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Impact of Noncoding Part of the Genome on the Proteome Plasticity of the Eukaryotic Cell

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Abstract

Recent studies revealed that about 80% of the eukaryotic genome is biochemically active; it produces not solely mRNA but also a large number of noncoding RNAs (ncRNAs). Thus, a large fraction of “ribonome” (the total cellular complement of RNAs and their regulatory factors) of the cell consists of a variety of noncoding RNAs (ncRNAs), while mRNAs occupy only a small part of it. It is well known that long noncoding RNAs (lncRNAs) are involved in the regulation of protein-coding gene expression by altering the chromatin structure, transcription regulation, and pre-mRNA splicing. MicroRNAs and small interfering RNAs trigger the RNA interference mechanism involved in the transcriptional and post-transcriptional regulation of gene expression. However, our knowledge of the role of noncoding part of the genome in proteome diversification and plasticity is scarce. In this mini-review, we discuss new data obtained over the past few years, which change our view of the role of noncoding part of the genome in the cell proteome formation.

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References

  1. Consortium Encode Project, Nature, 2012, vol. 489, pp. 57–74.

    Article  CAS  Google Scholar 

  2. Jacquier, A., Nat. Rev. Genet., 2009, vol. 10, pp. 833–844.

    Article  PubMed  CAS  Google Scholar 

  3. Geisler, S. and Coller, J., Nat. Rev. Mol. Cell. Biol., 2013, vol. 14, pp. 699–712.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., Bruhn, L., Yang, X., Amit, I., Meissner, A., Regev, A., Rinn, J.L., Root, D.E., and Lander, E.S., Nature, 2011, vol. 477, pp. 295–300.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Quinn, J.J. and Chang, H.Y., Nat. Rev. Genet., 2016, vol. 17, pp. 47–62.

    Article  PubMed  CAS  Google Scholar 

  6. Kapusta, A., Kronenberg, Z., Lynch, V.J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., and Feschotte, C., PLoS Genet., 2013, vol. 9. e1003470.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Kelley, D. and Rinn, J., Genome Biol., 2012, vol. 13, p. R107.

    Google Scholar 

  8. Lin, L., Jiang, P., Park, J.W., Wang, J., Lu, Z.X., Lam, M.P., Ping, P., and Xing, Y., Genome Biol., 2016, vol. 17, p. 15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Lorenc, A. and Makalowski, W., Genetics, 2003, vol. 118, pp. 183–191.

    CAS  Google Scholar 

  10. Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Brown, J.B., Lipovich, L., Gonzalez, J.M., Thomas, M., Davis, C.A., Shiekhattar, R., Gingeras, T.R., Hubbard, T.J., Notredame, C., Harrow, J., and Guigo, R., Genome Res., 2012, vol. 22, pp. 1775–1789.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Werner, A., RNA Biol., 2005, vol. 2, pp. 53–62.

    Article  PubMed  CAS  Google Scholar 

  12. Pelechano, V. and Steinmetz, L.M., Nat. Rev. Genet., 2013, vol. 14, pp. 880–893.

    Article  PubMed  CAS  Google Scholar 

  13. Good, L., Cell. Mol. Life Sci., 2003, vol. 60, pp. 854–861.

    Article  PubMed  CAS  Google Scholar 

  14. Darfeuille, F., Unoson, C., Vogel, J., and Wagner, E.G., Mol. Cell, 2007, vol. 26, pp. 381–392.

    Article  PubMed  CAS  Google Scholar 

  15. Carrieri, C., Cimatti, L., Biagioli, M., Beugnet, A., Zucchelli, S., Fedele, S., Pesce, E., Ferrer, I., Collavin, L., Santoro, C., Forrest, A.R., Carninci, P., Biffo, S., Stupka, E., and Gustincich, S., Nature, 2012, vol. 491, pp. 454–457.

    Article  PubMed  CAS  Google Scholar 

  16. Zucchelli, S., Cotella, D., Takahashi, H., Carrieri, C., Cimatti, L., Fasolo, F., Jones, M.H., Sblattero, D., Sanges, R., Santoro, C., Persichetti, F., Carninci, P., and Gustincich, S., RNA Biol., 2015, vol. 12, pp. 771–779.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Patrucco, L., Chiesa, A., Soluri, M.F., Fasolo, F., Takahashi, H., Carninci, P., Zucchelli, S., Santoro, C., Gustincich, S., Sblattero, D., and Cotella, D., Gene, 2015, vol. 569, pp. 287–293.

    Article  PubMed  CAS  Google Scholar 

  18. Lunyak, V.V., Prefontaine, G.G., Nunez, E., Cramer, T., Ju, B.G., Ohgi, K.A., Hutt, K., Roy, R., Garcia-Diaz, A., Zhu, X., Yung, Y., Montoliu, L., Glass, C.K., and Rosenfeld, M.G., Science, 2007, vol. 317, pp. 248–251.

    Article  PubMed  CAS  Google Scholar 

  19. Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F., Nat. Struct. Mol. Biol., 2004, vol. 11, pp. 816–821.

    Article  PubMed  CAS  Google Scholar 

  20. Blackwell, B.J., Lopez, M.F., Wang, J., Krastins, B., Sarracino, D., Tollervey, J.R., Dobke, M., Jordan, I.K., and Lunyak, V.V., Mobile Genet. Elem., 2012, vol. 2, pp. 26–35.

    Article  Google Scholar 

  21. Goodier, J.L., Cheung, L.E., and Kazazian, H.H., Jr., Nucleic Acids Res., 2013, vol. 41, pp. 7401–7419.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Yao, Y., Jin, S., Long, H., Yu, Y., Zhang, Z., Cheng, G., Xu, C., Ding, Y., Guan, Q., Li, N., Fu, S., Chen, X.J., Yan, Y.B., Zhang, H., Tong, P., Tan, Y., Yu, Y., Fu, S., Li, J., He, G.J., and Wu, Q., Nucleic Acids Res., 2015, vol. 43. e58.

  23. Jabnoune, M., Secco, D., Lecampion, C., Robaglia, C., Shu, Q., and Poirier, Y., Plant Cell, 2013, vol. 25, pp. 4166–4182.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Zywicki, M., Bakowska-Zywicka, K., and Polacek, N., Nucleic Acids Res., 2012, vol. 40, pp. 4013–4024.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Gebetsberger, J., Zywicki, M., Kunzi, A., and Polacek, N., Archaea, 2012, vol. 2012, p. 260909.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Pircher, A., Bakowska-Zywicka, K., Schneider, L., Zywicki, M., and Polacek, N., Mol. Cell, 2014, vol. 54, pp. 147–155.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Sobala, A. and Hutvagner, G., RNA Biol., 2013, vol. 10, pp. 553–563.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. van Heesch, S., van Iterson, M., Jacobi, J., Boymans, S., Essers, P.B., de Bruijn, E., Hao, W., Macinnes, A.W., Cuppen, E., and Simonis, M., Genome Biol., 2014, vol. 15, p. R6.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., et al., atInternational Human Genome Sequencing Consortium, Nature, 2001, vol. 409, pp. 860–921.

    PubMed  CAS  Google Scholar 

  30. Meyers, B.C., Tingey, S.V., and Morgante, M., Genome Res., 2001, vol. 11, pp. 1660–1676.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Jangam, D., Feschotte, C., and Betran, E., Trends Genet., 2017, vol. 33, pp. 817–831.

    Article  PubMed  CAS  Google Scholar 

  32. Nekrutenko, A. and Li, W.H., Trends Genet., 2001, vol. 17, pp. 619–621.

    Article  PubMed  CAS  Google Scholar 

  33. Gotea, V. and Makalowski, W., Trends Genet., 2006, vol. 22, pp. 260–267.

    Article  PubMed  CAS  Google Scholar 

  34. Ingolia, N.T., Lareau, L.F., and Weissman, J.S., Cell, 2011, vol. 147, pp. 789–802.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Guttman, M., Russell, P., Ingolia, N.T., Weissman, J.S., and Lander, E.S., Cell, 2013, vol. 154, pp. 240–251.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Bazzini, A.A., Johnstone, T.G., Christiano, R., Mackowiak, S.D., Obermayer, B., Fleming, E.S., Vejnar, C.E., Lee, M.T., Rajewsky, N., Walther, T.C., and Giraldez, A.J., EMBO J., 2014, vol. 33, pp. 981–993.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Housman, G. and Ulitsky, I., Biochim. Biophys. Acta, 2016, vol. 1859, pp. 31–40.

    Article  PubMed  CAS  Google Scholar 

  38. Magny, E.G., Pueyo, J.I., Pearl, F.M., Cespedes, M.A., Niven, J.E., Bishop, S.A., and Couso, J.P., Science, 2013, vol. 341, pp. 1116–1120.

