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Transcriptional and Posttranscriptional Programming by Long Noncoding RNAs

  • Radha Raman Pandey
  • Chandrasekhar KanduriEmail author
Chapter
Part of the Progress in Molecular and Subcellular Biology book series (PMSB, volume 51)

Abstract

Recently, several lines of evidence have suggested that noncoding RNAs, which include both small and long noncoding RNAs (ncRNAs), contribute to a significant portion of the transcriptome in eukaryotic organisms. However, the functional significance of this wide-spread occurrence of ncRNAs, and in particular, the long ncRNAs (lncRNAs), for organismal development and differentiation is unclear. The available evidence from a subset of lncRNAs suggests that certain lncRNAs, and/or the act of their transcription, are involved in important biological functions at the transcriptional and posttranscriptional level. This chapter discusses the epigenetic and nonepigenetic mechanisms by which lncRNAs and/or their transcription are involved in the programming of various biological functions in model systems, from yeast to mammals.

Keywords

Repressive Chromatin Preinitiation Complex Dosage Compensation Complex Transcriptional Interference Epigenetic Gene Silence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported by the grants from the Swedish Cancer Research foundation (Cancerfonden), Swedish Medical Research Council (VR-M), and Swedish Childhood Cancer Society (Barncancerfonden) to Chandrasekhar Kanduri. Chandrasekhar Kanduri is a Senior Research Fellow supported by VR-M.

