Mammalian Genome

, Volume 19, Issue 7–8, pp 454–492 | Cite as

Noncoding RNA in development

  • Paulo P. Amaral
  • John S. MattickEmail author


Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.



PPA is supported by a University of Queensland International Research Award. JSM is supported by a Federation Fellowship from the Australian Research Council. We thank our laboratory colleagues and collaborators for many stimulating discussions and for bringing many interesting papers to our attention. We also thank John Rinn for his helpful comments on the manuscript, and Carlo Brena, Yuji Kageyama, Tracy Young-Pearse, and the Allen Institute for Brain Science for providing high-resolution images of the figures.


  1. Abarrategui I, Krangel MS (2007) Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. EMBO J 26:4380–4390PubMedGoogle Scholar
  2. Abedin M, King N (2008) The premetazoan ancestry of cadherins. Science 319:946–948PubMedGoogle Scholar
  3. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758–762PubMedGoogle Scholar
  4. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V et al (2007) Deletion of ultraconserved elements yields viable mice. PLoS Biol 5:e234PubMedGoogle Scholar
  5. Akam ME, Martinez-Arias A, Weinzierl R, Wilde CD (1985) Function and expression of ultrabithorax in the Drosophila embryo. Cold Spring Harb Symp Quant Biol 50:195–200PubMedGoogle Scholar
  6. Akhtar A, Zink D, Becker PB (2000) Chromodomains are protein-RNA interaction modules. Nature 407:405–409PubMedGoogle Scholar
  7. Alfano G, Vitiello C, Caccioppoli C, Caramico T, Carola A et al (2005) Natural antisense transcripts associated with genes involved in eye development. Hum Mol Genet 14:913–923PubMedGoogle Scholar
  8. Allen L, Kloc M, Etkin LD (2003) Identification and characterization of the Xlsirt cis-acting RNA localization element. Differentiation 71:311–321PubMedGoogle Scholar
  9. Amack JD, Paguio AP, Mahadevan MS (1999) Cis and trans effects of the myotonic dystrophy (DM) mutation in a cell culture model. Hum Mol Genet 8:1975–1984PubMedGoogle Scholar
  10. Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008) The eukaryotic genome as an RNA machine. Science 319:1787–1789PubMedGoogle Scholar
  11. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13:807–818PubMedGoogle Scholar
  12. Andersen BB, Gundersen HJ, Pakkenberg B (2003) Aging of the human cerebellum: a stereological study. J Comp Neurol 466:356–365PubMedGoogle Scholar
  13. Angeleska A, Jonoska N, Saito M, Landweber LF (2007) RNA-guided DNA assembly. J Theor Biol 248:706–720PubMedGoogle Scholar
  14. Angelopoulou R, Lavranos G, Manolakou P (2008) Regulatory RNAs and chromatin modification in dosage compensation: a continuous path from flies to humans? Reprod Biol Endocrinol 6:12PubMedGoogle Scholar
  15. Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM et al (2001) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 11:1017–1027PubMedGoogle Scholar
  16. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D et al (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5:337–350PubMedGoogle Scholar
  17. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761–764PubMedGoogle Scholar
  18. Ashe HL, Monks J, Wijgerde M, Fraser P, Proudfoot NJ (1997) Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev 11:2494–2509PubMedGoogle Scholar
  19. Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F (2004) Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. Nucleic Acids Res 32:4646–4656PubMedGoogle Scholar
  20. Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (2007) Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 318:798–801PubMedGoogle Scholar
  21. Bachellerie JP, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84:775–790PubMedGoogle Scholar
  22. Bae E, Calhoun VC, Levine M, Lewis EB, Drewell RA (2002) Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci USA 99:16847–16852PubMedGoogle Scholar
  23. Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE et al (2007) Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J 51:991–1003PubMedGoogle Scholar
  24. Barboro P, D’Arrigo C, Diaspro A, Mormino M, Alberti I et al (2002) Unraveling the organization of the internal nuclear matrix: RNA-dependent anchoring of NuMA to a lamin scaffold. Exp Cell Res 279:202–218PubMedGoogle Scholar
  25. Bass BL (2002) RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71:817–846PubMedGoogle Scholar
  26. Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N et al (2008) PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell 31:67–78PubMedGoogle Scholar
  27. Bedford M, Arman E, Orr-Urtreger A, Lonai P (1995) Analysis of the Hoxd-3 gene: structure and localization of its sense and natural antisense transcripts. DNA Cell Biol 14:295–304PubMedGoogle Scholar
  28. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A et al (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441:87–90PubMedGoogle Scholar
  29. Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB et al (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22:756–769PubMedGoogle Scholar
  30. Bender W (2008) MicroRNAs in the Drosophila bithorax complex. Genes Dev 22:14–19PubMedGoogle Scholar
  31. Bender W, Fitzgerald DP (2002) Transcription activates repressed domains in the Drosophila bithorax complex. Development 129:4923–4930PubMedGoogle Scholar
  32. Benetti R, Gonzalo S, Jaco I, Munoz P, Gonzalez S et al (2008) A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol 15:268–279PubMedGoogle Scholar
  33. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S et al (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37:766–770PubMedGoogle Scholar
  34. Berdal A, Lezot F, Pibouin L, Hotton D, Ghoul-Mazgar S et al (2002) Msx1 homeogene antisense mRNA in mouse dental and bone cells. Connect Tissue Res 43:148–152PubMedGoogle Scholar
  35. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R et al (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38:1375–1377PubMedGoogle Scholar
  36. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669–681PubMedGoogle Scholar
  37. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19:1635–1655PubMedGoogle Scholar
  38. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H et al (2003) Dicer is essential for mouse development. Nat Genet 35:215–217PubMedGoogle Scholar
  39. Bernstein E, Duncan EM, Masui O, Gil J, Heard E et al (2006) Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol 26:2560–2569PubMedGoogle Scholar
  40. Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 22:615–626PubMedGoogle Scholar
  41. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE et al (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242–2246PubMedGoogle Scholar
  42. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816PubMedGoogle Scholar
  43. Bisoni L, Batlle-Morera L, Bird AP, Suzuki M, McQueen HA (2005) Female-specific hyperacetylation of histone H4 in the chicken Z chromosome. Chromosome Res 13:205–214PubMedGoogle Scholar
  44. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H et al (2004) Genomic analysis of mouse retinal development. PLoS Biol 2:E247PubMedGoogle Scholar
  45. Blin-Wakkach C, Lezot F, Ghoul-Mazgar S, Hotton D, Monteiro S et al (2001) Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc Natl Acad Sci USA 98:7336–7341PubMedGoogle Scholar
  46. Bollenbach T, Vetsigian K, Kishony R (2007) Evolution and multilevel optimization of the genetic code. Genome Res 17:401–404PubMedGoogle Scholar
  47. Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM et al (2008) Mapping of small RNAs in the human ENCODE regions. Am J Hum Genet 82:971–981PubMedGoogle Scholar
  48. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291PubMedGoogle Scholar
  49. Bowes Rickman C, Ebright JN, Zavodni ZJ, Yu L, Wang T et al (2006) Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Invest Ophthalmol Vis Sci 47:2305–2316PubMedGoogle Scholar
  50. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA et al (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441:349–353PubMedGoogle Scholar
  51. Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990) The product of the H19 gene may function as an RNA. Mol Cell Biol 10:28–36PubMedGoogle Scholar
  52. Brena C, Chipman AD, Minelli A, Akam M (2006) Expression of trunk Hox genes in the centipede Strigamia maritima: sense and anti-sense transcripts. Evol Dev 8:252–265PubMedGoogle Scholar
  53. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M et al (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089–1103PubMedGoogle Scholar
  54. Britten RJ, Davidson EH (1969) Gene regulation for higher cells: a theory. Science 165:349–357PubMedGoogle Scholar
  55. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190PubMedGoogle Scholar
  56. Brosius J (2003) How significant is 98.5% ‘junk’ in mammalian genomes? Bioinformatics 19(Suppl 2):II35Google Scholar
  57. Buhler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14:1041–1048PubMedGoogle Scholar
  58. Buhler M, Haas W, Gygi SP, Moazed D (2007) RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129:707–721PubMedGoogle Scholar
  59. Buiting K, Nazlican H, Galetzka D, Wawrzik M, Gross S et al (2007) C15orf2 and a novel noncoding transcript from the Prader-Willi/Angelman syndrome region show monoallelic expression in fetal brain. Genomics 89:588–595PubMedGoogle Scholar
  60. Bulfone A, Carotenuto P, Faedo A, Aglio V, Garzia L et al (2005) Telencephalic embryonic subtractive sequences: a unique collection of neurodevelopmental genes. J Neurosci 25:7586–7600PubMedGoogle Scholar
  61. Bushati N, Stark A, Brennecke J, Cohen SM (2008) Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol 18:501–506PubMedGoogle Scholar
  62. Cai X, Cullen BR (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13:313–316PubMedGoogle Scholar
  63. Calderwood MS, Gannoun-Zaki L, Wellems TE, Deitsch KW (2003) Plasmodium falciparum var genes are regulated by two regions with separate promoters, one upstream of the coding region and a second within the intron. J Biol Chem 278:34125–34132PubMedGoogle Scholar
  64. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R et al (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12:215–229PubMedGoogle Scholar
  65. Callahan KP, Butler JS (2008) Lifting the veil on the transcriptome. Genome Biol 9:218PubMedGoogle Scholar
  66. Callis TE, Chen JF, Wang DZ (2007) MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 26:219–225PubMedGoogle Scholar
