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Targeted Small Noncoding RNA-Directed Gene Activation in Human Cells

  • Caio Damski
  • Kevin V. MorrisEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1173)

Abstract

A growing body of evidence suggests that noncoding RNA (ncRNA) transcripts play a fundamental role in regulating gene expression via targeting epigenetic modifications to particular loci in the genome. Classical examples of such regulation are X-chromosome inactivation and genomic imprinting; however it is now clear that ncRNAs exert their influence over a wider array of genes throughout the metazoan genome. Accumulating evidence suggests that the ncRNAs act as guides for epigenetic silencing complexes to specific sites within the genome. Those ncRNAs involved in regulating the expression of particular protein-coding genes offer panoply of targets that when suppressed can result in derepression or activation of the ncRNA-targeted locus. Recent work has determined the underlying mechanisms involved in ncRNA-targeted epigenetic regulation in a subset of genes. These findings have resulted in a paradigm shift whereby targeted gene activation can be achieved, by targeting endogenous regulatory ncRNAs, producing potential novel treatments for genetic and infectious diseases where increases in gene expression are required.

Keywords

Long noncoding RNA Antisense transcripts Small noncoding RNAs X chromosome inactivation Genomic imprinting Gene silencing Gene activation DNA methylation Histone modification 

Notes

Acknowledgements

The project was supported by NIHLB R01AI084406, NIAID R56 AI096861-01, and PO1 AI099783-01 to KVM.