References

  1. Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project (2009) Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457:1028–1032CrossRefGoogle Scholar
  2. Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI (2006) High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev 20:848–857PubMedCrossRefGoogle Scholar
  3. Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI (2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134:599–609PubMedCrossRefGoogle Scholar
  4. Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19:454–492PubMedCrossRefGoogle Scholar
  5. Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008) The eukaryotic genome as an RNA machine. Science 319:1787–1789PubMedCrossRefGoogle Scholar
  6. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedCrossRefGoogle Scholar
  7. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233PubMedCrossRefGoogle Scholar
  8. Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, Bonilla F, de Herreros AG (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22:756–769PubMedCrossRefGoogle Scholar
  9. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19:1635–1655PubMedCrossRefGoogle Scholar
  10. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242–2246PubMedCrossRefGoogle Scholar
  11. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al (2007) Identification and analysis of functional elements in 1% ofthe human genome by the ENCODE pilot project. Nature 447:799–816PubMedCrossRefGoogle Scholar
  12. Blume SW, Meng Z, Shrestha K, Snyder RC, Emanuel PD (2003) The 5′-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter. J Cell Biochem 88:165–180PubMedCrossRefGoogle Scholar
  13. Brouwer R, Allmang C, Raijmakers R, van Aarssen Y, Egberts WV, Petfalski E, van Venrooij WJ, Tollervey D, Pruijn GJ (2001) Three novel components of the human exosome. J Biol Chem. 2;276(9):6177–84Google Scholar
  14. Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR (2009) Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106:18321–18326PubMedCrossRefGoogle Scholar
  15. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K et al (2005) The transcriptional landscape of the mammalian genome. Science 309:1559–1563PubMedCrossRefGoogle Scholar
  16. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499–509PubMedCrossRefGoogle Scholar
  17. Chaumeil J, Le Baccon P, Wutz A, Heard E (2006) A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 20:2223–2237PubMedCrossRefGoogle Scholar
  18. Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, Winston F (2008) Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol 6:e277PubMedCrossRefGoogle Scholar
  19. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845–1848PubMedCrossRefGoogle Scholar
  20. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103:5320–5325PubMedCrossRefGoogle Scholar
  21. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8:e1000384PubMedCrossRefGoogle Scholar
  22. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433–1445PubMedCrossRefGoogle Scholar
  23. Dobi KC, Winston F (2007) Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol 27:5575–5586PubMedCrossRefGoogle Scholar
  24. Ebisuya M, Yamamoto T, Nakajima M, Nishida E (2008) Ripples from neighbouring transcription. Nat Cell Biol 10:1106–1113PubMedCrossRefGoogle Scholar
  25. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M (2004) CREB binds to multiple loci on human chromosome 22. Mol Cell Biol 24:3804–3814PubMedCrossRefGoogle Scholar
  26. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14:723–730PubMedCrossRefGoogle Scholar
  27. Fitzpatrick GV, Soloway PD, Higgins MJ (2002) Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 32:426–431PubMedCrossRefGoogle Scholar
  28. Gelbart ME, Kuroda MI (2009) Drosophila dosage compensation: a complex voyage to the X chromosome. Development 136:1399–1410PubMedCrossRefGoogle Scholar
  29. Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI (2009) Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol 16:825–832PubMedCrossRefGoogle Scholar
  30. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108PubMedCrossRefGoogle Scholar
  31. Grewal SI, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8:35–46PubMedCrossRefGoogle Scholar
  32. Guaita S, Puig I, Franci C, Garrido M, Dominguez D, Batlle E, Sancho E, Dedhar S, De Herreros AG, Baulida J (2002) Snail induction of epithelial to mesenchymal transition in tumor cells is accompanied by MUC1 repression and ZEB1 expression. J Biol Chem 277:39209–39216PubMedCrossRefGoogle Scholar
  33. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:071–076Google Scholar
  34. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227PubMedCrossRefGoogle Scholar
  35. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The antisense transcriptomes of human cells. Science 322:1855–1857PubMedCrossRefGoogle Scholar
  36. Hongay CF, Grisafi PL, Galitski T, Fink GR (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127:735–745PubMedCrossRefGoogle Scholar
  37. Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S, Shiota K (2004) Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun 322:593–600PubMedCrossRefGoogle Scholar
  38. Kanduri M, Kanduri C, Mariano P, Vostrov AA, Quitschke W, Lobanenkov V, Ohlsson R (2002) Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region. Mol Cell Biol 22:3339–3344PubMedCrossRefGoogle Scholar
  39. Kanduri C, Thakur N, Pandey RR (2006) The length of the transcript encoded from the Kcnq1ot1 antisense promoter determines the degree of silencing. EMBO J 25:2096–2106PubMedCrossRefGoogle Scholar
  40. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007a) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484–1488PubMedCrossRefGoogle Scholar
  41. Kapranov P, Willingham AT, Gingeras TR (2007b) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413–423PubMedCrossRefGoogle Scholar
  42. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106:11667–11672PubMedCrossRefGoogle Scholar
  43. 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
  44. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3:ra8PubMedCrossRefGoogle Scholar
  45. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705PubMedCrossRefGoogle Scholar
  46. Lefevre P, Witham J, Lacroix CE, Cockerill PN, Bonifer C (2008) The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription. Mol Cell 32(1):129–139PubMedCrossRefGoogle Scholar
  47. Ligtenberg MJ, Kuiper RP, Chan TL, Goossens M, Hebeda KM, Voorendt M, Lee TY, Bodmer D, Hoenselaar E, Hendriks-Cornelissen SJ, Tsui WY, Kong CK, Brunner HG, van Kessel AG, Yuen ST, van Krieken JH, Leung SY, Hoogerbrugge N (2009) Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1. Nat Genet 41:112–117PubMedCrossRefGoogle Scholar
  48. 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 (2010) 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol 8:e1000276PubMedCrossRefGoogle Scholar
  49. Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668PubMedCrossRefGoogle Scholar
  50. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA (2008) Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 29:499–509PubMedCrossRefGoogle Scholar
  51. Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429:571–574PubMedCrossRefGoogle Scholar