  67. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131:706–717PubMedGoogle Scholar
  68. Cano A, Nieto MA (2008) Non-coding RNAs take centre stage in epithelial-to-mesenchymal transition. Trends Cell Biol 18:357–359Google Scholar
  69. Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH (2006) Noncoding RNAs in the mammalian central nervous system. Annu Rev Neurosci 29:77–103PubMedGoogle Scholar
  70. Carlile M, Nalbant P, Preston-Fayers K, McHaffie GS, Werner A (2008) Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs. Physiol Genomics 34:95–100PubMedGoogle Scholar
  71. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC et al (2005) The transcriptional landscape of the mammalian genome. Science 309:1559–1563PubMedGoogle Scholar
  72. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38:626–635PubMedGoogle Scholar
  73. Castanotto D, Tommasi S, Li M, Li H, Yanow S et al (2005) Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther 12:179–183PubMedGoogle Scholar
  74. Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI et al (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci USA 97:14311–14316PubMedGoogle Scholar
  75. Cavaille J, Vitali P, Basyuk E, Huttenhofer A, Bachellerie JP (2001) A novel brain-specific box C/D small nucleolar RNA processed from tandemly repeated introns of a noncoding RNA gene in rats. J Biol Chem 276:26374–26383PubMedGoogle Scholar
  76. Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP (2002) Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet 11:1527–1538PubMedGoogle Scholar
  77. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA et al (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499–509PubMedGoogle Scholar
  78. Cerutti H, Casas-Mollano JA (2006) On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet 50:81–99PubMedGoogle Scholar
  79. Chan WY, Wu SM, Ruszczyk L, Law E, Lee TL et al (2006) The complexity of antisense transcription revealed by the study of developing male germ cells. Genomics 87:681–692PubMedGoogle Scholar
  80. Chandler VL (2007) Paramutation: from maize to mice. Cell 128:641–645PubMedGoogle Scholar
  81. Chau YM, Pando S, Taylor HS (2002) HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the uterine endometrium. J Clin Endocrinol Metab 87:2674–2680PubMedGoogle Scholar
  82. Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R et al (2007) Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131:1340–1353PubMedGoogle Scholar
  83. Chen J, Sun M, Lee S, Zhou G, Rowley JD et al (2002) Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA 99:12257–12262PubMedGoogle Scholar
  84. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S et al (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154PubMedGoogle Scholar
  85. Cho YS, Iguchi N, Yang J, Handel MA, Hecht NB (2005) Meiotic messenger RNA and noncoding RNA targets of the RNA-binding protein Translin (TSN) in mouse testis. Biol Reprod 73:840–847PubMedGoogle Scholar
  86. Choi WY, Giraldez AJ, Schier AF (2007) Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 318:271–274PubMedGoogle Scholar
  87. Christov CP, Trivier E, Krude T (2008) Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98:981–988PubMedGoogle Scholar
  88. Chung WJ, Okamura K, Martin R, Lai EC (2008) Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr Biol 18:795–802PubMedGoogle Scholar
  89. Clamp M, Fry B, Kamal M, Xie X, Cuff J et al (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 104:19428–19433PubMedGoogle Scholar
  90. Clark RM, Wagler TN, Quijada P, Doebley J (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38:594–597PubMedGoogle Scholar
  91. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ et al (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613–619PubMedGoogle Scholar
  92. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X et al (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38:813–818PubMedGoogle Scholar
  93. Cocquet J, Pannetier M, Fellous M, Veitia RA (2005) Sense and antisense Foxl2 transcripts in mouse. Genomics 85:531–541PubMedGoogle Scholar
  94. Conaco C, Otto S, Han JJ, Mandel G (2006) Reciprocal actions of REST and a microRNA promote neuronal identity. Proc Natl Acad Sci USA 103:2422–2427PubMedGoogle Scholar
  95. Conley AB, Miller WJ, Jordan IK (2008) Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 24:53–56PubMedGoogle Scholar
  96. Corredor-Adamez M, Welten MC, Spaink HP, Jeffery JE, Schoon RT et al (2005) Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hox b 13a. Evol Dev 7:362–375PubMedGoogle Scholar
  97. Costa FF (2008) Non-coding RNAs, epigenetics and complexity. Gene 410:9–17PubMedGoogle Scholar
  98. Coudert AE, Pibouin L, Vi-Fane B, Thomas BL, Macdougall M et al (2005) Expression and regulation of the Msx1 natural antisense transcript during development. Nucleic Acids Res 33:5208–5218PubMedGoogle Scholar
  99. Crosthwaite SK (2004) Circadian clocks and natural antisense RNA. FEBS Lett 567:49–54PubMedGoogle Scholar
  100. Cumberledge S, Zaratzian A, Sakonju S (1990) Characterization of two RNAs transcribed from the cis-regulatory region of the abd-A domain within the Drosophila bithorax complex. Proc Natl Acad Sci USA 87:3259–3263PubMedGoogle Scholar
  101. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C et al (2008) An endogenous small interfering RNA pathway in Drosophila. Nature 453:798–802PubMedGoogle Scholar
  102. da Rocha ST, Edwards CA, Ito M, Ogata T, Ferguson-Smith AC (2008) Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet 24:306–316PubMedGoogle Scholar
  103. Dahary D, Elroy-Stein O, Sorek R (2005) Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res 15:364–368PubMedGoogle Scholar
  104. Dallosso AR, Hancock AL, Malik S, Salpekar A, King-Underwood L et al (2007) Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer. RNA 13:2287–2299PubMedGoogle Scholar
  105. Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ et al (2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell 31:79–90PubMedGoogle Scholar
  106. David L, Huber W, Granovskaia M, Toedling J, Palm CJ et al (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 103:5320–5325PubMedGoogle Scholar
  107. Davies W, Isles AR, Wilkinson LS (2005) Imprinted gene expression in the brain. Neurosci Biobehav Rev 29:421–430PubMedGoogle Scholar
  108. Davis BN, Hilyard AC, Lagna G, Hata A (2008) SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454:56–61PubMedGoogle Scholar
  109. Davis CA, Ares M Jr (2006) Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 103:3262–3267PubMedGoogle Scholar
  110. de la Calle-Mustienes E, Feijoo CG, Manzanares M, Tena JJ, Rodriguez-Seguel E et al (2005) A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res 15:1061–1072Google Scholar
  111. Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z et al (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res 16:20–29PubMedGoogle Scholar
  112. Deng X, Meller VH (2006) Non-coding RNA in fly dosage compensation. Trends Biochem Sci 31:526–532PubMedGoogle Scholar
  113. Dennis C (2002) The brave new world of RNA. Nature 418:122–124PubMedGoogle Scholar
  114. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R et al (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17:746–759PubMedGoogle Scholar
  115. Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (2007) The expanding RNA polymerase III transcriptome. Trends Genet 23:614–622PubMedCrossRefGoogle Scholar
  116. Ding F, Prints Y, Dhar MS, Johnson DK, Garnacho-Montero C et al (2005) Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models. Mamm Genome 16:424–431PubMedGoogle Scholar
  117. Ding F, Li HH, Zhang S, Solomon NM, Camper SA et al (2008) SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice. PLoS ONE 3:e1709PubMedGoogle Scholar
  118. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433–1445Google Scholar
  119. Dong XY, Rodriguez C, Guo P, Sun X, Talbot JT et al (2008) SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet 17:1031–1042PubMedGoogle Scholar
  120. Dorus S, Anderson JR, Vallender EJ, Gilbert SL, Zhang L et al (2006) Sonic Hedgehog, a key development gene, experienced intensified molecular evolution in primates. Hum Mol Genet 15:2031–2037PubMedGoogle Scholar
  121. Drewell RA, Bae E, Burr J, Lewis EB (2002) Transcription defines the embryonic domains of cis-regulatory activity at the Drosophila bithorax complex. Proc Natl Acad Sci USA 99:16853–16858PubMedGoogle Scholar
  122. Dumas C, Chow C, Muller M, Papadopoulou B (2006) A novel class of developmentally regulated noncoding RNAs in Leishmania. Eukaryot Cell 5:2033–2046PubMedGoogle Scholar
  123. Ebralidze AK, Guibal FC, Steidl U, Zhang P, Lee S et al (2008) PU. 1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Develop 22:2085–2092Google Scholar
  124. Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ et al (2008) Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2:437–447PubMedGoogle Scholar
  125. Elmendorf HG, Singer SM, Nash TE (2001) The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids Res 29:4674–4683PubMedGoogle Scholar
  126. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L et al (2006) Complex loci in human and mouse genomes. PLoS Genet 2:e47PubMedGoogle Scholar
  127. Espinoza CA, Goodrich JA, Kugel JF (2007) Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 13:583–596PubMedGoogle Scholar
  128. Esquela-Kerscher A, Slack FJ (2006) Oncomirs–microRNAs with a role in cancer. Nat Rev Cancer 6:259–269PubMedGoogle Scholar
  129. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL et al (2004) CREB binds to multiple loci on human chromosome 22. Mol Cell Biol 24:3804–3814PubMedGoogle Scholar
  130. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM et al (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of miRNA genes. PLoS ONE 2:e219PubMedGoogle Scholar
  131. Fan H, Villegas C, Huang A, Wright JA (1996) Suppression of malignancy by the 3′ untranslated regions of ribonucleotide reductase R1 and R2 messenger RNAs. Cancer Res 56:4366–4369PubMedGoogle Scholar
  132. Farazi TA, Juranek SA, Tuschl T (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135:1201–1214PubMedGoogle Scholar
  133. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20:1470–1484PubMedGoogle Scholar
  134. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114PubMedGoogle Scholar
  135. Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS (2006) Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276–279PubMedGoogle Scholar