    Article  PubMed  CAS  Google Scholar 

  39. Nelson, B.R., Makarewich, C.A., Anderson, D.M., Winders, B.R., Troupes, C.D., Wu, F., Reese, A.L., McAnally, J.R., Chen, X., Kavalali, E.T., Cannon, S.C., Houser, S.R., Bassel-Duby, R., and Olson, E.N., Science, 2016, vol. 351, pp. 271–275.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. D’Lima, N.G., Ma, J., Winkler, L., Chu, Q., Loh, K.H., Corpuz, E.O., Budnik, B.A., Lykke-Andersen, J., Saghatelian, A., and Slavoff, S.A., Nat. Chem. Biol., 2017, vol. 13, pp. 174–180.

    Article  PubMed  CAS  Google Scholar 

  41. Huang, J.Z., Chen, M., Chen GaoX.C., Zhu, S., Huang, H., Hu, M., Zhu, H., and Yan, G.R., Mol. Cell, 2017, vol. 68, pp. 171–184.

    Article  PubMed  CAS  Google Scholar 

  42. Matsumoto, A., Pasut, A., Matsumoto, M., Yamashita, R., Fung, J., Monteleone, E., Saghatelian, A., Nakayama, K.I., Clohessy, J.G., and Pandolfi, P.P., Nature, 2017, vol. 541, pp. 228–232.

    Article  PubMed  CAS  Google Scholar 

  43. Kondo, T., Hashimoto, Y., Kato, K., Inagaki, S., Hayashi, S., and Kageyama, Y., Nat. Cell Biol., 2007, vol. 9, pp. 660–665.

    Article  PubMed  CAS  Google Scholar 

  44. Andrews, S.J. and Rothnagel, J.A., Nat. Rev. Genet., 2014, vol. 15, pp. 193–204.

    Article  PubMed  CAS  Google Scholar 

  45. Tavormina, P., De Coninck, B., Nikonorova, N., De Smet, I., and Cammue, B.P., Plant Cell, 2015, vol. 27, pp. 2095–2118.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Couso, J.P. and Patraquim, P., Nat. Rev. Mol. Cell. Biol., 2017, vol. 18, pp. 575–589.

    Article  PubMed  CAS  Google Scholar 

  47. Slavoff, S.A., Mitchell, A.J., Schwaid, A.G., Cabili, M.N., Ma, J., Levin, J.Z., Karger, A.D., Budnik, B.A., Rinn, J.L., and Saghatelian, A., Nat. Chem. Biol., 2013, vol. 9, p. 59.

    Article  PubMed  CAS  Google Scholar 

  48. Ma, J., Diedrich, J.K., Jungreis, I., Donaldson, C., Vaughan, J., Kellis, M., Yates, J.R., and Saghatelian, A., 3rd, Anal. Chem., 2016, vol. 88, pp. 3967–3975.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Prabakaran, S., Hemberg, M., Chauhan, R., Winter, D., Tweedie-Cullen, R.Y., Dittrich, C., Hong, E., Gunawardena, J., Steen, H., Kreiman, G., and Steen, J.A., Nat. Commun., 2014, vol. 5, p. 5429.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Mackowiak, S.D., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M., and Obermayer, B., Genome Biol., 2015, vol. 16, p. 179.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Aspden, J.L., Eyre-Walker, Y.C., Phillips, R.J., Amin, U., Mumtaz, M.A., Brocard, M., and Couso, J.P., Elife, 2014, vol. 3. e03528.

    Google Scholar 

  52. Verheggen, K., Volders, P.J., Mestdagh, P., Menschaert, G., Van Damme, P., Gevaert, K., Martens, L., and Vandesompele, J., J. Proteome Res., 2017, vol. 16, pp. 2508–2515.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 119779, Russia

    I. A. Fesenko, I. V. Kirov & A. A. Filippova

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  1. I. A. Fesenko
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  2. I. V. Kirov
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  3. A. A. Filippova
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Correspondence to I. A. Fesenko.

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Original Russian Text © I.A. Fesenko, I.V. Kirov, A.A. Filippova, 2018, published in Bioorganicheskaya Khimiya, 2018, Vol. 44, No. 4, pp. 394–400.

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Fesenko, I.A., Kirov, I.V. & Filippova, A.A. Impact of Noncoding Part of the Genome on the Proteome Plasticity of the Eukaryotic Cell. Russ J Bioorg Chem 44, 397–402 (2018). https://doi.org/10.1134/S1068162018040076

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