Skip to main content

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε

  • Conference paper

Part of the Lecture Notes in Computer Science book series (LNBI,volume 6268)

Abstract

MALAT1 is one of the best-conserved long ncRNAs in mammals and shares several characteristics, among them nuclear retention and a non-standard processing of its 3’ end, with the longer, but less well conserved, adjacent MENβ RNA. We show that MALAT1 is conserved among gnathostomes (with the possible exception of birds), while MENβ likely originated in the mammalian stem lineage. Evolutionary conserved features of both transcripts are discussed, including RNA secondary structure motifs and short RNA processing products.

Keywords

  • MALAT1
  • MENβ
  • VINC
  • NEAT1
  • TncRNA

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-642-15060-9_1
  • Chapter length: 12 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   69.99
Price excludes VAT (USA)
  • ISBN: 978-3-642-15060-9
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   89.99
Price excludes VAT (USA)

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. The ENCODE Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)

    Google Scholar 

  2. Maeda, N., Kasukawa, T., Oyama, R., Gough, J., Frith, M., Engström, P.G., Lenhard, B., Aturaliya, R.N., Batalov, S., Beisel, K.W., Bult, C.J., Fletcher, C.F., Forrest, A.R., Furuno, M., Hill, D., Itoh, M., Kanamori-Katayama, M., Katayama, S., Katoh, M., Kawashima, T., Quackenbush, J., Ravasi, T., Ring, B.Z., Shibata, K., Sugiura, K., Takenaka, Y., Teasdale, R.D., Wells, C.A., Zhu, Y., Kai, C., Kawai, J., Hume, D.A., Carninci, P., Hayashizaki, Y.: Transcript annotation in FANTOM3: Mouse Gene Catalog based on physical cDNAs. PLoS Genetics 2, e62 (2006)

    CrossRef  Google Scholar 

  3. Ponjavic, J., Ponting, C.P., Lunter, G.: Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 17, 556–565 (2007)

    CrossRef  Google Scholar 

  4. Marques, A.C., Ponting, C.P.: Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol. 10, R124 (2009)

    CrossRef  Google Scholar 

  5. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P., Cabili, M.N., Jaenisch, R., Mikkelsen, T.S., Jacks, T., Hacohen, N., Bernstein, B.E., Kellis, M., Regev, A., Rinn, J.L., Lander, E.S.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009)

    CrossRef  Google Scholar 

  6. Pang, K.C., Frith, M.C., Mattick, J.S.: Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genetics 22, 1–5 (2006)

    CrossRef  Google Scholar 

  7. 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., Bateman, A.: Rfam: updates to the RNA families database. Nucleic Acids Res. 37, D136–D140 (2009)

    CrossRef  Google Scholar 

  8. Griffiths-Jones, S., Saini, H.K., van Dongen, S., Enright, A.J.: miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, 154–158 (2008)

    CrossRef  Google Scholar 

  9. Lestrade, L., Weber, M.J.: snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 34, D158–D162 (2006)

    CrossRef  Google Scholar 

  10. Smits, G., Mungall, A.J., Griffiths-Jones, S., Smith, P., Beury, D., Matthews, L., Rogers, J., Pask, A.J., Shaw, G., VandeBerg, J.L., McCarrey, J.R., SAVOIR Consortium,, Renfree, M.B., Reik, W., Dunham, I.: Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat. Genet. 40, 971–976 (2008)

    CrossRef  Google Scholar 

  11. Park, S.W., Kang, Y.I., Sypula, J.G., Choi, J., Oh, H., Park, Y.: An evolutionarily conserved domain of roX2 RNA is sufficient for induction of H4-Lys16 acetylation on the Drosophila X chromosome. Genetics 177, 1429–1437 (2007)

    CrossRef  Google Scholar 

  12. Duret, L., Chureau, C., Samain, S., Weissenbach, J., Avner, P.: The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312, 1653–1655 (2006)

    CrossRef  Google Scholar 

  13. Elisaphenko, E.A., Kolesnikov, N.N., Shevchenko, A.I., Rogozin, I.B., Nesterova, T.B., Brockdorff, N., Zakian, S.M.: A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS One 3, e2521 (2008)

    CrossRef  Google Scholar 

  14. Maenner, S., Blaud, M., Fouillen, L., Savoye, A., Marchand, V., Dubois, A., Sanglier-Cianférani, S., Van Dorsselaer, A., Clerc, P., Avner, P., Visvikis, A., Branlant, C.: 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol. 8, e1000276 (2010)

    CrossRef  Google Scholar 

  15. Hutchinson, J., Ensminger, A.W., Clemson, C.M., Lynch, C.R., Lawrence, J.B., Chess, A.: A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8, 39 (2007)

    CrossRef  Google Scholar 

  16. Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, P.P., Mattick, J.S., Spector, D.L.: MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 19, 347–359 (2009)

    CrossRef  Google Scholar 

  17. Wilusz, J.E., Freier, S.M., Spector, D.L.: 3’ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135, 919–932 (2008)