  136. Fitzpatrick GV, Pugacheva EM, Shin JY, Abdullaev Z, Yang Y et al (2007) Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1. Mol Cell Biol 27:2636–2647PubMedGoogle Scholar
  137. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG (2007) Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet 39:259–263PubMedGoogle Scholar
  138. Frederikse PH, Donnelly R, Partyka LM (2006) miRNA and Dicer in the mammalian lens: expression of brain-specific miRNAs in the lens. Histochem Cell Biol 126:1–8PubMedGoogle Scholar
  139. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407–415PubMedGoogle Scholar
  140. Frith MC, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13:894–897PubMedGoogle Scholar
  141. Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C et al (2006a) The abundance of short proteins in the mammalian proteome. PLoS Genet 2:e52PubMedGoogle Scholar
  142. Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J et al (2006b) Evolutionary turnover of mammalian transcription start sites. Genome Res 16:713–722PubMedGoogle Scholar
  143. Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC et al (2006) Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2:e37PubMedGoogle Scholar
  144. Gabory A, Ripoche MA, Yoshimizu T, Dandolo L (2006) The H19 gene: regulation and function of a non-coding RNA. Cytogenet Genome Res 113:188–193PubMedGoogle Scholar
  145. Gardiner DL, Holt DC, Thomas EA, Kemp DJ, Trenholme KR (2000) Inhibition of Plasmodium falciparum clag9 gene function by antisense RNA. Mol Biochem Parasitol 110:33–41PubMedGoogle Scholar
  146. Garzon R, Pichiorri F, Palumbo T, Iuliano R, Cimmino A et al (2006) MicroRNA fingerprints during human megakaryocytopoiesis. Proc Natl Acad Sci USA 103:5078–5083PubMedGoogle Scholar
  147. Gehring WJ (2005) New perspectives on eye development and the evolution of eyes and photoreceptors. J Hered 96:171–184PubMedGoogle Scholar
  148. Geirsson A, Lynch RJ, Paliwal I, Bothwell AL, Hammond GL (2003) Human trophoblast noncoding RNA suppresses CIITA promoter III activity in murine B-lymphocytes. Biochem Biophys Res Commun 301:718–724PubMedGoogle Scholar
  149. Geirsson A, Bothwell AL, Hammond GL (2004) Inhibition of alloresponse by a human trophoblast non-coding RNA suppressing class II transactivator promoter III and major histocompatibility class II expression in murine B-lymphocytes. J Heart Lung Transplant 23:1077–1081PubMedGoogle Scholar
  150. Geng X, Lavado A, Lagutin OV, Liu W, Oliver G (2007) Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns 7:252–257PubMedGoogle Scholar
  151. Ghildiyal M, Seitz H, Horwich MD, Li C, Du T et al (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077–1081PubMedGoogle Scholar
  152. Ginger MR, Gonzalez-Rimbau MF, Gay JP, Rosen JM (2001) Persistent changes in gene expression induced by estrogen and progesterone in the rat mammary gland. Mol Endocrinol 15:1993–2009PubMedGoogle Scholar
  153. Ginger MR, Shore AN, Contreras A, Rijnkels M, Miller J et al (2006) A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc Natl Acad Sci USA 103:5781–5786PubMedGoogle Scholar
  154. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM et al (2005) MicroRNAs regulate brain morphogenesis in zebrafish. Science 308:833–838PubMedGoogle Scholar
  155. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S et al (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312:75–79PubMedGoogle Scholar
  156. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP et al (2008a) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18:957–964PubMedGoogle Scholar
  157. Glazov EA, McWilliam S, Barris WC, Dalrymple BP (2008b) Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol 25:939–948PubMedGoogle Scholar
  158. Goodrich JA, Kugel JF (2006) Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 7:612–616PubMedGoogle Scholar
  159. Goodstadt L, Ponting CP (2006) Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 2:e133PubMedGoogle Scholar
  160. Graff J, Mansuy IM (2008) Epigenetic codes in cognition and behaviour. Behav Brain Res 1:70–87Google Scholar
  161. Graveley BR (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet 17:100–107PubMedGoogle Scholar
  162. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A et al (2008) The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol 10:593–601PubMedGoogle Scholar
  163. Gribnau J, Diderich K, Pruzina S, Calzolari R, Fraser P (2000) Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell 5:377–386PubMedGoogle Scholar
  164. Grimaud C, Bantignies F, Pal-Bhadra M, Ghana P, Bhadra U et al (2006) RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124:957–971PubMedGoogle Scholar
  165. Guenther MG, Jenner RG, Chevalier B, Nakamura T, Croce CM et al (2005) Global and Hox-specific roles for the MLL1 methyltransferase. Proc Natl Acad Sci USA 102:8603–8608PubMedGoogle Scholar
  166. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88PubMedGoogle Scholar
  167. Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J et al (2004) Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol 136:35–42PubMedGoogle Scholar
  168. Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R et al (2006) The complexity of the mammalian transcriptome. J Physiol 575:321–332PubMedGoogle Scholar
  169. Haddad F, Bodell PW, Qin AX, Giger JM, Baldwin KM (2003) Role of antisense RNA in coordinating cardiac myosin heavy chain gene switching. J Biol Chem 278:37132–37138PubMedGoogle Scholar
  170. Haddad F, Qin AX, Bodell PW, Jiang W, Giger JM et al (2008) Intergenic transcription and developmental regulation of cardiac myosin heavy chain genes. Am J Physiol Heart Circ Physiol 294:H29–H40PubMedGoogle Scholar
  171. Hale CJ, Stonaker JL, Gross SM, Hollick JB (2007) A novel Snf2 protein maintains trans-generational regulatory states established by paramutation in maize. PLoS Biol 5:2156–2165Google Scholar
  172. Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952PubMedGoogle Scholar
  173. Han J, Kim D, Morris KV (2007) Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci USA 104:12422–12427PubMedGoogle Scholar
  174. Hardiman KE, Brewster R, Khan SM, Deo M, Bodmer R (2002) The bereft gene, a potential target of the neural selector gene cut, contributes to bristle morphogenesis. Genetics 161:231–247PubMedGoogle Scholar
  175. Hasler J, Samuelsson T, Strub K (2007) Useful ‘junk’: Alu RNAs in the human transcriptome. Cell Mol Life Sci 64:1793–1800PubMedGoogle Scholar
  176. Hatada I, Morita S, Obata Y, Sotomaru Y, Shimoda M et al (2001) Identification of a new imprinted gene, Rian, on mouse chromosome 12 by fluorescent differential display screening. J Biochem (Tokyo) 130:187–190Google Scholar
  177. Haussecker D, Proudfoot NJ (2005) Dicer-dependent turnover of intergenic transcripts from the human beta-globin gene cluster. Mol Cell Biol 25:9724–9733PubMedGoogle Scholar
  178. He H, Wang J, Liu T, Liu XS, Li T et al (2007) Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 17:1471–1477PubMedGoogle Scholar
  179. Heard E, Disteche CM (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20:1848–1867PubMedGoogle Scholar
  180. Heasman J, Wessely O, Langland R, Craig EJ, Kessler DS (2001) Vegetal localization of maternal mRNAs is disrupted by VegT depletion. Dev Biol 240:377–386PubMedGoogle Scholar
  181. Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ (2008) MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci USA 105:2946–2950PubMedGoogle Scholar
  182. Herrera L, Ottolenghi C, Garcia-Ortiz JE, Pellegrini M, Manini F et al (2005) Mouse ovary developmental RNA and protein markers from gene expression profiling. Dev Biol 279:271–290PubMedGoogle Scholar
  183. Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A et al (2006) The expansion of the metazoan microRNA repertoire. BMC Genomics 7:25PubMedGoogle Scholar
  184. Hildebrandt M, Nellen W (1992) Differential antisense transcription from the Dictyostelium EB4 gene locus: implications on antisense-mediated regulation of mRNA stability. Cell 69:197–204PubMedGoogle Scholar
  185. Hinas A, Soderbom F (2007) Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum. Curr Genet 51:141–159PubMedGoogle Scholar
  186. Hinas A, Reimegard J, Wagner EG, Nellen W, Ambros VR et al (2007) The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. Nucleic Acids Res 35:6714–6726PubMedGoogle Scholar
  187. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G et al (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34:D590–D598PubMedGoogle Scholar
  188. Hirai H, Pang Z, Bao D, Miyazaki T, Li L et al (2005) Cbln1 is essential for synaptic integrity and plasticity in the cerebellum. Nat Neurosci 8:1534–1541PubMedGoogle Scholar
  189. Hogga I, Karch F (2002) Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. Development 129:4915–4922PubMedGoogle Scholar
  190. Hogness DS, Lipshitz HD, Beachy PA, Peattie DA, Saint RB et al (1985) Regulation and products of the Ubx domain of the bithorax complex. Cold Spring Harb Symp Quant Biol 50:181–194PubMedGoogle Scholar
  191. Holmes R, Williamson C, Peters J, Denny P, Wells C (2003) A comprehensive transcript map of the mouse Gnas imprinted complex. Genome Res 13:1410–1415PubMedGoogle Scholar
  192. Hornstein E, Mansfield JH, Yekta S, Hu JK, Harfe BD et al (2005) The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 438:671–674PubMedGoogle Scholar
  193. Houbaviy HB, Murray MF, Sharp PA (2003) Embryonic stem cell-specific microRNAs. Dev Cell 5:351–358PubMedGoogle Scholar
  194. Houseley J, Kotovic K, El Hage A, Tollervey D (2007) Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 26:4996–5006PubMedGoogle Scholar
  195. Hsieh-Li HM, Witte DP, Weinstein M, Branford W, Li H et al (1995) Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility. Development 121:1373–1385PubMedGoogle Scholar
  196. Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB et al (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8:39PubMedGoogle Scholar
  197. Iguchi N, Xu M, Hori T, Hecht NB (2007) Noncoding RNAs of the mammalian testis: the meiotic transcripts Nct1 and Nct2 encode piRNAs. Ann N Y Acad Sci 1120:84–94PubMedGoogle Scholar
  198. Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S et al (2004) Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun 322:593–600PubMedGoogle Scholar
  199. Imanishi T, Itoh T, Suzuki Y, O’Donovan C, Fukuchi S et al (2004) Integrative annotation of 21, 037 human genes validated by full-length cDNA clones. PLoS Biol 2:856–875Google Scholar
  200. Inagaki S, Numata K, Kondo T, Tomita M, Yasuda K et al (2005) Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells 10:1163–1173PubMedGoogle Scholar