  52. Martens JA, Py Wu, Winston F (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 19:2695–2704PubMedCrossRefGoogle Scholar
  53. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666–670PubMedCrossRefGoogle Scholar
  54. Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5:316–323PubMedCrossRefGoogle Scholar
  55. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15:R17PubMedCrossRefGoogle Scholar
  56. Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (2006) Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 22:351–361PubMedCrossRefGoogle Scholar
  57. Meller VH, Rattner BP (2002) The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J 21:1084–1091PubMedCrossRefGoogle Scholar
  58. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105:716–721PubMedCrossRefGoogle Scholar
  59. Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri C (2008) Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 28:3713–3728PubMedCrossRefGoogle Scholar
  60. Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C (2010) Characterization of the RNA content of chromatin. Genome Res 20(7):899–907PubMedCrossRefGoogle Scholar
  61. 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:e1000258PubMedCrossRefGoogle Scholar
  62. Murakami K, Oshimura M, Kugoh H (2007) Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 52:926–933PubMedCrossRefGoogle Scholar
  63. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349PubMedCrossRefGoogle Scholar
  64. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717–1720PubMedCrossRefGoogle Scholar
  65. Navarro P, Chambers I, Karwacki-Neisius V, Chureau C, Morey C, Rougeulle C, Avner P (2008) Molecular coupling of Xist regulation and pluripotency. Science 321:693–695Google Scholar
  66. Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457:1038–1042PubMedCrossRefGoogle Scholar
  67. Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V, Schmitz MH, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J (2010) Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464:721–727PubMedCrossRefGoogle Scholar
  68. Nobori T, Miura K, Wu DJ, Lois A, Takabayashi K, Carson DA (1994) Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature 368:753–756PubMedCrossRefGoogle Scholar
  69. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563–573PubMedCrossRefGoogle Scholar
  70. Pandey RR, Ceribelli M, Singh PB, Ericsson J, Mantovani R, Kanduri C (2004) NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of he Kcnq1 imprinting control region. J Biol Chem 279:52685–52693PubMedCrossRefGoogle Scholar
  71. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232–246PubMedCrossRefGoogle Scholar
  72. Payer B, Lee JT (2008) X chromosome dosage compensation: how mammals keep the balance. Annu Rev Genet 42:733–772PubMedCrossRefGoogle Scholar
  73. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35:e128PubMedCrossRefGoogle Scholar
  74. Phillips JE, Corces VG (2009) CTCF: master weaver of the genome. Cell 137:1194–1211PubMedCrossRefGoogle Scholar
  75. Ponjavic J, Ponting CP, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17:556–565PubMedCrossRefGoogle Scholar
  76. Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum. Genes Dev 21:11–42PubMedCrossRefGoogle Scholar
  77. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science 322:1851–1854PubMedCrossRefGoogle Scholar
  78. Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, Nagano T, Cobb BS, Fraser P, Reik W (2009) The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136:25–30CrossRefGoogle Scholar
  79. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323PubMedCrossRefGoogle Scholar
  80. Rossignol F, Vache C, Clottes E (2002) Natural antisense transcripts of hypoxia-inducible factor 1alpha are detected in different normal and tumour human tissues. Gene 299:135–140PubMedCrossRefGoogle Scholar
  81. Rossignol F, de Laplanche E, Mounier R, Bonnefont J, Cayre A, Godinot C, Simonnet H, Clottes E (2004) Natural antisense transcripts of HIF-1alpha are conserved in rodents. Gene 339:121–130PubMedCrossRefGoogle Scholar
  82. Samanta MP, Tongprasit W, Sethi H, Chin CS, Stolc V (2006) Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc Natl Acad Sci U S A 103:4192–4197PubMedCrossRefGoogle Scholar
  83. Sanchez-Elsner T, Gou D, Kremmer E, Sauer F (2006) Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311:1118–1123PubMedCrossRefGoogle Scholar
  84. Shamovsky I, Nudler E (2008) New insights into the mechanism of heat shock response activation. Cell Mol Life Sci 65:855–861PubMedCrossRefGoogle Scholar
  85. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100:15776–15781PubMedCrossRefGoogle Scholar
  86. Sleutels F, Zwart R, Barlow DP (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415:810–813PubMedCrossRefGoogle Scholar
  87. Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB (2008) The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex. PLoS Genet 4:e1000302PubMedCrossRefGoogle Scholar
  88. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19:347–359PubMedCrossRefGoogle Scholar
  89. Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI (2008) The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nat Struct Mol Biol 15:1318–1325PubMedCrossRefGoogle Scholar
  90. Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29:288–299PubMedCrossRefGoogle Scholar
  91. Thakur N, Tiwari VK, Thomassin H, Pandey RR, Kanduri M, Göndör A, Grange T, Ohlsson R, Kanduri C (2004) An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol 24:7855–7862PubMedCrossRefGoogle Scholar
  92. Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet 34:157–165PubMedCrossRefGoogle Scholar
  93. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487PubMedCrossRefGoogle Scholar
  94. Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK (2010) Visualization of image data from cells to organisms. Nat Methods 7:S26–S41PubMedCrossRefGoogle Scholar
  95. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454:126–130PubMedCrossRefGoogle Scholar
  96. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309:1570–1573PubMedCrossRefGoogle Scholar
  97. Woo CJ, Kingston RE (2007) HOTAIR lifts noncoding RNAs to new levels. Cell 129:1257–1259PubMedCrossRefGoogle Scholar
  98. Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30:167–174PubMedCrossRefGoogle Scholar
  99. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737PubMedCrossRefGoogle Scholar
  100. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457(7232):1033–1037PubMedCrossRefGoogle Scholar
  101. Yakovchuk P, Goodrich JA, Kugel JF (2009) B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A 106:5569–5574PubMedCrossRefGoogle Scholar
  102. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846PubMedCrossRefGoogle Scholar
  103. 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 451:202–206PubMedCrossRefGoogle Scholar
  104. Zhang LF, Huynh KD, Lee JT (2007) Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 129:693–706PubMedCrossRefGoogle Scholar
  105. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322:750–756PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  1. 1.Department of Genetics and Pathology, Rudbeck LaboratoryUppsala UniversityUppsalaSweden

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