    CrossRef  Google Scholar 

  18. Marz, M., Stadler, P.F.: Homology search for small structured ncRNAs. In: Hartmann, R., Bindereif, A., Schön, A., Westhof, E. (eds.) Handbook of RNA Biochemistry, 2nd edn., Wiley VCH, Weinheim (2010)

    Google Scholar 

  19. Ji, P., Diederichs, S., Wang, W., Böing, S., Metzger, R., Schneider, P.M., Tidow, N., Brandt, B., Buerger, H., Bulk, E., Thomas, M., Berdel, W.E., Serve, H., Müller-Tidow, C.: MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 8031–8041 (2003)

    CrossRef  Google Scholar 

  20. Lin, R., Maeda, S., Liu, C., Karin, M., Edgington, T.S.: A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26, 851–858 (2007)

    CrossRef  Google Scholar 

  21. Guffanti, A., Iacono, M., Pelucchi, P., Kim, N., Soldà, G., Croft, L.J., Taft, R.J., Rizzi, E., Askarian-Amiri, M., Bonnal, R.J., Callari, M., Mignone, F., Pesole, G., Bertalot, G., Rossi Bernardi, L., Albertini, A., Lee, C., Mattick, J.S., Zucchi, I., De Bellis, G.: A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 10, 163 (2009)

    CrossRef  Google Scholar 

  22. Guo, F., Li, Y., Liu, Y., Wang, J., Li, Y., Li, G.: Inhibition of metastasis-associated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion. Acta. Biochim. Biophys. Sin. (Shanghai) 42, 224–229 (2010)

    CrossRef  Google Scholar 

  23. Saha, S., Rangarajan, P.N.: Common host genes are activated in mouse brain by Japanese encephalitis and rabies viruses. J. Gen. Virol. 84, 1729–1735 (2003)

    CrossRef  Google Scholar 

  24. Saha, S., Murthy, S., Rangarajan, P.N.: Identification and characterization of a virus-inducible non-coding RNA in mouse brain. J. Gen. Virol. 87, 1991–1995 (2006)

    CrossRef  Google Scholar 

  25. Sasaki, Y.T.F., Ideue, T., Sano, M., Mituyama, T., Hirose, T.: MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl. Acad. Sci. USA 106, 2525–2530 (2009)

    CrossRef  Google Scholar 

  26. Peyman, J.A.: Mammalian expression cloning of two human trophoblast suppressors of major histocompatibility complex genes. Am. J. Reprod. Immunol. 45, 382–392 (2001)

    CrossRef  Google Scholar 

  27. Geirsson, A., Paliwal, I., Lynch, R.J., Bothwell, A.L., Hammond, G.L.: Class II transactivator promoter activity is suppressed through regulation by a trophoblast noncoding RNA. Transplantation 76, 387–394 (2003)

    CrossRef  Google Scholar 

  28. Geirsson, A., Lynch, R.J., Paliwal, I., Bothwell, A.L., Hammond, G.L.: Altered nuclear retention of Human trophoblast noncoding RNA suppresses CIITA promoter III activity in murine B-lymphocytes. Biochem. Biophys. Res. Commun. 301, 718–724 (2003)

    CrossRef  Google Scholar 

  29. Lehnert, S.A., Reverter, A., Byrne, K.A., Wang, Y., Nattrass, G.S., Hudson, N.J., Greenwood, P.L.: Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC Dev. Biol. 7, 95 (2007)

    CrossRef  Google Scholar 

  30. Chen, L., Carmichael, G.: RNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA. Mol. Cell 35, 467–478 (2009)

    CrossRef  Google Scholar 

  31. Clemson, C.M., Hutchinson, J.N., Sara, S.A., Ensminger, A.W., Fox, A.H., Chess, A., Lawrence, J.B.: An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33, 717–726 (2009)

    CrossRef  Google Scholar 

  32. Bond, C.S., Fox, A.H.: Paraspeckles: nuclear bodies built on long noncoding RNA. J. Cell Biol. 186, 637–644 (2009)

    CrossRef  Google Scholar 

  33. Murthy, S.U.M., Rangarajan, P.N.: Identification of protein interaction regions of VINC/NEAT1/Men epsilon RNA. FEBS Lett. 584, 1531–1535 (2010)

    CrossRef  Google Scholar 

  34. Scadden, D.: A NEAT way of regulating nuclear export of mRNAs. Mol. Cell 35, 395–396 (2009)

    CrossRef  Google Scholar 

  35. Douaud, M., Fève, K., Gerus, M., Fillon, V., Bardes, S., Gourichon, D., Dawson, D.A., Hanotte, O., Burke, T., Vignoles, F., Morisson, M., Tixier-Boichard, M., Vignal, A., Pitel, F.: Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics 9, 129 (2008)