  201. Inoue A, Kobayashi Y, Ishizuka M, Hirose S, Hagiwara H (2002) Identification of a novel osteoblastic gene, inducible by C-type natriuretic peptide, whose transcript might function in mineralization as a noncoding RNA. Calcif Tissue Int 70:111–116PubMedGoogle Scholar
  202. Ioudinkova E, Razin SV, Borunova V, de Conto F, Rynditch A et al (2005) RNA-dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes. J Cell Biochem 94:529–539PubMedGoogle Scholar
  203. Itoh Y, Melamed E, Yang X, Kampf K, Wang S et al (2007) Dosage compensation is less effective in birds than in mammals. J Biol 6:2PubMedGoogle Scholar
  204. Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17:405–412PubMedGoogle Scholar
  205. Jacob F (1977) Evolution and tinkering. Science 196:1161–1166PubMedGoogle Scholar
  206. Jady BE, Bertrand E, Kiss T (2004) Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body-specific localization signal. J Cell Biol 164:647–652PubMedGoogle Scholar
  207. Jeffery L, Nakielny S (2004) Components of the DNA methylation system of chromatin control are RNA-binding proteins. J Biol Chem 279:49479–49487PubMedGoogle Scholar
  208. Jenny A, Hachet O, Zavorszky P, Cyrklaff A, Weston MD et al (2006) A translation-independent role of oskar RNA in early Drosophila oogenesis. Development 133:2827–2833PubMedGoogle Scholar
  209. Jin H, Vacic V, Girke T, Lonardi S, Zhu JK (2008) Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 9:6PubMedGoogle Scholar
  210. Jin Z, Xie T (2007) Dcr-1 maintains Drosophila ovarian stem cells. Curr Biol 17:539–544PubMedGoogle Scholar
  211. Jöchl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL et al (2008) Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res 36:2677–2689PubMedGoogle Scholar
  212. Johnnidis JB, Harris MH, Wheeler RT, Stehling-Sun S, Lam MH et al (2008) Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451:1125–1129PubMedGoogle Scholar
  213. Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426:845–849PubMedGoogle Scholar
  214. Jones EA, Flavell RA (2005) Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster. J Immunol 175:7437–7446PubMedGoogle Scholar
  215. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53PubMedGoogle Scholar
  216. Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD et al (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15:1007–1014PubMedGoogle Scholar
  217. Juan V, Crain C, Wilson C (2000) Evidence for evolutionarily conserved secondary structure in the H19 tumor suppressor RNA. Nucleic Acids Res 28:1221–1227PubMedGoogle Scholar
  218. Jupe ER, Liu XT, Kiehlbauch JL, McClung JK, Dell’Orco RT (1996) The 3′ untranslated region of prohibitin and cellular immortalization. Exp Cell Res 224:128–135PubMedGoogle Scholar
  219. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL et al (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296:916–919PubMedGoogle Scholar
  220. Kapranov P, Drenkow J, Cheng J, Long J, Helt G et al (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15:987–997PubMedGoogle Scholar
  221. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R et al (2007a) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484–1488PubMedGoogle Scholar
  222. Kapranov P, Willingham AT, Gingeras TR (2007b) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413–423PubMedGoogle Scholar
  223. Karali M, Peluso I, Marigo V, Banfi S (2007) Identification and characterization of microRNAs expressed in the mouse eye. Invest Ophthalmol Vis Sci 48:509–515PubMedGoogle Scholar
  224. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M et al (2005) Antisense transcription in the mammalian transcriptome. Science 309:1564–1566PubMedGoogle Scholar
  225. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S et al (2008) Hidden layers of human small RNAs. BMC Genomics 9:157PubMedGoogle Scholar
  226. Kawamura Y, Saito K, Kin T, Ono Y, Asai K et al (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453:793–797PubMedGoogle Scholar
  227. Kim A, Zhao H, Ifrim I, Dean A (2007) Beta-globin intergenic transcription and histone acetylation dependent on an enhancer. Mol Cell Biol 27:2980–2986PubMedGoogle Scholar
  228. Kim J, Bergmann A, Wehri E, Lu X, Stubbs L (2001) Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain. Genomics 77:91–98PubMedGoogle Scholar
  229. Kim M, Patel B, Schroeder KE, Raza A, Dejong J (2008) Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10. RNA 14:1005–1011PubMedGoogle Scholar
  230. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188:107–116PubMedGoogle Scholar
  231. King N, Hittinger CT, Carroll SB (2003) Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301:361–363PubMedGoogle Scholar
  232. Kishore S, Stamm S (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311:230–232PubMedGoogle Scholar
  233. Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145–148PubMedGoogle Scholar
  234. Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S et al (2005) Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development 132:3445–3457PubMedGoogle Scholar
  235. Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP et al (2008) Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proc Natl Acad Sci USA 105:1949–1954PubMedGoogle Scholar
  236. Kohtz JD, Fishell G (2004) Developmental regulation of EVF-1, a novel non-coding RNA transcribed upstream of the mouse Dlx6 gene. Gene Expr Patterns 4:407–412PubMedGoogle Scholar
  237. Komine Y, Tanaka NK, Yano R, Takai S, Yuasa S et al (1999) A novel type of non-coding RNA expressed in the rat brain. Brain Res Mol Brain Res 66:1–13PubMedGoogle Scholar
  238. Komine Y, Nakamura K, Katsuki M, Yamamori T (2006) Novel transcription factor zfh-5 is negatively regulated by its own antisense RNA in mouse brain. Mol Cell Neurosci 31:273–283PubMedGoogle Scholar
  239. Koralov SB, Muljo SA, Galler GR, Krek A, Chakraborty T et al (2008) Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage. Cell 132:860–874PubMedGoogle Scholar
  240. Korpal M, Lee ES, Hu G, Kang Y (2008) The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J Biol Chem 283:14910–14914PubMedGoogle Scholar
  241. Kosik KS (2006) The neuronal microRNA system. Nat Rev Neurosci 7:911–920PubMedGoogle Scholar
  242. Kotlikova IV, Demakova OV, Semeshin VF, Shloma VV, Boldyreva LV et al (2006) The Drosophila dosage compensation complex binds to polytene chromosomes independently of developmental changes in transcription. Genetics 172:963–974PubMedGoogle Scholar
  243. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705PubMedGoogle Scholar
  244. Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421:948–952PubMedGoogle Scholar
  245. Kuehbacher A, Urbich C, Zeiher AM, Dimmeler S (2007) Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ Res 101:59–68PubMedGoogle Scholar
  246. Kumimoto H, Yoshida H, Okamoto K (1995) RNA polymerase II transcribes Dictyostelium untranslatable gene, dutA, specifically in the developmental phase. Biochem Biophys Res Commun 216:273–278PubMedGoogle Scholar
  247. Kumimoto H, Yoshida H, Okamoto K (1996) Expression of Dictyostelium early gene, dutA, is independent of cAMP pulses but dependent on protein kinase A. FEMS Microbiol Lett 140:121–124PubMedGoogle Scholar
  248. Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116:779–793PubMedGoogle Scholar
  249. Kyes S, Christodoulou Z, Pinches R, Newbold C (2002) Stage-specific merozoite surface protein 2 antisense transcripts in Plasmodium falciparum. Mol Biochem Parasitol 123:79–83PubMedGoogle Scholar
  250. Lai EC, Tam B, Rubin GM (2005) Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev 19:1067–1080PubMedGoogle Scholar
  251. Lakshmipathy U, Love B, Goff LA, Jornsten R, Graichen R et al (2007) MicroRNA expression pattern of undifferentiated and differentiated human embryonic stem cells. Stem Cells Dev 16:1003–1016PubMedGoogle Scholar
  252. Landers M, Bancescu DL, Le Meur E, Rougeulle C, Glatt-Deeley H et al (2004) Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res 32:3480–3492PubMedGoogle Scholar
  253. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414PubMedGoogle Scholar
  254. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J et al (1999) A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97:17–27PubMedGoogle Scholar
  255. Lanz RB, Razani B, Goldberg AD, O’Malley BW (2002) Distinct RNA motifs are important for coactivation of steroid hormone receptors by steroid receptor RNA activator (SRA). Proc Natl Acad Sci USA 99:16081–16086PubMedGoogle Scholar
  256. Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM et al (2008) Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 25:980–996PubMedGoogle Scholar
  257. Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T et al (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131:174–187PubMedGoogle Scholar
  258. Lee JT, Lu N, Han Y (1999) Genetic analysis of the mouse X inactivation center defines an 80-kb multifunction domain. Proc Natl Acad Sci USA 96:3836–3841PubMedGoogle Scholar
  259. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS et al (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125:301–313PubMedGoogle Scholar
  260. Legube G, McWeeney SK, Lercher MJ, Akhtar A (2006) X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev 20:871–883PubMedGoogle Scholar
  261. Lei EP, Corces VG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38:936–941PubMedGoogle Scholar
  262. Leighton PA, Ingram RS, Eggenschwiler J, Efstratiadis A, Tilghman SM (1995) Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375:34–39PubMedGoogle Scholar
  263. Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918–1922PubMedGoogle Scholar
  264. Lempradl A, Ringrose L (2008) How does noncoding transcription regulate Hox genes? Bioessays 30:110–121PubMedGoogle Scholar
  265. Lepère G, Bétermier M, Meyer E, Duharcourt S (2008) Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev 22:1501–1512PubMedGoogle Scholar
  266. Lestrade L, Weber MJ (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34:D158–D162PubMedGoogle Scholar
  267. Levine M, Davidson EH (2005) Gene regulatory networks for development. Proc Natl Acad Sci USA 102:4936–4942PubMedGoogle Scholar
  268. Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P et al (2004) Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav Brain Res 154:273–289PubMedCrossRefGoogle Scholar
  269. Lewis A, Mitsuya K, Umlauf D, Smith P, Dean W et al (2004) Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet 36:1291–1295PubMedGoogle Scholar
  270. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565–570PubMedGoogle Scholar
  271. Leygue E (2007) Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer. Nucl Recept Signal 5:e006PubMedGoogle Scholar
  272. Li T, Vu TH, Lee KO, Yang Y, Nguyen CV et al (2002) An imprinted PEG1/MEST antisense expressed predominantly in human testis and in mature spermatozoa. J Biol Chem 277:13518–13527PubMedGoogle Scholar
  273. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB et al (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–819PubMedGoogle Scholar
  274. Lipovich L, Vanisri RR, Kong SL, Lin CY, Liu ET (2006) Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. J Mol Evol 62:73–88PubMedGoogle Scholar
  275. Lipshitz HD, Peattie DA, Hogness DS (1987) Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev 1:307–322PubMedGoogle Scholar
  276. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536PubMedGoogle Scholar
  277. Liu AY, Torchia BS, Migeon BR, Siliciano RF (1997a) The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4 + T cells. Genomics 39:171–184PubMedGoogle Scholar
  278. Liu JK, Ghattas I, Liu S, Chen S, Rubenstein JL (1997b) Dlx genes encode DNA-binding proteins that are expressed in an overlapping and sequential pattern during basal ganglia differentiation. Dev Dyn 210:498–512PubMedGoogle Scholar
  279. Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF et al (2007) RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev 21:1530–1545PubMedGoogle Scholar
  280. Louro R, Nakaya HI, Amaral PP, Festa F, Sogayar MC et al (2007) Androgen responsive intronic non-coding RNAs. BMC Biol 5:4PubMedGoogle Scholar
  281. Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K et al (2008) Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci USA 105:4951–4956PubMedGoogle Scholar
  282. Lunyak VV, Prefontaine GG, Nunez E, Cramer T, Ju BG et al (2007) Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317:248–251PubMedGoogle Scholar
  283. Luther HP, Haase H, Hohaus A, Beckmann G, Reich J et al (1998) Characterization of naturally occurring myosin heavy chain antisense mRNA in rat heart. J Cell Biochem 70:110–120PubMedGoogle Scholar
  284. Lyle R, Watanabe D, te Vruchte D, Lerchner W, Smrzka OW et al (2000) The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat Genet 25:19–21PubMedGoogle Scholar
  285. Madamanchi NR, Hu ZY, Li F, Horaist C, Moon SK et al (2002) A noncoding RNA regulates human protease-activated receptor-1 gene during embryogenesis. Biochim Biophys Acta 1576:237–245PubMedGoogle Scholar
  286. Maeda M, Sakamoto H, Iranfar N, Fuller D, Maruo T et al (2003) Changing patterns of gene expression in dictyostelium prestalk cell subtypes recognized by in situ hybridization with genes from microarray analyses. Eukaryot Cell 2:627–637PubMedGoogle Scholar
  287. Mager J, Montgomery ND, de Villena FP, Magnuson T (2003) Genome imprinting regulated by the mouse Polycomb group protein Eed. Nat Genet 33:502–507PubMedGoogle Scholar
  288. Makeyev EV, Maniatis T (2008) MicroRNAs target global regulators of transcription and alternative splicing. Science 319:1789–1790PubMedGoogle Scholar
  289. Makrinou E, Fox M, Lovett M, Haworth K, Cameron JM et al (2001) Tty2: a multicopy y-linked gene family. Genome Res 11:935–945PubMedGoogle Scholar
  290. Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F et al (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet 38:1151–1158PubMedGoogle Scholar
  291. Manji SS, Sorensen BS, Klockars T, Lam T, Hutchison W et al (2006) Molecular characterization and expression of maternally expressed gene 3 (Meg3/Gtl2) RNA in the mouse inner ear. J Neurosci Res 83:181–190PubMedGoogle Scholar
  292. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J et al (2004) MicroRNA-responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet 36:1079–1083PubMedGoogle Scholar
  293. Maraia RJ, Driscoll CT, Bilyeu T, Hsu K, Darlington GJ (1993) Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol 13:4233–4241PubMedGoogle Scholar
  294. Margueron R, Trojer P, Reinberg D (2005) The key to development: interpreting the histone code? Curr Opin Genet Dev 15:163–176PubMedGoogle Scholar
  295. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD et al (2008) Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 29:499–509PubMedGoogle Scholar
  296. Martello G, Zacchigna L, Inui M, Montagner M, Adorno M et al (2007) MicroRNA control of Nodal signalling. Nature 449:183–188PubMedGoogle Scholar
  297. 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 445:666–670PubMedGoogle Scholar
  298. Martinez AM, Cavalli G (2006) The role of polycomb group proteins in cell cycle regulation during development. Cell Cycle 5:1189–1197PubMedGoogle Scholar
  299. Mattick JS (1994) Introns: evolution and function. Curr Opin Genet Dev 4:823–831PubMedGoogle Scholar
  300. Mattick JS (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2:986–991PubMedGoogle Scholar
  301. Mattick JS (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25:930–939PubMedGoogle Scholar
  302. Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5:316–323PubMedGoogle Scholar
  303. Mattick JS (2007) A new paradigm for developmental biology. J Exp Biol 210:1526–1547PubMedGoogle Scholar
  304. Mattick JS, Gagen MJ (2001) The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 18:1611–1630PubMedGoogle Scholar
  305. Mattick JS, Gagen MJ (2005) Accelerating networks. Science 307:856–858PubMedGoogle Scholar
  306. Mattick JS, Makunin IV (2005) Small regulatory RNAs in mammals. Hum Mol Genet 14:R121–R132PubMedGoogle Scholar
  307. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15:R17–R29PubMedGoogle Scholar
  308. Mattick JS, Mehler MF (2008) RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci 31:227–233PubMedGoogle Scholar
  309. Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (2006) Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 22:351–361PubMedGoogle Scholar
  310. Mazumder B, Seshadri V, Fox PL (2003) Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 28:91–98PubMedGoogle Scholar
  311. Meehan RR, Kao CF, Pennings S (2003) HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain. EMBO J 22:3164–3174PubMedGoogle Scholar
  312. Megosh HB, Cox DN, Campbell C, Lin H (2006) The role of PIWI and the miRNA machinery in Drosophila germline determination. Curr Biol 16:1884–1894PubMedGoogle Scholar
  313. Mehler MF, Mattick JS (2006) Non-coding RNAs in the nervous system. J Physiol 575:333–341PubMedGoogle Scholar
  314. Mehler MF, Mattick JS (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 87:799–823PubMedGoogle Scholar
  315. Meins F Jr, Si-Ammour A, Blevins T (2005) RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol 21:297–318PubMedGoogle Scholar
  316. Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biol 8:R202PubMedGoogle Scholar
  317. 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 USA 105:716–712PubMedGoogle Scholar
  318. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M et al (2004) Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 22:1006–1011PubMedGoogle Scholar
  319. Michel U, Kallmann B, Rieckmann P, Isbrandt D (2002) UM 9(5)h and UM 9(5)p, human and porcine noncoding transcripts with preferential expression in the cerebellum. RNA 8:153–547Google Scholar
  320. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560PubMedGoogle Scholar
  321. Militello KT, Patel V, Chessler AD, Fisher JK, Kasper JM et al (2005) RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. RNA 11:365–370PubMedGoogle Scholar
  322. Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS et al (2000) Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum Mol Genet 9:1415–1423PubMedGoogle Scholar
  323. Mineno J, Okamoto S, Ando T, Sato M, Chono H et al (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Res 34:1765–1771PubMedGoogle Scholar
  324. Miska EA, Alvarez-Saavedra E, Abbott AL, Lau NC, Hellman AB et al (2007) Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3:e215PubMedGoogle Scholar
  325. Miyoshi N, Wagatsuma H, Wakana S, Shiroishi T, Nomura M et al (2000) Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q. Genes Cells 5:211–220PubMedGoogle Scholar
  326. Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T et al (2008) Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 28:3713–3728PubMedGoogle Scholar
  327. Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447:1126–1129PubMedGoogle Scholar
  328. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V et al (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18:571–584PubMedGoogle Scholar
  329. Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289–1292PubMedGoogle Scholar
  330. Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP et al (2008) Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Res 18:281–292PubMedGoogle Scholar
  331. Muchardt C, Guillemé M, Seeler J, Trouche D, Dejean A et al (2002) Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1. EMBO Rep 3:975–981PubMedGoogle Scholar
  332. Munroe SH, Lazar MA (1991) Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem 266:22083–22086PubMedGoogle Scholar
  333. Murakami H, Goto DB, Toda T, Chen ES, Grewal SI et al (2007a) Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS ONE 2:e317PubMedGoogle Scholar
  334. Murakami K, Oshimura M, Kugoh H (2007b) Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 52:926–933PubMedGoogle Scholar
  335. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ et al (2007) Critical roles for Dicer in the female germline. Genes Dev 21:682–693PubMedGoogle Scholar
  336. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D et al (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349PubMedGoogle Scholar
  337. Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R et al (2006) The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation. Nat Cell Biol 8:278–284PubMedGoogle Scholar
  338. Nakabayashi K, Bentley L, Hitchins MP, Mitsuya K, Meguro M et al (2002) Identification and characterization of an imprinted antisense RNA (MESTIT1) in the human MEST locus on chromosome 7q32. Hum Mol Genet 11:1743–1756PubMedGoogle Scholar
  339. Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA et al (2007) Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 8:R43PubMedGoogle Scholar
  340. Navarro P, Page DR, Avner P, Rougeulle C (2006) Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes Dev 20:2787–2792PubMedGoogle Scholar
  341. Nguyen VT, Kiss T, Michels AA, Bensaude O (2001) 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414:322–325PubMedGoogle Scholar
  342. Nickerson J (2001) Experimental observations of a nuclear matrix. J Cell Sci 114:463–474PubMedGoogle Scholar
  343. Nicolas E, Yamada T, Cam HP, Fitzgerald PC, Kobayashi R et al (2007) Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat Struct Mol Biol 14:372–380PubMedGoogle Scholar
  344. Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM (2004) Megabase deletions of gene deserts result in viable mice. Nature 431:988–993PubMedGoogle Scholar
  345. Noonan FC, Goodfellow PJ, Staloch LJ, Mutch DG, Simon TC (2003) Antisense transcripts at the EMX2 locus in human and mouse. Genomics 81:58–66PubMedGoogle Scholar
  346. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG et al (2007) RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451:153–158PubMedGoogle Scholar
  347. Numata K, Kanai A, Saito R, Kondo S, Adachi J et al (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res 13:1301–1306PubMedGoogle Scholar
  348. O’Rourke JR, Georges SA, Seay HR, Tapscott SJ, McManus MT et al (2007) Essential role for Dicer during skeletal muscle development. Dev Biol 311:359–368PubMedGoogle Scholar
  349. Ogawa Y, Lee JT (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 11:731–743PubMedGoogle Scholar
  350. Ogawa Y, Sun BK, Lee JT (2008) Intersection of the RNA interference and X-inactivation pathways. Science 320:1336–1341PubMedGoogle Scholar
  351. Okafuji T, Abe F, Maeda Y (1997) Antisense-mediated regulation of Annexin VII gene expression during the transition from growth to differentiation in Dictyostelium discoideum. Gene 189:49–56PubMedGoogle Scholar
  352. Okamura K, Chung WJ, Ruby JG, Guo H, Bartel DP et al (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453:803–806PubMedGoogle Scholar
  353. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H et al (2002) Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature 420:563–573PubMedGoogle Scholar
  354. Ooi L, Wood IC (2007) Chromatin crosstalk in development and disease: lessons from REST. Nat Rev Genet 8:544–554PubMedGoogle Scholar
  355. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T et al (2004) Complete sequencing and characterization of 21, 243 full-length human cDNAs. Nat Genet 36:40–45PubMedGoogle Scholar
  356. Pagano A, Castelnuovo M, Tortelli F, Ferrari R, Dieci G et al (2007) New small nuclear RNA gene-like transcriptional units as sources of regulatory transcripts. PLoS Genet 3:e1PubMedGoogle Scholar
  357. Pandorf CE, Haddad F, Roy RR, Qin AX, Edgerton VR et al (2006) Dynamics of myosin heavy chain gene regulation in slow skeletal muscle: role of natural antisense RNA. J Biol Chem 281:38330–38342PubMedGoogle Scholar
  358. Pang KC, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22:1–5PubMedGoogle Scholar
  359. Pang KC, Stephen S, Dinger ME, Engstrom PG, Lenhard B et al (2007) RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 35:D178–D182PubMedGoogle Scholar
  360. Park JK, Liu X, Strauss TJ, McKearin DM, Liu Q (2007) The miRNA pathway intrinsically controls self-renewal of Drosophila germline stem cells. Curr Biol 17:533–538PubMedGoogle Scholar
  361. Park Y, Oh H, Meller VH, Kuroda MI (2005) Variable splicing of non-coding roX2 RNAs influences targeting of MSL dosage compensation complexes in Drosophila. RNA Biol 2:157–164PubMedGoogle Scholar
  362. Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF (2001) Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol Biol Cell 12:3114–3125PubMedGoogle Scholar
  363. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA et al (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444:499–502PubMedGoogle Scholar
  364. Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996) Requirement for Xist in X chromosome inactivation. Nature 379:131–137PubMedGoogle Scholar
  365. Perez DS, Hoage TR, Pritchett JR, Ducharme-Smith AL, Halling ML et al (2008) Long, abundantly-expressed non-coding transcripts are altered in cancer. Hum Mol Genet 17:642–655PubMedGoogle Scholar
  366. Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F et al (2006) Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 127:1209–1221PubMedGoogle Scholar
  367. Peyman JA (1999) Repression of major histocompatibility complex genes by a human trophoblast ribonucleic acid. Biol Reprod 60:23–31PubMedGoogle Scholar
  368. Pheasant M, Mattick JS (2007) Raising the estimate of functional human sequences. Genome Res 17:1245–1253PubMedGoogle Scholar
  369. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA et al (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135PubMedGoogle Scholar
  370. Plath K, Talbot D, Hamer KM, Otte AP, Yang TP et al (2004) Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosome. J Cell Biol 167:1025–1035PubMedGoogle Scholar
  371. Poirier F, Chan CT, Timmons PM, Robertson EJ, Evans MJ et al (1991) The murine H19 gene is activated during embryonic stem cell differentiation in vitro and at the time of implantation in the developing embryo. Development 113:1105–1114PubMedGoogle Scholar
  372. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S et al (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167–172PubMedGoogle Scholar
  373. Ponjavic J, Ponting CP, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17:556–565PubMedGoogle Scholar
  374. Potter SS, Branford WW (1998) Evolutionary conservation and tissue-specific processing of Hoxa 11 antisense transcripts. Mamm Genome 9:799–806PubMedGoogle Scholar
  375. Potts JD, Vincent EB, Runyan RB, Weeks DL (1992) Sense and antisense TGF beta 3 mRNA levels correlate with cardiac valve induction. Dev Dyn 193:340–345PubMedGoogle Scholar
  376. Prabhakar S, Noonan JP, Paabo S, Rubin EM (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314:786PubMedGoogle Scholar
  377. Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum. Genes Dev 21:11–42PubMedGoogle Scholar
  378. Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM et al (2005) Regulating gene expression through RNA nuclear retention. Cell 123:249–263PubMedGoogle Scholar
  379. Prochnik SE, Rokhsar DS, Aboobaker AA (2007) Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol 217:73–77PubMedGoogle Scholar
  380. Prud’homme B, Gompel N, Carroll SB (2007) Emerging principles of regulatory evolution. Proc Natl Acad Sci USA 104(Suppl 1):8605-8612Google Scholar
  381. Pruunsild P, Kazantseva A, Aid T, Palm K, Timmusk T (2007) Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. Genomics 90:397–406PubMedGoogle Scholar
  382. Qiu GF, Weber GM, Rexroad CE 3rd, Yao J (2008) Identification of RtGST-1, a novel germ cell-specific mRNA-like transcript predominantly expressed in early previtellogenic oocytes in rainbow trout (Oncorhynchus mykiss). Mol Reprod Dev 75:723–730PubMedGoogle Scholar
  383. Rank G, Prestel M, Paro R (2002) Transcription through intergenic chromosomal memory elements of the Drosophila bithorax complex correlates with an epigenetic switch. Mol Cell Biol 22:8026–8034PubMedGoogle Scholar
  384. Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I et al (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441:469–474PubMedGoogle Scholar
  385. Rastinejad F, Blau HM (1993) Genetic complementation reveals a novel regulatory role for 3′ untranslated regions in growth and differentiation. Cell 72:903–917PubMedGoogle Scholar
  386. Rastinejad F, Conboy MJ, Rando TA, Blau HM (1993) Tumor suppression by RNA from the 3′ untranslated region of alpha-tropomyosin. Cell 75:1107–1117PubMedGoogle Scholar
  387. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M et al (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16:11–19PubMedGoogle Scholar
  388. Razin SV, Rynditch A, Borunova V, Ioudinkova E, Smalko V et al (2004) The 33 kb transcript of the chicken alpha-globin gene domain is part of the nuclear matrix. J Cell Biochem 92:445–457PubMedGoogle Scholar
  389. Reik W, Lewis A (2005) Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet 6:403–410PubMedGoogle Scholar
  390. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906PubMedGoogle Scholar
  391. Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart AV et al (2004) Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene 23:6684–6692PubMedGoogle Scholar
  392. Reis EM, Ojopi EP, Alberto FL, Rahal P, Tsukumo F et al (2005) Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer. Cancer Res 65:1693–1699PubMedGoogle Scholar
  393. Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38:413–443PubMedGoogle Scholar
  394. Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134:223–232PubMedGoogle Scholar
  395. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM et al (2003) The transcriptional activity of human chromosome 22. Genes Dev 17:529–540PubMedGoogle Scholar
  396. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323PubMedGoogle Scholar
  397. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14:1902–1910PubMedGoogle Scholar
  398. Rogan DF, Cousins DJ, Santangelo S, Ioannou PA, Antoniou M et al (2004) Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster. Proc Natl Acad Sci USA 101:2446–2451PubMedGoogle Scholar
  399. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC (2005) The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev 19:2947–2952PubMedGoogle Scholar
  400. Royo H, Cavaille J (2008) Non-coding RNAs in imprinted gene clusters. Biol Cell 100:149–166PubMedGoogle Scholar
  401. Royo H, Basyuk E, Marty V, Marques M, Bertrand E et al (2007) Bsr, a nuclear-retained RNA with monoallelic expression. Mol Biol Cell 18:2817–2827PubMedGoogle Scholar
  402. Ruby JG, Jan C, Player C, Axtell MJ, Lee W et al (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207PubMedGoogle Scholar
  403. Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B et al (2001) The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 10:2687–2700PubMedGoogle Scholar
  404. Ryan DG, Oliveira-Fernandes M, Lavker RM (2006) MicroRNAs of the mammalian eye display distinct and overlapping tissue specificity. Mol Vis 12:1175–1184PubMedGoogle Scholar
  405. Sado T, Wang Z, Sasaki H, Li E (2001) Regulation of imprinted X-chromosome inactivation in mice by Tsix. Development 128:1275–1286PubMedGoogle Scholar
  406. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ et al (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20:508–512PubMedGoogle Scholar
  407. Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU et al (2008) Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet 40:719–721PubMedGoogle Scholar
  408. Sanchez-Elsner T, Gou D, Kremmer E, Sauer F (2006) Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311:1118–1123PubMedGoogle Scholar
  409. Sanchez-Herrero E, Akam M (1989) Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 107:321–329PubMedGoogle Scholar
  410. Sarin S, O’Meara MM, Flowers EB, Antonio C, Poole RJ et al (2007) Genetic screens for Caenorhabditis elegans mutants defective in left/right asymmetric neuronal fate specification. Genetics 176:2109–2130PubMedGoogle Scholar
  411. Sasaki H, Matsui Y (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 9:129–140PubMedGoogle Scholar
  412. Sasaki YT, Sano M, Ideue T, Kin T, Asai K et al (2007a) Identification and characterization of human non-coding RNAs with tissue-specific expression. Biochem Biophys Res Commun 357:991–996PubMedGoogle Scholar
  413. Sasaki YT, Sano M, Kin T, Asai K, Hirose T (2007b) Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem Biophys Res Commun 357:724–730PubMedGoogle Scholar
  414. Satterlee JS, Barbee S, Jin P, Krichevsky A, Salama S et al (2007) Noncoding RNAs in the brain. J Neurosci 27:11856–11859PubMedGoogle Scholar
  415. Sauman I, Reppert SM (1996) Circadian clock neurons in the silkmoth Antheraea pernyi: novel mechanisms of Period protein regulation. Neuron 17:889–900PubMedGoogle Scholar
  416. Sawata M, Yoshino D, Takeuchi H, Kamikouchi A, Ohashi K et al (2002) Identification and punctate nuclear localization of a novel noncoding RNA, Ks-1, from the honeybee brain. RNA 8:772–785PubMedGoogle Scholar
  417. Sawata M, Takeuchi H, Kubo T (2004) Identification and analysis of the minimal promoter activity of a novel noncoding nuclear RNA gene, AncR-1, from the honeybee (Apis mellifera L.). RNA 10:1047–1058PubMedGoogle Scholar
  418. Scalbert E, Bril A (2008) Implication of microRNAs in the cardiovascular system. Curr Opin Pharmacol 8:181–188PubMedGoogle Scholar
  419. Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L et al (2004) A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 5:R73PubMedGoogle Scholar
  420. Schmitt S, Prestel M, Paro R (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19:697–708PubMedGoogle Scholar
  421. Schoeftner S, Blasco MA (2008) Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 10:228–236PubMedGoogle Scholar
  422. Schoenfelder S, Smits G, Fraser P, Reik W, Paro R (2007) Non-coding transcripts in the H19 imprinting control region mediate gene silencing in transgenic Drosophila. EMBO Rep 8:1068–1073PubMedGoogle Scholar
  423. Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME et al (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439:283–289PubMedGoogle Scholar
  424. Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128:735–745PubMedGoogle Scholar
  425. Schuster-Gossler K, Bilinski P, Sado T, Ferguson-Smith A, Gossler A (1998) The mouse Gtl2 gene is differentially expressed during embryonic development, encodes multiple alternatively spliced transcripts, and may act as an RNA. Dev Dyn 212:214–228PubMedGoogle Scholar
  426. Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP et al (2008) Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 15:842–848Google Scholar
  427. Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8:9–22PubMedGoogle Scholar
  428. Schwartz YB, Pirrotta V (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20:266–273PubMedGoogle Scholar
  429. Seim I, Collet C, Herington AC, Chopin LK (2007) Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts. BMC Genomics 8:298PubMedGoogle Scholar
  430. Seki M, Satou M, Sakurai T, Akiyama K, Iida K et al (2004) RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. J Exp Bot 55:213–223PubMedGoogle Scholar
  431. Sempere LF, Cole CN, McPeek MA, Peterson KJ (2006) The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol 306:575–588PubMedGoogle Scholar
  432. Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G et al (2007) Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 13:223–239PubMedGoogle Scholar
  433. Shaikh TH, Roy AM, Kim J, Batzer MA, Deininger PL (1997) cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J Mol Biol 271:222–234PubMedGoogle Scholar
  434. Shimada N, Kawata T (2007) Evidence that noncoding RNA dutA is a multicopy suppressor of Dictyostelium discoideum STAT protein Dd-STATa. Eukaryot Cell 6:1030–1040PubMedGoogle Scholar
  435. Shippy TD, Ronshaugen M, Cande J, He J, Beeman RW et al (2008) Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Dev Genes Evol 218:127–139PubMedGoogle Scholar
  436. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C et al (2005) A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6 J mouse tissues and cells. Proc Natl Acad Sci USA 102:18485–18490PubMedGoogle Scholar
  437. Singh SK, Kagalwala MN, Parker-Thornburg J, Adams H, Majumder S (2008) REST maintains self-renewal and pluripotency of embryonic stem cells. Nature 453:223–227PubMedGoogle Scholar
  438. Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F et al (2008) MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 15:259–267PubMedGoogle Scholar
  439. Skeiky YA, Iatrou K (1990) Silkmoth chorion antisense RNA. Structural characterization, developmental regulation and evolutionary conservation. J Mol Biol 213:53–66PubMedGoogle Scholar
  440. Skryabin BV, Kremerskothen J, Vassilacopoulou D, Disotell TR, Kapitonov VV et al (1998) The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). J Mol Evol 47:677–685PubMedGoogle Scholar
  441. Sleutels F, Zwart R, Barlow DP (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415:810–813PubMedGoogle Scholar
  442. Smilinich NJ, Day CD, Fitzpatrick GV, Caldwell GM, Lossie AC et al (1999) A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci USA 96:8064–8069PubMedGoogle Scholar
  443. Smit M, Segers K, Carrascosa LG, Shay T, Baraldi F et al (2003) Mosaicism of Solid Gold supports the causality of a noncoding A-to-G transition in the determinism of the callipyge phenotype. Genetics 163:453–456PubMedGoogle Scholar
  444. Smith NG, Brandstrom M, Ellegren H (2004) Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics 84:806–813PubMedGoogle Scholar
  445. Sone M, Hayashi T, Tarui H, Agata K, Takeichi M et al (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120:2498–2506PubMedGoogle Scholar
  446. Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila microRNA targets. PLoS Biol 1:E60PubMedGoogle Scholar
  447. Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E et al (2007) Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 17:1865–1879PubMedGoogle Scholar
  448. Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E et al (2008) A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev 22:8–13PubMedGoogle Scholar
  449. Stefani G, Slack FJ (2008) Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 9:219–230PubMedGoogle Scholar
  450. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR et al (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1:E45PubMedGoogle Scholar
  451. Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF et al (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306:655–660PubMedGoogle Scholar
  452. Stuckenholz C, Meller VH, Kuroda MI (2003) Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster. Genetics 164:1003–1014PubMedGoogle Scholar
  453. Su XZ, Heatwole VM, Wertheimer SP, Guinet F, Herrfeldt JA et al (1995) The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82:89–100PubMedGoogle Scholar
  454. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, epub ahead of printGoogle Scholar
  455. Sun BK, Deaton AM, Lee JT (2006) A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 21:617–628PubMedGoogle Scholar
  456. Swalla BJ, Jeffery WR (1995) A maternal RNA localized in the yellow crescent is segregated to the larval muscle cells during ascidian development. Dev Biol 170:353–364PubMedGoogle Scholar
  457. Swalla BJ, Jeffery WR (1996) PCNA mRNA has a 3′UTR antisense to yellow crescent RNA and is localized in ascidian eggs and embryos. Dev Biol 178:23–34PubMedGoogle Scholar
  458. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2005) A new frontier for molecular medicine: noncoding RNAs. Biochim Biophys Acta 1756:65–75PubMedGoogle Scholar
  459. Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29:288–299PubMedGoogle Scholar
  460. Takeda K, Ichijo H, Fujii M, Mochida Y, Saitoh M et al (1998) Identification of a novel bone morphogenetic protein-responsive gene that may function as a noncoding RNA. J Biol Chem 273:17079–17085PubMedGoogle Scholar
  461. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP et al (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534–538PubMedGoogle Scholar
  462. Tanaka R, Satoh H, Moriyama M, Satoh K, Morishita Y et al (2000) Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma. Genes Cells 5:277–287PubMedGoogle Scholar
  463. Tang F, Kaneda M, O’Carroll D, Hajkova P, Barton SC et al (2007) Maternal microRNAs are essential for mouse zygotic development. Genes Dev 21:644–648PubMedGoogle Scholar
  464. Taniura H, Sng JC, Yoneda Y (2007) Histone modifications in the brain. Neurochem Int 51:85–91PubMedGoogle Scholar
  465. Tay YM, Tam WL, Ang YS, Gaughwin PM, Yang H et al (2008) MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells 26:17–29PubMedGoogle Scholar
  466. Taylor HM, Kyes SA, Harris D, Kriek N, Newbold CI (2000) A study of var gene transcription in vitro using universal var gene primers. Mol Biochem Parasitol 105:13–23PubMedGoogle Scholar
  467. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y et al (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2:e30PubMedGoogle Scholar
  468. Teodorovic S, Walls CD, Elmendorf HG (2007) Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res 35:2544–2553PubMedGoogle Scholar
  469. Teranishi M, Shimada Y, Hori T, Nakabayashi O, Kikuchi T et al (2001) Transcripts of the MHM region on the chicken Z chromosome accumulate as non-coding RNA in the nucleus of female cells adjacent to the DMRT1 locus. Chromosome Res 9:147–165PubMedGoogle Scholar
  470. Thakur N, Tiwari VK, Thomassin H, Pandey RR, Kanduri M et al (2004) An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol 24:7855–7862PubMedGoogle Scholar
  471. Thompson DM, Parker R (2007) Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol Cell Biol 27:92–101PubMedGoogle Scholar
  472. Thrash-Bingham CA, Tartof KD (1999) aHIF: a natural antisense transcript overexpressed in human renal cancer and during hypoxia. J Natl Cancer Inst 91:143–151PubMedGoogle Scholar
