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Volumn 8, Issue 6, 2009, Pages 424-436

Establishing legitimacy and function in the new transcriptome

Author keywords

Hidden transcriptome; Noncoding RNA; RNA seq; Tiling arrays; Transcription

Indexed keywords

ARGONAUTE PROTEIN; COMPLEMENTARY DNA; CYCLIN D1; LARGE INTERVENING NON CODING RNA; MICRORNA; PASRNA; PIWI INTERACTING RNA; POLYADENYLATED RNA; QIRNA; RNA; SMALL INTERFERING RNA; SMALL NUCLEOLAR RNA; TRANSCRIPTION FACTOR NFAT; TRANSCRIPTOME; TRANSFER RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

EID: 70449723389     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elp037     Document Type: Article
Times cited : (60)

References (134)
  • 1
    • 65649092633 scopus 로고    scopus 로고
    • The genetic signatures of noncoding RNAs
    • Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet 2009;5:e1000459.
    • (2009) PLoS Genet , vol.5
    • Mattick, J.S.1
  • 3
    • 33845474731 scopus 로고    scopus 로고
    • Non-coding RNAs: lost in translation?
    • Costa FF. Non-coding RNAs: lost in translation? Gene 2007;386:1-10.
    • (2007) Gene , vol.386 , pp. 1-10
    • Costa, F.F.1
  • 4
    • 41349116135 scopus 로고    scopus 로고
    • The eukaryotic genome as an RNA machine
    • Amaral PP, Dinger ME, Mercer TR, et al. The eukaryotic genome as an RNA machine. Science 2008;319:1787-9.
    • (2008) Science , vol.319 , pp. 1787-1789
    • Amaral, P.P.1    Dinger, M.E.2    Mercer, T.R.3
  • 5
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments
    • Johnson JM, Edwards S, Shoemaker D, et al. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 2005;21:93-102.
    • (2005) Trends Genet , vol.21 , pp. 93-102
    • Johnson, J.M.1    Edwards, S.2    Shoemaker, D.3
  • 6
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007;8:413-23.
    • (2007) Nat Rev Genet , vol.8 , pp. 413-423
    • Kapranov, P.1    Willingham, A.T.2    Gingeras, T.R.3
  • 8
    • 0242300620 scopus 로고    scopus 로고
    • Empirical analysis of transcriptional activity in the Arabidopsis genome
    • Yamada K, Lim J, Dale JM, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003;302:842-6.
    • (2003) Science , vol.302 , pp. 842-846
    • Yamada, K.1    Lim, J.2    Dale, J.M.3
  • 9
    • 0016293335 scopus 로고
    • The diversity of the messenger RNA population in growing Friend cells
    • Birnie GD, MacPhail E, Young BD, et al. The diversity of the messenger RNA population in growing Friend cells. Cell Differ 1974;3:221-32.
    • (1974) Cell Differ , vol.3 , pp. 221-232
    • Birnie, G.D.1    MacPhail, E.2    Young, B.D.3
  • 10
    • 0016612014 scopus 로고
    • A kinetic estimation of base sequence complexity of nuclear poly(A)-containing RNA in mouse Friend cells
    • Getz MJ, Birnie GD, Young BD, et al. A kinetic estimation of base sequence complexity of nuclear poly(A)-containing RNA in mouse Friend cells. Cell 1975;4:121-9.
    • (1975) Cell , vol.4 , pp. 121-129
    • Getz, M.J.1    Birnie, G.D.2    Young, B.D.3
  • 11
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science 2005; 309:1559-63.
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1    Kasukawa, T.2    Katayama, S.3
  • 12
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002;420:563-73.
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1    Furuno, M.2    Kasukawa, T.3
  • 13
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • Kapranov P, Drenkow J, Cheng J, et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 2005; 15:987-997.
    • (2005) Genome Res , vol.15 , pp. 987-997
    • Kapranov, P.1    Drenkow, J.2    Cheng, J.3
  • 14
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Birney E, Stamatoyannopoulos JA, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3
  • 15
    • 30044445670 scopus 로고    scopus 로고
    • Tandem chimerism as a means to increase protein complexity in the human genome
    • Parra G, Reymond A, Dabbouseh N, et al. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 2006;16:37-44.
    • (2006) Genome Res , vol.16 , pp. 37-44
    • Parra, G.1    Reymond, A.2    Dabbouseh, N.3
  • 16
    • 30044431810 scopus 로고    scopus 로고
    • Transcription mediated gene fusion in the human genome
    • Akiva P, Toporik A, Edelheit S, et al. Transcription mediated gene fusion in the human genome. