOME ANALYSIS; HELA CELL; HUMAN; HUMAN CELL; INTRON; MOUSE; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROTEOMICS; RNA ANALYSIS; RNA SEQUENCE; VALIDATION PROCESS; ANIMAL; BRAIN LEVEL; CHEMISTRY; CLASSIFICATION; EXON; GENE EXPRESSION PROFILING; GENE LIBRARY; ISOLATION AND PURIFICATION; METABOLISM; NUCLEOTIDE SEQUENCE;

EUKARYOTA;

ANIMALS; BASE SEQUENCE; BRAIN CHEMISTRY; CONSERVED SEQUENCE; EXONS; GENE EXPRESSION PROFILING; GENE LIBRARY; HELA CELLS; HUMANS; INTRONS; MICE; REPETITIVE SEQUENCES, NUCLEIC ACID; RIBONUCLEOPROTEINS; RNA, UNTRANSLATED;

EID: 77954117695     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq057     Document Type: Article

References (69)

1. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
2. Mattick, J.S. and Makunin, I.V. (2005) Small regulatory RNAs in mammals. Hum. Mol. Genet., 14(Spec No 1), R121-132.
3. Willingham, A.T. and Gingeras, T.R. (2006) TUF love for "junk" DNA. Cell, 125, 1215-1220.
4. Huttenhofer, A., Schattner, P. and Polacek, N. (2005) Non-coding RNAs: hope or hype? Trends Genet., 21, 289-297.
5. Brosius, J. (2005) Waste not, want not-transcript excess in multicellular eukaryotes. Trends Genet., 21, 287-288.
6. Eddy, S.R. (2001) Non-coding RNA genes and the modern RNA world. Nature Rev., 2, 919-929.
7. Huttenhofer, A. and Schattner, P. (2006) The principles of guiding by RNA: chimeric RNA-protein enzymes. Nature Rev., 7, 475-482.
8. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
9. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
10. Bachellerie, J.P., Cavaille, J. and Huttenhofer, A. (2002) The expanding snoRNA world. Biochimie, 84, 775-790.
11. Huttenhofer, A., Brosius, J. and Bachellerie, J.P. (2002) RNomics: identification and function of small, non-messenger RNAs. Curr. Opin. Chem. Biol., 6, 835-843.
12. Huttenhofer, A., Cavaille, J. and Bachellerie, J.P. (2004) Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms. Methods Mol. Biol., 265, 409-428.
13. Huttenhofer, A. and Vogel, J. (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res., 34, 635-646.
14. Jochl, C., Rederstorff, M., Hertel, J., Stadler, P.F., Hofacker, I.L., Schrettl, M., Haas, H. and Huttenhofer, A. (2008) Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res., 36, 2677-2689.
15. Lung, B., Zemann, A., Madej, M.J., Schuelke, M., Techritz, S., Ruf, S., Bock, R. and Huttenhofer, A. (2006) Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res., 34, 3842-3852.
16. Madej, M.J., Alfonzo, J.D. and Huttenhofer, A. (2007) Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae. Nucleic Acids Res., 35, 1544-1554.
17. Mrazek, J., Kreutmayer, S.B., Grasser, F.A., Polacek, N. and Huttenhofer, A. (2007) Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells. Nucleic Acids Res., 35, e73.
18. Ender, C., Krek, A., Friedlander, M.R., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N. and Meister, G. (2008) A human snoRNA with microRNA-like functions. Mol. Cell, 32, 519-528.
19. Sittka, A., Lucchini, S., Papenfort, K., Sharma, C.M., Rolle, K., Binnewies, T.T., Hinton, J.C. and Vogel, J. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genetics, 4, e1000163.
20. Dignam, J.D., Lebovitz, R.M. and Roeder, R.G. (1983) Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res., 11, 1475-1489.
21. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
22. Hoffmann, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., Stadler, P.F. and Hackermuller, J. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput. Biol., 5, e1000502.
23. Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
24. Juhling, F., Morl, M., Hartmann, R.K., Sprinzl, M., Stadler, P.F. and Putz, J. (2009) tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res., 37, D159-D162.
25. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pheasant, M. et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
26. Mituyama, T., Yamada, K., Hattori, E., Okida, H., Ono, Y., Terai, G., Yoshizawa, A., Komori, T. and Asai, K. (2009) The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res., 37, D89-D92.
27. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol Biol., 215, 403-410.
28. Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
29. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
30. Washietl, S., Hofacker, I.L. and Stadler, P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454-2459.
31. Hertel, J., Hofacker, I.L. and Stadler, P.F. (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics, 24, 158-164.
32. Reichow, S.L., Hamma, T., Ferre-D'Amare, A.R. and Varani, G. (2007) The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res., 35, 1452-1464.
33. Ryckelynck, M., Giege, R. and Frugier, M. (2005) tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations. Biochimie, 87, 835-845.
34. Huttenhofer, A., Kiefmann, M., Meier-Ewert, S., O'Brien, J., Lehrach, H., Bachellerie, J.P. and Brosius, J. (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J., 20, 2943-2953.
35. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
36. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nature Biotechnol., 26, 407-415.
37. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
38. Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M.J., Kuramochi-Miyagawa, S., Nakano, T. et al. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442, 203-207.
39. Verma, I.M. and Baltimore, D. (1974) Purification of the RNA-directed DNA polymerase from avian myeloblastosis virus and its assay with polynucleotide templates. Methods Enzymol., 29, 125-130.
40. Wittig, B. and Wittig, S. (1978) Reverse transcription of tRNA. Nucleic Acids Res., 5, 1165-1178.
41. Fu, H., Feng, J., Liu, Q., Sun, F., Tie, Y., Zhu, J., Xing, R., Sun, Z. and Zheng, X. (2009) Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett., 583, 437-442.
42. Thompson, D.M., Lu, C., Green, P.J. and Parker, R. (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA, 14, 2095-2103.
43. Yamasaki, S., Ivanov, P., Hu, G.F. and Anderson, P. (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J. Cell Biol., 185, 35-42.
44. Cavaille, J., Buiting, K., Kiefmann, M., Lalande, M., Brannan, C.I., Horsthemke, B., Bachellerie, J.P., Brosius, J. and Huttenhofer, A. (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl Acad. Sci. USA, 97, 14311-14316.
45. Li, Z., Liu, M., Zhang, L., Zhang, W., Gao, G., Zhu, Z., Wei, L., Fan, Q. and Long, M. (2009) Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. Nucleic Acids Res., 37, 4308-4314.
46. Amaral, P.P., Dinger, M.E., Mercer, T.R. and Mattick, J.S. (2008) The eukaryotic genome as an RNA machine. Science, 319, 1787-1789.
47. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
48. Mattick, J.S. (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays, 25, 930-939.
49. Yan, M.D., Hong, C.C., Lai, G.M., Cheng, A.L., Lin, Y.W. and Chuang, S.E. (2005) Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum. Mol. Genet., 14, 1465-1474.
50. Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L. and Thanaraj, T.A. (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res., 34, D46-D55.
51. Cullen, B.R. (2009) Viral RNAs: lessons from the enemy. Cell, 136, 592-597.
52. Umbach, J.L., Kramer, M.F., Jurak, I., Karnowski, H.W., Coen, D.M. and Cullen, B.R. (2008) MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature, 454, 780-783.
53. Sleutels, F., Zwart, R. and Barlow, D.P. (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature, 415, 810-813.
54. Faghihi, M.A., Modarresi, F., Khalil, A.M., Wood, D.E., Sahagan, B.G., Morgan, T.E., Finch, C.E., St Laurent, G., Kenny, P.J. 3rd and Wahlestedt, C. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nature Med., 14, 723-730.
55. Scheele, C., Petrovic, N., Faghihi, M.A., Lassmann, T., Fredriksson, K., Rooyackers, O., Wahlestedt, C., Good, L. and Timmons, J.A. (2007) The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genomics, 8, 74.
56. Camblong, J., Beyrouthy, N., Guffanti, E., Schlaepfer, G., Steinmetz, L.M. and Stutz, F. (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev., 23, 1534-1545.
57. Wagner, E.G., Altuvia, S. and Romby, P. (2002) Antisense RNAs in bacteria and their genetic elements. Adv. Genet., 46, 361-398.
58. Kim, J., Martignetti, J.A., Shen, M.R., Brosius, J. and Deininger, P. (1994) Rodent BC1 RNA gene as a master gene for ID element amplification. Proc. Natl Acad. Sci. USA, 91, 3607-3611.
59. Quentin, Y. (1992) Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res., 20, 3397-3401.
60. Smalheiser, N.R. and Torvik, V.I. (2005) Mammalian microRNAs derived from genomic repeats. Trends Genet., 21, 322-326.
61. Margulies, E.H., Blanchette, M., Haussler, D. and Green, E.D. (2003) Identification and characterization of multi-species conserved sequences. Genome Res., 13, 2507-2518.
62. Muddashetty, R., Khanam, T., Kondrashov, A., Bundman, M., Iacoangeli, A., Kremerskothen, J., Duning, K., Barnekow, A., Huttenhofer, A., Tiedge, H. et al. (2002) Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol., 321, 433-445.
63. Kawaji, H. and Hayashizaki, Y. (2008) Exploration of small RNAs. PLoS Genetics, 4, e22.
64. Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. Nature Rev., 10, 155-159.
65. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
66. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
67. Kapranov, P., Willingham, A.T. and Gingeras, T.R. (2007) Genome-wide transcription and the implications for genomic organization. Nature Rev., 8, 413-423.
68. Ploner, A., Ploner, C., Lukasser, M., Niederegger, H. and Huttenhofer, A. (2009) Methodological obstacles in knocking down small noncoding RNAs. RNA, 15, 1797-1804.
69. Gruber, A.R., Lorenz, R., Bernhart, S.H., Neubock, R. and Hofacker, I.L. (2008) The Vienna RNA websuite. Nucleic Acids Res., 36, W70-W74.