  473. Tierling S, Dalbert S, Schoppenhorst S, Tsai CE, Oliger S et al (2006) High-resolution map and imprinting analysis of the Gtl2-Dnchc1 domain on mouse chromosome 12. Genomics 87:225–235PubMedGoogle Scholar
  474. Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J (2006) Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res 16:885–889PubMedGoogle Scholar
  475. Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C et al (2008) Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res 18:242–251PubMedGoogle Scholar
  476. Trang le TD, Sehadova H, Ichihara N, Iwai S, Mita K et al (2006) Casein kinases I of the silkworm, Bombyx mori: their possible roles in circadian timing and developmental determination. J Biol Rhythms 21:335-349Google Scholar
  477. Tresaugues L, Dehe PM, Guerois R, Rodriguez-Gil A, Varlet I et al (2006) Structural characterization of Set1 RNA recognition motifs and their role in histone H3 lysine 4 methylation. J Mol Biol 359:1170–1181PubMedGoogle Scholar
  478. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP et al (2004) An abundance of bidirectional promoters in the human genome. Genome Res 14:62–66PubMedGoogle Scholar
  479. Tsutsumi M, Itoh M (2007) Novel transcript nort is a downstream target gene of the Notch signaling pathway in zebrafish. Gene Expr Patterns 7:227–232PubMedGoogle Scholar
  480. 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 34:157–165PubMedGoogle Scholar
  481. Tupy JL, Bailey AM, Dailey G, Evans-Holm M, Siebel CW et al (2005) Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci USA 102:5495–5500PubMedGoogle Scholar
  482. Tyler DM, Okamura K, Chung WJ, Hagen JW, Berezikov E et al (2008) Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev 22:26–36PubMedGoogle Scholar
  483. Uchida T, Rossignol F, Matthay MA, Mounier R, Couette S et al (2004) Prolonged hypoxia differentially regulates hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha expression in lung epithelial cells: implication of natural antisense HIF-1alpha. J Biol Chem 279:14871–14878PubMedGoogle Scholar
  484. Uhler JP, Hertel C, Svejstrup JQ (2007) A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci USA 104:8011–8016PubMedGoogle Scholar
  485. Ullu E, Lujan HD, Tschudi C (2005) Small sense and antisense RNAs derived from a telomeric retroposon family in Giardia intestinalis. Eukaryot Cell 4:1155–1157PubMedGoogle Scholar
  486. Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A et al (2004) Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36:1296–1300PubMedGoogle Scholar
  487. Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R et al (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129:1543–1552PubMedGoogle Scholar
  488. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C et al (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832–836PubMedGoogle Scholar
  489. van Noort V, Huynen MA (2006) Combinatorial gene regulation in Plasmodium falciparum. Trends Genet 22:73–78PubMedGoogle Scholar
  490. Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S (2008) Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell 29:313–323PubMedGoogle Scholar
  491. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771PubMedGoogle Scholar
  492. Velleca MA, Wallace MC, Merlie JP (1994) A novel synapse-associated noncoding RNA. Mol Cell Biol 14:7095–7104PubMedGoogle Scholar
  493. Ventura A, Young AG, Winslow MM, Lintault L, Meissner A et al (2008) Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132:875–886PubMedGoogle Scholar
  494. Visvanathan J, Lee S, Lee B, Lee JW, Lee SK (2007) The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 21:744–749PubMedGoogle Scholar
  495. Vogels A, Fryns JP (2002) The Prader-Willi syndrome and the Angelman syndrome. Genet Couns 13:385–396PubMedGoogle Scholar
  496. von Allmen N, Bienz M, Hemphill A, Muller N (2005) Quantitative assessment of sense and antisense transcripts from genes involved in antigenic variation (vsp genes) and encystation (cwp 1 gene) of Giardia lamblia clone GS/M-83-H7. Parasitology 130:389–396Google Scholar
  497. Wagner LA, Christensen CJ, Dunn DM, Spangrude GJ, Georgelas A et al (2007) EGO, a novel, non-coding RNA gene, regulates eosinophil granule protein transcript expression. BloodGoogle Scholar
  498. Wang G, Reinke V (2008) A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol 18:861–867PubMedGoogle Scholar
  499. Wang H, Iacoangeli A, Popp S, Muslimov IA, Imataka H et al (2002) Dendritic BC1 RNA: functional role in regulation of translation initiation. J Neurosci 22:10232–10241PubMedGoogle Scholar
  500. Wang H, Iacoangeli A, Lin D, Williams K, Denman RB et al (2005) Dendritic BC1 RNA in translational control mechanisms. J Cell Biol 171:811–821PubMedGoogle Scholar
  501. Wang X, Arai S, Song X, Reichart D, Du K et al (2008a) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454:126–130PubMedGoogle Scholar
  502. Wang F, Li X, Xie X, Zhao L, Chen W (2008b) UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. FEBS Letters 582:1919–1927Google Scholar
  503. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP et al (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175–183PubMedGoogle Scholar
  504. Watanabe T, Miyashita K, Saito TT, Yoneki T, Kakihara Y et al (2001) Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Nucleic Acids Res 29:2327–2337PubMedGoogle Scholar
  505. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S et al (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–543PubMedGoogle Scholar
  506. Watanabe Y, Yamamoto M (1994) S. pombe mei2 + encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78:487–498PubMedGoogle Scholar
  507. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562PubMedGoogle Scholar
  508. Watson JB, Sutcliffe JG (1987) Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol Cell Biol 7:3324–3327PubMedGoogle Scholar
  509. Werner A (2005) Natural antisense transcripts. RNA Biol 2:53–62PubMedGoogle Scholar
  510. Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579:5911–5922PubMedGoogle Scholar
  511. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG et al (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309:1570–1573PubMedGoogle Scholar
  512. Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8:206–216PubMedGoogle Scholar
  513. Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30:167–174PubMedGoogle Scholar
  514. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME et al (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737PubMedGoogle Scholar
  515. Xiao C, Calado DP, Galler G, Thai TH, Patterson HC et al (2007) MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 131:146–159PubMedGoogle Scholar
  516. Xie J, Zhang M, Zhou T, Hua X, Tang L et al (2007) Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res 35:D183–D187PubMedGoogle Scholar
  517. Xu S, Witmer PD, Lumayag S, Kovacs B, Valle D (2007) MicroRNA (miRNA) transcriptome of mouse retina and identification of a sensory organ-specific miRNA cluster. J Biol Chem 282:25053–25066PubMedGoogle Scholar
  518. Yamada K, Lim J, Dale JM, Chen H, Shinn P et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846PubMedGoogle Scholar
  519. Yan MD, Hong CC, Lai GM, Cheng AL, Lin YW et al (2005) Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 14:1465–1474PubMedGoogle Scholar
  520. Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB et al (2006) snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res 34:5112–5123PubMedGoogle Scholar
  521. Yang Y, Li Z, Fan Q, Long M, Zhang W (2007) Significant divergence of sex-related non-coding RNA expression patterns among closely related species in Drosophila. Chinese Sci Bull 52:748–754Google Scholar
  522. Yao MC (2008) Molecular biology. RNA rules. Nature 451:131–132Google Scholar
  523. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594–596PubMedGoogle Scholar
  524. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O et al (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechol 21:379–386Google Scholar
  525. Yi R, Poy MN, Stoffel M, Fuchs E (2008) A skin microRNA promotes differentiation by repressing ‘stemness’. Nature 452:225–229PubMedGoogle Scholar
  526. Yoshida H, Kumimoto H, Okamoto K (1994) dutA RNA functions as an untranslatable RNA in the development of Dictyostelium discoideum. Nucleic Acids Res 22:41–46PubMedGoogle Scholar
  527. Young TL, Matsuda T, Cepko CL (2005) The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 15:501–512PubMedGoogle Scholar
  528. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J et al (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451:202–206PubMedGoogle Scholar
  529. Yuan G, Klambt C, Bachellerie JP, Brosius J, Huttenhofer A (2003) RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res 31:2495–2507PubMedGoogle Scholar
  530. Zearfoss NR, Chan AP, Kloc M, Allen LH, Etkin LD (2003) Identification of new Xlsirt family members in the Xenopus laevis oocyte. Mech Dev 120:503–509PubMedGoogle Scholar
  531. Zhai J, Liu J, Liu B, Li P, Meyers BC et al (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet 4:e1000056PubMedGoogle Scholar
  532. Zhang H, Christoforou A, Aravind L, Emmons SW, van den Heuvel S et al (2004) The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein. Mol Cell 14:841–847PubMedGoogle Scholar
  533. Zhang J, Webb DM (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet 13:1785–1791PubMedGoogle Scholar
  534. Zhang X, Zhou Y, Mehta KR, Danila DC, Scolavino S et al (2003) A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab 88:5119–5126PubMedGoogle Scholar
  535. Zhang Z, Pang AW, Gerstein M (2007) Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol Biol 7(Suppl 1):S14PubMedGoogle Scholar
  536. Zhao T, Li G, Mi S, Li S, Hannon GJ et al (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 21:1190–1203PubMedGoogle Scholar
  537. Zhao Y, He S, Liu C, Ru S, Zhao H et al (2008) MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Genet 24:323–327PubMedGoogle Scholar
  538. Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL et al (2007) Activation of p53 by MEG3 non-coding RNA. J Biol Chem 282:24731–24742PubMedGoogle Scholar
  539. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC et al (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14:1214–1220PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular BioscienceUniversity of QueenslandSt. LuciaAustralia

Personalised recommendations