References

  1. 1.
    Lee J (2012) Epigenetic regulation by long noncoding RNAs. Science 338:1435–1439PubMedCrossRefGoogle Scholar
  2. 2.
    Ponting C (2008) The functional repertoires of metazoan genomes. Nat Rev Genet 9:689–698PubMedCrossRefGoogle Scholar
  3. 3.
    Morris K (2009) RNA-directed transcriptional gene silencing and activation in human cells. Oligonucleotides 19:299–306PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Kung J, Colognori D, Lee J (2013) Long noncoding RNAs: past, present, and future. Genetics 193:651–669PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Morris K (2009) Non-coding RNAs, epigenetic memory and the passage of information to progeny. RNA Biol 6(3):242–247PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, Cuzin F (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441:469–474PubMedCrossRefGoogle Scholar
  7. 7.
    Davidson B, Fasman GD (1969) The single-stranded polyadenylic acid-poly-L-lysine complex. A conformational study and characterization. Biochemistry 8:4116–4126PubMedCrossRefGoogle Scholar
  8. 8.
    Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356PubMedCrossRefGoogle Scholar
  9. 9.
    Banfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L (2012) Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 22:1646–1657PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic V, Brenner S, Batalov S, Forrest AR, Zavolan M, Davis M, Wilming L, Aidinis V, Allen J, Ambesi-Impiombato A, Apweiler R, Aturaliya R, Bailey T, Bansal M, Baxter L, Beisel K, Bersano T, Bono H, Chalk A, Chiu K, Choudhary V, Christoffels A, Clutterbuck D, Crowe M, Dalla E, Dalrymple B, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher C, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras T, Gojobori T, Green R, Gustincich S, Harbers M, Hayashi Y, Hensch T, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan S, Kruger A, Kummerfeld S, Kurochkin I, Lareau L, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S (2005) The transcriptional landscape of the mammalian genome. Science 309:1559–1563PubMedCrossRefGoogle Scholar
  11. 11.
    Amaral P, Mattick J (2008) Noncoding RNA in development. Mamm Genome 19:454–492PubMedCrossRefGoogle Scholar
  12. 12.
    Lucchesi J, Kelly W, Panning B (2005) Chromatin remodeling in dosage compensation. Annu Rev Genet 39:615–651PubMedCrossRefGoogle Scholar
  13. 13.
    Lee J (2010) The X as model for RNA’s niche in epigenomic regulation. Cold Spring Harb Perspect Biol 2:a003749PubMedCentralPubMedGoogle Scholar
  14. 14.
    Wutz A (2003) RNAs templating chromatin structure for dosage compensation in animals. Bioessays 25:434–442PubMedCrossRefGoogle Scholar
  15. 15.
    Lyon MF (1961) Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190:372–373PubMedCrossRefGoogle Scholar
  16. 16.
    Brown C, Lafreniere R, Powers V, Sebastio G, Ballabio A, Pettigrew A, Ledbetter D, Levy E, Craig I, Willard H (1991) Localization of the X inactivation centre on the human X chromosome in Xq13. Nature 349:82–84PubMedCrossRefGoogle Scholar
  17. 17.
    Rastan S, Robertson EJ (1985) X-chromosome deletions in embryo-derived (EK) cell lines associated with lack of X-chromosome inactivation. J Embryol Exp Morphol 90:379–388PubMedGoogle Scholar
  18. 18.
    Cattanach B, Isaacson J (1967) Controlling elements in the mouse X chromosome. Genetics 57:331–346PubMedCentralPubMedGoogle Scholar
  19. 19.
    Kay GF, Barton SC, Surani MA, Rastan S (1994) Imprinting and X chromosome counting mechanisms determine Xist expression in early mouse development. Cell 77:639–650PubMedCrossRefGoogle Scholar
  20. 20.
    Lyon MF (1999) Imprinting and X-chromosome inactivation. Results Probl Cell Differ 25:73–90PubMedCrossRefGoogle Scholar
  21. 21.
    Avner P, Heard E (2001) X-chromosome inactivation: counting, choice and initiation. Nat Rev Genet 2:59–67PubMedCrossRefGoogle Scholar
  22. 22.
    Boumil RM, Lee JT (2001) Forty years of decoding the silence in X-chromosome inactivation. Hum Mol Genet 10:2225–2232PubMedCrossRefGoogle Scholar
  23. 23.
    Namekawa SH, Payer B, Huynh KD, Jaenisch R, Lee JT (2010) Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Mol Cell Biol 30:3187–3205PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Xu N, Donohoe ME, Silva SS, Lee JT (2007) Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 39:1390–1396PubMedCrossRefGoogle Scholar
  25. 25.
    Xu N, Tsai CL, Lee JT (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311:1149–1152PubMedCrossRefGoogle Scholar
  26. 26.
    Bacher C, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E (2006) Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8:293–299PubMedCrossRefGoogle Scholar
  27. 27.
    Edwards C, Ferguson-Smith A (2007) Mechanisms regulating imprinted genes in clusters. Curr Opin Cell Biol 19:281–289PubMedCrossRefGoogle Scholar
  28. 28.
    Sleutels F, Barlow DP (2002) The origins of genomic imprinting in mammals. Adv Genet 46:119–163PubMedCrossRefGoogle Scholar
  29. 29.
    Bartolomei MS, Ferguson-Smith AC (2011) Mammalian genomic imprinting. Cold Spring Harb Perspect Biol. 3(7). pii: a002592. doi: 10.1101/cshperspect.a002592Google Scholar
  30. 30.
    Lee JT (2003) Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting? Curr Biol 13(6):R242–54CrossRefGoogle Scholar
  31. 31.
    Cai X, Cullen B (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13:313–316PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Kevin V, M. (2009) RNA-directed control of transcription in human cells: specifically turning genes ON or OFF. Gene Ther Reg 04Google Scholar
  33. 33.
    Weinberg M, Morris K (2013) Long non-coding RNA targeting and transcriptional de-repression. Nucleic Acid Ther 23:9–14PubMedCentralPubMedGoogle Scholar
  34. 34.
    Leung AK, Sharp PA (2006) Function and localization of microRNAs in mammalian cells. Cold Spring Harb Symp Quant Biol 71:29–38PubMedCrossRefGoogle Scholar
  35. 35.
    Turner AM, Morris KV (2010) Controlling transcription with noncoding RNAs in mammalian cells. Biotechniques 48:ix–xviPubMedCrossRefGoogle Scholar
  36. 36.
    Ackley A, Lenox A, Stapleton K, Knowling S, Lu T, Sabir KS, Vogt PK, Morris KV (2013) An algorithm for generating small RNAs capable of epigenetically modulating transcriptional gene silencing and activation in human cells. Mol Ther Nucleic Acids 2:e104PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Hawkins P, Santoso S, Adams C, Anest V, Morris K (2009) Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res 37:2984–2995PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Kim DH, Villeneuve LM, Morris KV, Rossi JJ (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat Struct Mol Biol 13:793–797PubMedCrossRefGoogle Scholar
  39. 39.
    Suzuki K, Juelich T, Lim H, Ishida T, Watanebe T, Cooper DA, Rao S, Kelleher AD (2008) Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J Biol Chem 283:23353–23363PubMedCentralPubMedCrossRefGoogle Scholar
  40. 40.
    Weinberg MS, Villeneuve LM, Ehsani A, Amarzguioui M, Aagaard L, Chen ZX, Riggs AD, Rossi JJ, Morris KV (2006) The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12:256–262PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
    Han J, Kim D, Morris K (2007) Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci U S A 104:12422–12427PubMedCentralPubMedCrossRefGoogle Scholar
  42. 42.
    Knowling S, Morris KV (2011) Epigenetic regulation of gene expression in human cells by noncoding RNAs. Prog Mol Biol Transl Sci 102:1–10PubMedCrossRefGoogle Scholar
  43. 43.
    Hawkins P, Morris K (2008) RNA and transcriptional modulation of gene expression. Cell Cycle 7:602–607PubMedCentralPubMedCrossRefGoogle Scholar
  44. 44.
    Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Grander D, Morris KV (2013) A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 20(4):440–446PubMedCentralPubMedCrossRefGoogle Scholar
  45. 45.
    Braunschweig M, Jagannathan V, Gutzwiller A, Bee G (2012) Investigations on transgenerational epigenetic response down the male line in F2 pigs. PLoS One 7:e30583PubMedCentralPubMedCrossRefGoogle Scholar
  46. 46.
    Janowski B, Younger S, Hardy D, Ram R, Huffman K, Corey D (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol 3:166–173PubMedCrossRefGoogle Scholar
  47. 47.
    Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103:17337–17342PubMedCentralPubMedCrossRefGoogle Scholar
  48. 48.
    Morris KV, Santoso S, Turner AM, Pastori C, Hawkins PG (2008) Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 4:e1000258PubMedCentralPubMedCrossRefGoogle Scholar
  49. 49.
    Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP, Corey DR, Janowski BA (2008) Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 15:842–848PubMedCentralPubMedCrossRefGoogle Scholar
  50. 50.
    Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451:202–206PubMedCentralPubMedCrossRefGoogle Scholar
  51. 51.
    Hawkins PG, Morris KV (2010) Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 1:165–175PubMedCentralPubMedCrossRefGoogle Scholar
  52. 52.
    Modarresi F, Faghihi M, Lopez-Toledano M, Fatemi R, Magistri M, Brothers S, van der Brug M, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30:453–459PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Biotechnology and Biomedical SciencesThe University of New South WalesSydneyAustralia
  2. 2.Molecular and Experimental MedicineThe Scripps Research InstituteLa JollaUSA

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