Noncoding RNA in development
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Abarrategui I, Krangel MS (2007) Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. EMBO J 26:4380–4390
Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758–762
Ahituv N, Zhu Y, Visel A, Holt A, Afzal V et al (2007) Deletion of ultraconserved elements yields viable mice. PLoS Biol 5:e234
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 50:195–200
Akhtar A, Zink D, Becker PB (2000) Chromodomains are protein-RNA interaction modules. Nature 407:405–409
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 14:913–923
Allen L, Kloc M, Etkin LD (2003) Identification and characterization of the Xlsirt cis-acting RNA localization element. Differentiation 71:311–321
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 8:1975–1984
Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008) The eukaryotic genome as an RNA machine. Science 319:1787–1789
Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13:807–818
Andersen BB, Gundersen HJ, Pakkenberg B (2003) Aging of the human cerebellum: a stereological study. J Comp Neurol 466:356–365
Angeleska A, Jonoska N, Saito M, Landweber LF (2007) RNA-guided DNA assembly. J Theor Biol 248:706–720
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 6:12
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 11:1017–1027
Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D et al (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5:337–350
Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761–764
Ashe HL, Monks J, Wijgerde M, Fraser P, Proudfoot NJ (1997) Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev 11:2494–2509
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 32:4646–4656
Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (2007) Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 318:798–801
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 99:16847–16852
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 51:991–1003
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 279:202–218
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 31:67–78
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 14:295–304
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 441:87–90
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 22:756–769
Bender W, Fitzgerald DP (2002) Transcription activates repressed domains in the Drosophila bithorax complex. Development 129:4923–4930
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 15:268–279
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S et al (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37:766–770
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 43:148–152
Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R et al (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38:1375–1377
Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H et al (2003) Dicer is essential for mouse development. Nat Genet 35:215–217
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 26:2560–2569
Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 22:615–626
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE et al (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242–2246
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 447:799–816
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 13:205–214
Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H et al (2004) Genomic analysis of mouse retinal development. PLoS Biol 2:E247
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 98:7336–7341
Bollenbach T, Vetsigian K, Kishony R (2007) Evolution and multilevel optimization of the genetic code. Genome Res 17:401–404
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 82:971–981
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 123:1279–1291
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 47:2305–2316
Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA et al (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441:349–353
Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990) The product of the H19 gene may function as an RNA. Mol Cell Biol 10:28–36
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 8:252–265
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 128:1089–1103
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190
Brosius J (2003) How significant is 98.5% ‘junk’ in mammalian genomes? Bioinformatics 19(Suppl 2):II35
Buhler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14:1041–1048
Buhler M, Haas W, Gygi SP, Moazed D (2007) RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129:707–721
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 89:588–595
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 25:7586–7600
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 18:501–506
Cai X, Cullen BR (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13:313–316
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 278:34125–34132
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 12:215–229
Callis TE, Chen JF, Wang DZ (2007) MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 26:219–225
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 131:706–717
Cano A, Nieto MA (2008) Non-coding RNAs take centre stage in epithelial-to-mesenchymal transition. Trends Cell Biol 18:357–359
Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH (2006) Noncoding RNAs in the mammalian central nervous system. Annu Rev Neurosci 29:77–103
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 34:95–100
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC et al (2005) The transcriptional landscape of the mammalian genome. Science 309:1559–1563
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38:626–635
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 12:179–183
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 97:14311–14316
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 276:26374–26383
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 11:1527–1538
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 116:499–509
Cerutti H, Casas-Mollano JA (2006) On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet 50:81–99
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 87:681–692
Chau YM, Pando S, Taylor HS (2002) HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the uterine endometrium. J Clin Endocrinol Metab 87:2674–2680
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 131:1340–1353
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 99:12257–12262
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S et al (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154
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 73:840–847
Choi WY, Giraldez AJ, Schier AF (2007) Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 318:271–274
Christov CP, Trivier E, Krude T (2008) Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98:981–988
Chung WJ, Okamura K, Martin R, Lai EC (2008) Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr Biol 18:795–802
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 104:19428–19433
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 38:594–597
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ et al (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613–619
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 38:813–818
Cocquet J, Pannetier M, Fellous M, Veitia RA (2005) Sense and antisense Foxl2 transcripts in mouse. Genomics 85:531–541
Conaco C, Otto S, Han JJ, Mandel G (2006) Reciprocal actions of REST and a microRNA promote neuronal identity. Proc Natl Acad Sci USA 103:2422–2427
Conley AB, Miller WJ, Jordan IK (2008) Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 24:53–56
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 7:362–375
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 33:5208–5218
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 87:3259–3263
Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C et al (2008) An endogenous small interfering RNA pathway in Drosophila. Nature 453:798–802
da Rocha ST, Edwards CA, Ito M, Ogata T, Ferguson-Smith AC (2008) Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet 24:306–316
Dahary D, Elroy-Stein O, Sorek R (2005) Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res 15:364–368
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 13:2287–2299
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 31:79–90
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 103:5320–5325
Davies W, Isles AR, Wilkinson LS (2005) Imprinted gene expression in the brain. Neurosci Biobehav Rev 29:421–430
Davis BN, Hilyard AC, Lagna G, Hata A (2008) SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454:56–61
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 103:3262–3267
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 15:1061–1072
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 16:20–29
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 17:746–759
Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (2007) The expanding RNA polymerase III transcriptome. Trends Genet 23:614–622
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 16:424–431
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:e1709
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 18:1433–1445
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 17:1031–1042
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 15:2031–2037
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 99:16853–16858
Dumas C, Chow C, Muller M, Papadopoulou B (2006) A novel class of developmentally regulated noncoding RNAs in Leishmania. Eukaryot Cell 5:2033–2046
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 22:2085–2092
Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ et al (2008) Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2:437–447
Elmendorf HG, Singer SM, Nash TE (2001) The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids Res 29:4674–4683
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L et al (2006) Complex loci in human and mouse genomes. PLoS Genet 2:e47
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 13:583–596
Esquela-Kerscher A, Slack FJ (2006) Oncomirs–microRNAs with a role in cancer. Nat Rev Cancer 6:259–269
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 24:3804–3814
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:e219
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 56:4366–4369
Farazi TA, Juranek SA, Tuschl T (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135:1201–1214
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 20:1470–1484
Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS (2006) Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276–279
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 27:2636–2647
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 39:259–263
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 126:1–8
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407–415
Frith MC, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13:894–897
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:e52
Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J et al (2006b) Evolutionary turnover of mammalian transcription start sites. Genome Res 16:713–722
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:e37
Gabory A, Ripoche MA, Yoshimizu T, Dandolo L (2006) The H19 gene: regulation and function of a non-coding RNA. Cytogenet Genome Res 113:188–193
Gardiner DL, Holt DC, Thomas EA, Kemp DJ, Trenholme KR (2000) Inhibition of Plasmodium falciparum clag9 gene function by antisense RNA. Mol Biochem Parasitol 110:33–41
Garzon R, Pichiorri F, Palumbo T, Iuliano R, Cimmino A et al (2006) MicroRNA fingerprints during human megakaryocytopoiesis. Proc Natl Acad Sci USA 103:5078–5083
Gehring WJ (2005) New perspectives on eye development and the evolution of eyes and photoreceptors. J Hered 96:171–184
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 301:718–724
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 23:1077–1081
Geng X, Lavado A, Lagutin OV, Liu W, Oliver G (2007) Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns 7:252–257
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 320:1077–1081
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 15:1993–2009
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 103:5781–5786
Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM et al (2005) MicroRNAs regulate brain morphogenesis in zebrafish. Science 308:833–838
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 312:75–79
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 18:957–964
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 25:939–948
Goodrich JA, Kugel JF (2006) Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 7:612–616
Goodstadt L, Ponting CP (2006) Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 2:e133
Graveley BR (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet 17:100–107
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 10:593–601
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 5:377–386
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 124:957–971
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 102:8603–8608
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88
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 136:35–42
Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R et al (2006) The complexity of the mammalian transcriptome. J Physiol 575:321–332
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 278:37132–37138
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–H40
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 5:2156–2165
Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952
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 104:12422–12427
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 161:231–247
Hasler J, Samuelsson T, Strub K (2007) Useful ‘junk’: Alu RNAs in the human transcriptome. Cell Mol Life Sci 64:1793–1800
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) 130:187–190
Haussecker D, Proudfoot NJ (2005) Dicer-dependent turnover of intergenic transcripts from the human beta-globin gene cluster. Mol Cell Biol 25:9724–9733
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 17:1471–1477
Heard E, Disteche CM (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20:1848–1867
Heasman J, Wessely O, Langland R, Craig EJ, Kessler DS (2001) Vegetal localization of maternal mRNAs is disrupted by VegT depletion. Dev Biol 240:377–386
Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ (2008) MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci USA 105:2946–2950
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 279:271–290
Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A et al (2006) The expansion of the metazoan microRNA repertoire. BMC Genomics 7:25
Hildebrandt M, Nellen W (1992) Differential antisense transcription from the Dictyostelium EB4 gene locus: implications on antisense-mediated regulation of mRNA stability. Cell 69:197–204
Hinas A, Soderbom F (2007) Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum. Curr Genet 51:141–159
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 35:6714–6726
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–D598
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 8:1534–1541
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 129:4915–4922
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 50:181–194
Holmes R, Williamson C, Peters J, Denny P, Wells C (2003) A comprehensive transcript map of the mouse Gnas imprinted complex. Genome Res 13:1410–1415
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 438:671–674
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 26:4996–5006
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 121:1373–1385
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 8:39
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 1120:84–94
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 322:593–600
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 2:856–875
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 10:1163–1173
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 70:111–116
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 94:529–539
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 6:2
Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17:405–412
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 164:647–652
Jeffery L, Nakielny S (2004) Components of the DNA methylation system of chromatin control are RNA-binding proteins. J Biol Chem 279:49479–49487
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 133:2827–2833
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 9:6
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 36:2677–2689
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 451:1125–1129
Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426:845–849
Jones EA, Flavell RA (2005) Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster. J Immunol 175:7437–7446
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
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 15:1007–1014
Juan V, Crain C, Wilson C (2000) Evidence for evolutionarily conserved secondary structure in the H19 tumor suppressor RNA. Nucleic Acids Res 28:1221–1227
Jupe ER, Liu XT, Kiehlbauch JL, McClung JK, Dell’Orco RT (1996) The 3′ untranslated region of prohibitin and cellular immortalization. Exp Cell Res 224:128–135
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL et al (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296:916–919
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 15:987–997
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 316:1484–1488
Kapranov P, Willingham AT, Gingeras TR (2007b) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413–423
Karali M, Peluso I, Marigo V, Banfi S (2007) Identification and characterization of microRNAs expressed in the mouse eye. Invest Ophthalmol Vis Sci 48:509–515
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M et al (2005) Antisense transcription in the mammalian transcriptome. Science 309:1564–1566
Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S et al (2008) Hidden layers of human small RNAs. BMC Genomics 9:157
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 453:793–797
Kim A, Zhao H, Ifrim I, Dean A (2007) Beta-globin intergenic transcription and histone acetylation dependent on an enhancer. Mol Cell Biol 27:2980–2986
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 77:91–98
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 14:1005–1011
King N, Hittinger CT, Carroll SB (2003) Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301:361–363
Kishore S, Stamm S (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311:230–232
Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145–148
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 132:3445–3457
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 105:1949–1954
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 4:407–412
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 66:1–13
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 31:273–283
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 132:860–874
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 283:14910–14914
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 172:963–974
Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421:948–952
Kuehbacher A, Urbich C, Zeiher AM, Dimmeler S (2007) Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ Res 101:59–68
Kumimoto H, Yoshida H, Okamoto K (1995) RNA polymerase II transcribes Dictyostelium untranslatable gene, dutA, specifically in the developmental phase. Biochem Biophys Res Commun 216:273–278
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 140:121–124
Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116:779–793
Kyes S, Christodoulou Z, Pinches R, Newbold C (2002) Stage-specific merozoite surface protein 2 antisense transcripts in Plasmodium falciparum. Mol Biochem Parasitol 123:79–83
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 19:1067–1080
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 16:1003–1016
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 32:3480–3492
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 129:1401–1414
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 97:17–27
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 99:16081–16086
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 25:980–996
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 131:174–187
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 96:3836–3841
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 125:301–313
Legube G, McWeeney SK, Lercher MJ, Akhtar A (2006) X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev 20:871–883
Lei EP, Corces VG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38:936–941
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 375:34–39
Lempradl A, Ringrose L (2008) How does noncoding transcription regulate Hox genes? Bioessays 30:110–121
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 22:1501–1512
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–D162
Levine M, Davidson EH (2005) Gene regulatory networks for development. Proc Natl Acad Sci USA 102:4936–4942
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 154:273–289
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 36:1291–1295
Leygue E (2007) Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer. Nucl Recept Signal 5:e006
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 277:13518–13527
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 438:803–819
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 62:73–88
Lipshitz HD, Peattie DA, Hogness DS (1987) Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev 1:307–322
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 133:523–536
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 39:171–184
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 210:498–512
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 21:1530–1545
Louro R, Nakaya HI, Amaral PP, Festa F, Sogayar MC et al (2007) Androgen responsive intronic non-coding RNAs. BMC Biol 5:4
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 105:4951–4956
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 317:248–251
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 70:110–120
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 25:19–21
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 1576:237–245
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 2:627–637
Mager J, Montgomery ND, de Villena FP, Magnuson T (2003) Genome imprinting regulated by the mouse Polycomb group protein Eed. Nat Genet 33:502–507
Makeyev EV, Maniatis T (2008) MicroRNAs target global regulators of transcription and alternative splicing. Science 319:1789–1790
Makrinou E, Fox M, Lovett M, Haworth K, Cameron JM et al (2001) Tty2: a multicopy y-linked gene family. Genome Res 11:935–945
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 38:1151–1158
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 83:181–190
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 36:1079–1083
Maraia RJ, Driscoll CT, Bilyeu T, Hsu K, Darlington GJ (1993) Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol 13:4233–4241
Margueron R, Trojer P, Reinberg D (2005) The key to development: interpreting the histone code? Curr Opin Genet Dev 15:163–176
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 29:499–509
Martello G, Zacchigna L, Inui M, Montagner M, Adorno M et al (2007) MicroRNA control of Nodal signalling. Nature 449:183–188
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 445:666–670
Martinez AM, Cavalli G (2006) The role of polycomb group proteins in cell cycle regulation during development. Cell Cycle 5:1189–1197
Mattick JS (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25:930–939
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 18:1611–1630
Mattick JS, Mehler MF (2008) RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci 31:227–233
Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (2006) Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 22:351–361
Mazumder B, Seshadri V, Fox PL (2003) Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 28:91–98
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 22:3164–3174
Megosh HB, Cox DN, Campbell C, Lin H (2006) The role of PIWI and the miRNA machinery in Drosophila germline determination. Curr Biol 16:1884–1894
Mehler MF, Mattick JS (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 87:799–823
Meins F Jr, Si-Ammour A, Blevins T (2005) RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol 21:297–318
Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biol 8:R202
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 105:716–712
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 22:1006–1011
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 8:153–547
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 448:553–560
Militello KT, Patel V, Chessler AD, Fisher JK, Kasper JM et al (2005) RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. RNA 11:365–370
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 9:1415–1423
Mineno J, Okamoto S, Ando T, Sato M, Chono H et al (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Res 34:1765–1771
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:e215
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 5:211–220
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 28:3713–3728
Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447:1126–1129
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 18:571–584
Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289–1292
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 18:281–292
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 3:975–981
Munroe SH, Lazar MA (1991) Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem 266:22083–22086
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:e317
Murakami K, Oshimura M, Kugoh H (2007b) Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 52:926–933
Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ et al (2007) Critical roles for Dicer in the female germline. Genes Dev 21:682–693
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 320:1344–1349
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 8:278–284
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 11:1743–1756
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:R43
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 20:2787–2792
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 414:322–325
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 14:372–380
Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM (2004) Megabase deletions of gene deserts result in viable mice. Nature 431:988–993
Noonan FC, Goodfellow PJ, Staloch LJ, Mutch DG, Simon TC (2003) Antisense transcripts at the EMX2 locus in human and mouse. Genomics 81:58–66
Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG et al (2007) RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451:153–158
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 13:1301–1306
O’Rourke JR, Georges SA, Seay HR, Tapscott SJ, McManus MT et al (2007) Essential role for Dicer during skeletal muscle development. Dev Biol 311:359–368
Ogawa Y, Lee JT (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 11:731–743
Ogawa Y, Sun BK, Lee JT (2008) Intersection of the RNA interference and X-inactivation pathways. Science 320:1336–1341
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 189:49–56
Okamura K, Chung WJ, Ruby JG, Guo H, Bartel DP et al (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453:803–806
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 420:563–573
Ooi L, Wood IC (2007) Chromatin crosstalk in development and disease: lessons from REST. Nat Rev Genet 8:544–554
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 36:40–45
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:e1
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 281:38330–38342
Pang KC, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22:1–5
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–D182
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 17:533–538
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 2:157–164
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 12:3114–3125
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA et al (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444:499–502
Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996) Requirement for Xist in X chromosome inactivation. Nature 379:131–137
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 17:642–655
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 127:1209–1221
Peyman JA (1999) Repression of major histocompatibility complex genes by a human trophoblast ribonucleic acid. Biol Reprod 60:23–31
Pheasant M, Mattick JS (2007) Raising the estimate of functional human sequences. Genome Res 17:1245–1253
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 300:131–135
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 167:1025–1035
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 113:1105–1114
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 443:167–172
Ponjavic J, Ponting CP, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17:556–565
Potter SS, Branford WW (1998) Evolutionary conservation and tissue-specific processing of Hoxa 11 antisense transcripts. Mamm Genome 9:799–806
Potts JD, Vincent EB, Runyan RB, Weeks DL (1992) Sense and antisense TGF beta 3 mRNA levels correlate with cardiac valve induction. Dev Dyn 193:340–345
Prabhakar S, Noonan JP, Paabo S, Rubin EM (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314:786
Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum. Genes Dev 21:11–42
Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM et al (2005) Regulating gene expression through RNA nuclear retention. Cell 123:249–263
Prochnik SE, Rokhsar DS, Aboobaker AA (2007) Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol 217:73–77
Prud’homme B, Gompel N, Carroll SB (2007) Emerging principles of regulatory evolution. Proc Natl Acad Sci USA 104(Suppl 1):8605-8612
Pruunsild P, Kazantseva A, Aid T, Palm K, Timmusk T (2007) Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. Genomics 90:397–406
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 75:723–730
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 22:8026–8034
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 441:469–474
Rastinejad F, Blau HM (1993) Genetic complementation reveals a novel regulatory role for 3′ untranslated regions in growth and differentiation. Cell 72:903–917
Rastinejad F, Conboy MJ, Rando TA, Blau HM (1993) Tumor suppression by RNA from the 3′ untranslated region of alpha-tropomyosin. Cell 75:1107–1117
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 16:11–19
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 92:445–457
Reik W, Lewis A (2005) Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet 6:403–410
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 403:901–906
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 23:6684–6692
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 65:1693–1699
Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38:413–443
Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134:223–232
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM et al (2003) The transcriptional activity of human chromosome 22. Genes Dev 17:529–540
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 129:1311–1323
Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14:1902–1910
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 101:2446–2451
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 19:2947–2952
Royo H, Basyuk E, Marty V, Marques M, Bertrand E et al (2007) Bsr, a nuclear-retained RNA with monoallelic expression. Mol Biol Cell 18:2817–2827
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 127:1193–1207
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 10:2687–2700
Ryan DG, Oliveira-Fernandes M, Lavker RM (2006) MicroRNAs of the mammalian eye display distinct and overlapping tissue specificity. Mol Vis 12:1175–1184
Sado T, Wang Z, Sasaki H, Li E (2001) Regulation of imprinted X-chromosome inactivation in mice by Tsix. Development 128:1275–1286
Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ et al (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20:508–512
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 40:719–721
Sanchez-Elsner T, Gou D, Kremmer E, Sauer F (2006) Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311:1118–1123
Sanchez-Herrero E, Akam M (1989) Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 107:321–329
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 176:2109–2130
Sasaki H, Matsui Y (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 9:129–140
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 357:991–996
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 357:724–730
Satterlee JS, Barbee S, Jin P, Krichevsky A, Salama S et al (2007) Noncoding RNAs in the brain. J Neurosci 27:11856–11859
Sauman I, Reppert SM (1996) Circadian clock neurons in the silkmoth Antheraea pernyi: novel mechanisms of Period protein regulation. Neuron 17:889–900
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 8:772–785
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 10:1047–1058
Scalbert E, Bril A (2008) Implication of microRNAs in the cardiovascular system. Curr Opin Pharmacol 8:181–188
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:R73
Schmitt S, Prestel M, Paro R (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19:697–708
Schoeftner S, Blasco MA (2008) Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 10:228–236
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 8:1068–1073
Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME et al (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439:283–289
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128:735–745
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 212:214–228
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 15:842–848
Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8:9–22
Schwartz YB, Pirrotta V (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20:266–273
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 8:298
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 55:213–223
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 306:575–588
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 13:223–239
Shaikh TH, Roy AM, Kim J, Batzer MA, Deininger PL (1997) cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J Mol Biol 271:222–234
Shimada N, Kawata T (2007) Evidence that noncoding RNA dutA is a multicopy suppressor of Dictyostelium discoideum STAT protein Dd-STATa. Eukaryot Cell 6:1030–1040
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 218:127–139
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 102:18485–18490
Singh SK, Kagalwala MN, Parker-Thornburg J, Adams H, Majumder S (2008) REST maintains self-renewal and pluripotency of embryonic stem cells. Nature 453:223–227
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 15:259–267
Skeiky YA, Iatrou K (1990) Silkmoth chorion antisense RNA. Structural characterization, developmental regulation and evolutionary conservation. J Mol Biol 213:53–66
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 47:677–685
Sleutels F, Zwart R, Barlow DP (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415:810–813
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 96:8064–8069
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 163:453–456
Smith NG, Brandstrom M, Ellegren H (2004) Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics 84:806–813
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 120:2498–2506
Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila microRNA targets. PLoS Biol 1:E60
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 17:1865–1879
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 22:8–13
Stefani G, Slack FJ (2008) Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 9:219–230
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:E45
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 306:655–660
Stuckenholz C, Meller VH, Kuroda MI (2003) Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster. Genetics 164:1003–1014
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 82:89–100
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 print
Sun BK, Deaton AM, Lee JT (2006) A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 21:617–628
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 170:353–364
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 178:23–34
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2005) A new frontier for molecular medicine: noncoding RNAs. Biochim Biophys Acta 1756:65–75
Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29:288–299
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 273:17079–17085
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 453:534–538
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 5:277–287
Tang F, Kaneda M, O’Carroll D, Hajkova P, Barton SC et al (2007) Maternal microRNAs are essential for mouse zygotic development. Genes Dev 21:644–648
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 26:17–29
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 105:13–23
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y et al (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2:e30
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 35:2544–2553
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 9:147–165
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 24:7855–7862
Thompson DM, Parker R (2007) Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol Cell Biol 27:92–101
Thrash-Bingham CA, Tartof KD (1999) aHIF: a natural antisense transcript overexpressed in human renal cancer and during hypoxia. J Natl Cancer Inst 91:143–151
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 87:225–235
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 16:885–889
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 18:242–251
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 21:335-349
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 359:1170–1181
Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP et al (2004) An abundance of bidirectional promoters in the human genome. Genome Res 14:62–66
Tsutsumi M, Itoh M (2007) Novel transcript nort is a downstream target gene of the Notch signaling pathway in zebrafish. Gene Expr Patterns 7:227–232
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 34:157–165
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 102:5495–5500
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 22:26–36
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 279:14871–14878
Uhler JP, Hertel C, Svejstrup JQ (2007) A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci USA 104:8011–8016
Ullu E, Lujan HD, Tschudi C (2005) Small sense and antisense RNAs derived from a telomeric retroposon family in Giardia intestinalis. Eukaryot Cell 4:1155–1157
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 36:1296–1300
Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R et al (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129:1543–1552
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 425:832–836
van Noort V, Huynen MA (2006) Combinatorial gene regulation in Plasmodium falciparum. Trends Genet 22:73–78
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 29:313–323
Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771
Velleca MA, Wallace MC, Merlie JP (1994) A novel synapse-associated noncoding RNA. Mol Cell Biol 14:7095–7104
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 132:875–886
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 21:744–749
Vogels A, Fryns JP (2002) The Prader-Willi syndrome and the Angelman syndrome. Genet Couns 13:385–396
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 130:389–396
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. Blood
Wang G, Reinke V (2008) A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol 18:861–867
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 22:10232–10241
Wang H, Iacoangeli A, Lin D, Williams K, Denman RB et al (2005) Dendritic BC1 RNA in translational control mechanisms. J Cell Biol 171:811–821
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 454:126–130
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 582:1919–1927
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 453:175–183
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 29:2327–2337
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 453:539–543
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 78:487–498
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562
Watson JB, Sutcliffe JG (1987) Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol Cell Biol 7:3324–3327
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 309:1570–1573
Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30:167–174
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 121:725–737
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 131:146–159
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–D187
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 282:25053–25066
Yamada K, Lim J, Dale JM, Chen H, Shinn P et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846
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 14:1465–1474
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 34:5112–5123
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 52:748–754
Yao MC (2008) Molecular biology. RNA rules. Nature 451:131–132
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O et al (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechol 21:379–386
Yi R, Poy MN, Stoffel M, Fuchs E (2008) A skin microRNA promotes differentiation by repressing ‘stemness’. Nature 452:225–229
Yoshida H, Kumimoto H, Okamoto K (1994) dutA RNA functions as an untranslatable RNA in the development of Dictyostelium discoideum. Nucleic Acids Res 22:41–46
Young TL, Matsuda T, Cepko CL (2005) The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 15:501–512
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 451:202–206
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 31:2495–2507
Zearfoss NR, Chan AP, Kloc M, Allen LH, Etkin LD (2003) Identification of new Xlsirt family members in the Xenopus laevis oocyte. Mech Dev 120:503–509
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:e1000056
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 14:841–847
Zhang J, Webb DM (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet 13:1785–1791
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 88:5119–5126
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):S14
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 21:1190–1203
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 24:323–327
Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL et al (2007) Activation of p53 by MEG3 non-coding RNA. J Biol Chem 282:24731–24742