    CrossRef  Google Scholar 

  36. Thompson, J.D., Higgs, D.G., Gibson, T.J.: CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucl. Acids Res. 22, 4673–4680 (1994)

    CrossRef  Google Scholar 

  37. Koshimizu, T.A., Fujiwara, Y., Sakai, N., Shibata, K., Tsuchiya, H.: Oxytocin stimulates expression of a noncoding RNA tumor marker in a human neuroblastoma cell line. Life Sci. 86, 455–460 (2010)

    CrossRef  Google Scholar 

  38. Washietl, S., Hofacker, I.L., Stadler, P.F.: Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102, 2454–2459 (2005)

    CrossRef  Google Scholar 

  39. Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W., Haussler, D.: Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33 (2006)

    CrossRef  Google Scholar 

  40. Moazed, D.: Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009)

    CrossRef  Google Scholar 

  41. Tanzer, A., Riester, M., Hertel, J., Bermudez-Santana, C.I., Gorodkin, J., Hofacker, I.L., Stadler, P.F.: Evolutionary genomics of microRNAs and their relatives. In: Caetano-Anolles, G. (ed.) Evolutionary genomics and System Biology, pp. 295–327. Wiley-Blackwell, Hoboken (2010)

    Google Scholar 

  42. Kapranov, P., Cheng, J., Dike, S., Nix, D., Duttagupta, R., Willingham, A.T., Stadler, P.F., Hertel, J., Hackermüller, J., Hofacker, I.L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Madhavan, G., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T.R.: RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007)

    CrossRef  Google Scholar 

  43. Taft, R.J., Kaplan, C.D., Simons, C., Mattick, J.S.: Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8, 2332–2338 (2009)

    Google Scholar 

  44. Shi, W., Hendrix, D., Levine, M., Haley, B.: A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat. Struct. Mol. Biol. 16, 183–189 (2009)

    CrossRef  Google Scholar 

  45. Langenberger, D., Bermudez-Santana, C., Hertel, J., Hoffmann, S., Khaitovich, S., Stadler, P.F.: Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 25, 2298–2301 (2009)

    CrossRef  Google Scholar 

  46. Jöchl, C., Rederstorff, M., Hertel, J., Stadler, P.F., Hofacker, I.L., Schrettl, M., Haas, H., Hüttenhofer, A.: Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis. Nucleic Acids Res. 36, 2677–2689 (2008)

    CrossRef  Google Scholar 

  47. Kawaji, H., Hayashizaki, Y.: Exploration of small RNAs. PLoS Genet. 4, e22 (2008)

    CrossRef  Google Scholar 

  48. Cole, C., Sobala, A., Lu, C., Thatcher, S.R., Bowman, A., Brown, J.W., Green, P.J., Barton, G.J., Hutvagner, G.: Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15, 2147–2160 (2009)

    CrossRef  Google Scholar 

  49. Lee, Y.S., Shibata, Y., Malhotra, A., Dutta, A.: A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 23, 2639–2649 (2009)

    CrossRef  Google Scholar 

  50. Ender, C., Krek, A., Friedländer, M.R., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N., Meister, G.: A human snoRNA with microRNA-like functions. Mol. Cell 32, 519–528 (2008)

    CrossRef  Google Scholar 

  51. Stadler, P.F., Chen, J.J.L., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., Kretzschmar, A.K., Mosig, A., Prohaska, S.J., Qi, X., Schutt, K., Ullmann, K.: Evolution of vault RNAs. Mol. Biol. Evol. 26, 1975–1991 (2009)

    CrossRef  Google Scholar 

  52. Persson, H., Kvist, A., Vallon-Christersson, J., Medstrand, P., Borg, A., Rovira, C.: The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat. Cell Biol. 11, 1268–1271 (2009)

    CrossRef  Google Scholar 

  53. Langenberger, D., Bermudez-Santana, C., Stadler, P.F., Hoffmann, S.: Identification and classification of small RNAs in transcriptome sequence data. In: Pac. Symp. Biocomput., vol. 15, pp. 80–87 (2010)

    Google Scholar 

  54. Hoffmann, S., Otto, C., Kurtz, S., Sharma, C., Khaitovich, P., Stadler, P.F., Hackermüller, J.: Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comp. Biol. 5, e1000502 (2009)

    CrossRef  Google Scholar 

  55. Babiarz, J.E., Ruby, J.G., Wang, Y., Bartel, D.P., Blelloch, R.: Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 22, 2773–2785 (2008)

    CrossRef  Google Scholar 

  56. Volff, J.-N., Brosius, J.: Modern genomes with retro-look: Retrotransposed elements, retroposition and the origin of new genes. Genome Dyn. 3, 175–190 (2007)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Stadler, P.F. (2010). Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε . In: Ferreira, C.E., Miyano, S., Stadler, P.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2010. Lecture Notes in Computer Science(), vol 6268. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15060-9_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-15060-9_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15059-3

  • Online ISBN: 978-3-642-15060-9

  • eBook Packages: Computer ScienceComputer Science (R0)