Skip to main content

The RNA Gene Information: Retroelement-MicroRNA Entangling as the RNA Quantum Code

  • Protocol
  • First Online:
MicroRNA Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 936))

Abstract

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.

2011.11th.March.14:46. This paper is Requiem for our lost people in Tsunami Japan.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kimura M (1983) Neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  2. Ohno S (1972) So much “junk” DNA in our genome. Brookhaven Symp Biol 23:366–370

    PubMed  CAS  Google Scholar 

  3. Ohno S, Yomo T (1991) The grammatical rule for all DNA: junk and coding sequences. Electrophoresis 12:103–108

    Article  PubMed  CAS  Google Scholar 

  4. Gibson HL, May TW, Wilks AV (1981) Genetic variation at the alcohol dehydrogenase locus in Drosophila melanogaster in relation to environmental variation. Oecologica 51:191–198

    Article  Google Scholar 

  5. Miranda R (2010) The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise. BMC Biol 8:97

    Article  Google Scholar 

  6. Dawkins R (1976) The selfish gene. Oxford University Press, Oxford

    Google Scholar 

  7. Kosaka N, Izumi H, Sekine K, Ochiya T (2010) microRNA as a new immune-regulatory agent in breast milk. Silence 1:7

    Article  PubMed  Google Scholar 

  8. Go AT, van Vugt JM, Oudejans CB (2011) Non-invasive aneuploidy using free fetal DNA and RNA in maternal plasma: recent progress and future possibilities. Hum Reprod Update 17(3):372–382

    Article  PubMed  CAS  Google Scholar 

  9. Srikantan S, Marasa BS, Becker KG, Gorospe M, Abdelmohsen K (2011) Paradoxical microRNAs: individual gene repressors, global translation enhancers. Cell Cycle 10:751–759

    Article  PubMed  CAS  Google Scholar 

  10. Navarro A, Monzó M (2010) MicroRNAs in human embryonic and cancer stem cells. Yonsei Med J 51:622–632

    Article  PubMed  CAS  Google Scholar 

  11. Hanina SA, Mifsud W, Down TA, Hayashi K, O’Carroll D, Lao K, Miska EA, Surani MA (2010) Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells. PLoS Genet 6:e1001163

    Article  PubMed  Google Scholar 

  12. Parra P, Serra F, Palou A (2010) Expression of adipose microRNAs is sensitive to dietary conjugated linoleic acid treatment in mice. PLoS One 5:e13005

    Article  PubMed  Google Scholar 

  13. Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y (2010) Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ-stimulated HeLa cells. PLoS One 5:e11794

    Article  PubMed  Google Scholar 

  14. Potenza N, Papa U, Mosca N, Zerbini F, Nobile V, Russo A (2011) Human microRNA hsa-miR-125a-5p interferes with expression of hepatitis B virus surface antigen. Nucleic Acids Res 39(12):5157–5163

    Article  PubMed  CAS  Google Scholar 

  15. Hooten NN, Abdelmohsen K, Gorospe M, Ejiogu N, Zonderman AB, Evans MK (2010) microRNA expression patterns reveal differential expression of target genes with age. PLoS One 5:e10724

    Article  Google Scholar 

  16. Mariño G, Ugalde AP, Femández AF, Osorio FG, Fueyo A, Freije JM, López-Otin C (2010) Insulin-like growth factor 1 treatment extends longevity in a mouse model of human premature aging by restoring somatotroph axis function. Proc Natl Acad Sci USA 37:16268–16273

    Article  Google Scholar 

  17. Farazi T, Spitzer J, Morozov P, Tuschl T (2010) miRNAs in human cancer. J Pathol 223:102–115

    Article  PubMed  Google Scholar 

  18. Smits M, Nilsson J, Mir SE, van der Stoop PM, Hulleman E, Niers JM, de Witt Hamer PC, Marquez VE, Cloos J, Krichevsky AM, Noske DP, Tannous BA, Würdinger T (2010) miR-101 is down-regulated in glioblastoma resulting in EZH2-induced proliferation, migration, and angiogenesis. Oncotarget 7:710–720

    Google Scholar 

  19. Niu Y, Mo D, Qin L, Wang C, Li A, Zhao X, Wang X, Xiao S, Wang Q, Xie Y, He Z, Cong P, Chen Y (2011) Lipopolysaccharide-induced miR-1224 negatively regulates tumor necrosis factor-α gene expression by modulating Sp1. Immunology 133(1):8–20

    Article  PubMed  CAS  Google Scholar 

  20. Sotillo E, Laver T, Mellert H, Schelter JM, Cleary MA, McMahon S, Thomas-Tikhonenko A (2011) Myc overexpression brings out unexpected antiapoptotoc effects of miR-34a. Oncogene 30(22):2587–2594

    Article  PubMed  CAS  Google Scholar 

  21. Tang S, Bertke AS, Patel A, Margolis TP, Krause PR (2011) Herpes simplex virus-2 miR-H6 is a novel LAT-associated microRNA, but reduction of its expression does not influence viral latency establishment or recurrence phenotype. J Virol 85(9):4501–4509

    Article  PubMed  CAS  Google Scholar 

  22. Tang B, Xiao B, Liu Z, Li N, Zhu E-D, Li B-S, Xie Q-H, Zhuang Y, Zou Q-M, Mao X-H (2010) Identification of MyD88 as a novel target of miR-155, involved in negative regulation of Helicobacter pylori-induced inflammation. FEBS Lett 584:854–863

    Google Scholar 

  23. Sonkoly E, Pivarcsi A (2011) MicroRNAs in inflammation and response to injuries induced by environmental pollution. Mutat Res 717:46–53

    Article  PubMed  CAS  Google Scholar 

  24. Zhang X, Wan G, Berger FG, He X, Lu X (2011) The ATM kinase induces microRNA biogenesis in the DNA damage response. Mol Cell 41:371–383

    Article  PubMed  CAS  Google Scholar 

  25. Elyakim E, Sitbon E, Faeman A, Tabak S, Montia E, Belanis L, Dov A, Marcusson EG, Bennett CF, Chajut A, Cohen D, Yerushalmi N (2010) hsa-miR-191 is a candidate oncogene target for hepatocellular carcinoma therapy. Ther Targ Chem Biol 70:8077–8087

    CAS  Google Scholar 

  26. Izzotti A, Larghero P, Cartiglia C, Longobardi M, Pfeffer U, Steele VE, de Flora S (2010) Modulation of microRNA expression by budesonide, phenethyl iosthiocyanate, and cigarette smoking in mouse liver and lung. Carcinogenesis 31:894–901

    Article  PubMed  CAS  Google Scholar 

  27. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124–1128

    Article  PubMed  CAS  Google Scholar 

  28. Yuan A, Farber EL, Rapoport AL, Tejada D, Deniskin R, Akhmedov NB, Farber DB (2009) Transfer of microRNAs by embryonic stem cell microvesicles. PLoS One 4:e4722

    Article  PubMed  Google Scholar 

  29. Smalheiser NR, Torvik VI (2004) A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions. BMC Bioinformatics 5:139

    Article  PubMed  Google Scholar 

  30. Croce CM (2009) Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 10:704–714

    Article  PubMed  CAS  Google Scholar 

  31. Sonoki T, Asou N (2008) Insertion of miRNA 125b-1 into innunoglobulin heavy chain gene locus mediated by V(D)J recombination in precursor B cell acute lymphoblastic leukemia. In: Appasani K (ed) MicroRNAs. Cambridge University Press, Cambridge, pp 372–379

    Google Scholar 

  32. Lee H-C, Yang C-W, Chen C-Y, Au L-C (2011) Single point mutation of microRNA may cause butterfly effect on alteration of global gene expression. Biochem Biophys Res Commun 404:1065–1069

    Article  PubMed  CAS  Google Scholar 

  33. Ren J, Jin P, Wang E, Marinocola FM, Stroncek DF (2009) MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells. J Trans Med 7:20

    Article  Google Scholar 

  34. Costa FF (2010) Epigenomics in cancer management. Cancer Manage Res 2:255–265

    CAS  Google Scholar 

  35. Tana PR, Tana NR, Kühl M, Sirbu IO (2011) Identification of a novel epigenetic regulatory region within the pluripotency associated microRNA cluster, EEmiRC. Nucleic Acids Res 90:124–128

    Google Scholar 

  36. Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, Pasquinelli AE (2011) LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nat Struct Mol Biol 18:302–308

    Article  PubMed  Google Scholar 

  37. Kim YJ, Zheng B, Yu Y, Won SY, Mo B, Chen X (2011) The role of mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J 30:814–822

    Article  PubMed  CAS  Google Scholar 

  38. Li N, Flynt AS, Kim HR, Solnica-Krezel L, Patton JG (2008) Dispatched Homolog 2 is ­targeted by miR-214 through a combination of three weak microRNA recognition sites. Nucleic Acids Res 36:4277–4285

    Article  PubMed  CAS  Google Scholar 

  39. Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024

    Article  PubMed  CAS  Google Scholar 

  40. Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Molecular computation: RNA solutions to chess problem. Proc Natl Acad Sci USA 97:1385–1389

    Article  PubMed  CAS  Google Scholar 

  41. Fujii YR (2008) Formulation of new algorithmics for miRNAs. Open Virol J 2:37–43

    Article  PubMed  CAS  Google Scholar 

  42. Fujii YR (2008) The quantum theory of RNA waves for microRNAs. Proceedings of 2008 international symposium on physics of quantum technology. Nara, p 177

    Google Scholar 

  43. Bailey VJ, Puleo CM, Ho YP, Yeh HC, Wang TH (2009) Quantum dots in molecular detection of disease. Conf Proc IEEE Eng Med Biol Soc 2009:4089–4092

    PubMed  CAS  Google Scholar 

  44. Bailey VJ, Easwaran H, Zhang Y, Griffiths E, Belinsky SA, Herman JG, Baylin SB, Carraway HE, Wang T-H (2009) MS-qFRET: a quantum dot-based method for analysis of DNA methylation. Genome Res 19:1455–1461

    Article  PubMed  CAS  Google Scholar 

  45. Fujii YR (2010) RNA genes: retroelements and virally retroposable microRNAs in human embryonic stem cells. Open Virol J 4:63–75

    Article  PubMed  CAS  Google Scholar 

  46. Feynman R (1982) Quantum mechanical computers. Int J Theo Phys 21:467–488

    Article  Google Scholar 

  47. Sober E (1993) Phylosophy of biology. Oxford University Press, Oxford

    Google Scholar 

  48. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Kariko K, Yoo JW, Lee D, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJC, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MMW, Provost P, Kugel JF, Goodrich JA, Dunaief JL, Baffi JZ, Ambati J (2010) DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature 471:325–330

    Article  Google Scholar 

  49. Balaj L, Lessard R, Dai L, Cho YJ, Pomeroy SL, Breakefield XO, Skog J (2011) Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. Nat Commun 2:180

    Article  PubMed  Google Scholar 

  50. Ritz T, Thalau P, Phillips JB, Wiltschko R, Wiltschko W (2004) Resonance effects indicate a radical-pair mechanism for avian magnetic compass. Nature 429:177–180

    Article  PubMed  CAS  Google Scholar 

  51. Hwang HW, Wentzel EA, Mendell JT (2007) A hexanucleotide element directs microRNA nuclear import. Science 315:97–100

    Article  PubMed  CAS  Google Scholar 

  52. Jeffries CD, Fried HM, Perkins DO (2011) Nuclear and cytoplasmic localization of neural stem cell microRNAs. RNA 17:675–686

    Article  PubMed  CAS  Google Scholar 

  53. Regan C, Zuker M, Regan MA (2011) Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLoS Comput Biol 7:e10001090

    Google Scholar 

  54. Astolfi PA, Salamini F, Sgaramella V (2010) Are we genomic mosaics? Variations of the genome of somatic cells can contribute to diversify our phenotypes. Curr Genomics 11:379–386

    Article  PubMed  CAS  Google Scholar 

  55. Kurth HM, Mochizuki K (2009) Non-coding RNA: a bridge between small RNA and DNA. RNA Biol 6:2

    Article  Google Scholar 

  56. Dwivedi RS, Herman JG, McCaffrey TA, Raj DSC (2010) Beyond genetics: epigenetic code in chronic kidney disease. Kidney Int 79:23–32

    Article  PubMed  Google Scholar 

  57. Schrödinger E (1944) What is life. The physical aspect of the living cell. Cambridge University Press, Cambridge

    Google Scholar 

  58. Otake K, Ohta M, Minowada J, Hatama S, Takahashi E, Ikemoto A, Okuyama H, Fujii YR (2000) Extracellular Nef of HIV-1 can target CD4 memory T population. AIDS 14:1662–1664

    Article  PubMed  CAS  Google Scholar 

  59. Fujii Y, Otake K, Tashiro M, Adachi A (1996) Soluble Nef antigen of HIV-1 is cytotoxic for human CD4+ T cells. FEBS Lett 393:93–96

    Article  PubMed  CAS  Google Scholar 

  60. Raymond AD, Campbell-Sims TC, Khan M, Lang M, Huang MB, Bond VC, Powell MD (2010) HIV type 1 Nef is released from infected cells in CD45+ microvesicles and is present in the plasma of HIV-infected individuals. AIDS Res Hum Retroviruses 26:167–178

    Google Scholar 

  61. Meckes DG Jr, Shair KHY, Marquitz AR, Kung C-P, Edwards RH, Raab-Traub N (2010) Human tumor virus utilizes exosomes for intercellular communication. Proc Natl Acad Soci USA 107:20370–20375

    Article  Google Scholar 

  62. Younger ST, Corey DR (2011) Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoter. Nucleic Acids Res 39(13):5682–5691

    Article  PubMed  CAS  Google Scholar 

  63. Piriyapongsa J, Polavarapu N, Borodovsky M, McDonald J (2007) Exonization of the LTR transposable elements in human genome. BMC Genomics 8:291

    Article  PubMed  Google Scholar 

  64. Lu Y, Li C, Zhang K, Sun H, Tao D, Liu Y, Zhang S, Ma Y (2010) Identification of piRNAs in HeLa cells by massive parallel sequencing. BMB Rep 45:635–641

    Article  Google Scholar 

  65. Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J (2009) Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One 4:e7686

    Article  PubMed  Google Scholar 

  66. Chuma S, Pillai RS (2009) Retrotransposon silencing by piRNAs: ping-pong players mark their sub-cellular boundaries. PLoS Genet 5:e1000770

    Article  PubMed  Google Scholar 

  67. Pélisson A, Sarot E, Payen-Groshêne G, Bucheton A (2007) A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J Virol 81:1951–1960

    Article  PubMed  Google Scholar 

  68. Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL (2010) The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS One 5:e8638

    Article  PubMed  Google Scholar 

  69. Ruse M (2003) Darwin and design: does evolution have a purpose? Harvard University Press, Cambridge

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yoichi Robertus Fujii .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Fujii, Y.R. (2013). The RNA Gene Information: Retroelement-MicroRNA Entangling as the RNA Quantum Code. In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology, vol 936. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-083-0_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-083-0_4

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-082-3

  • Online ISBN: 978-1-62703-083-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics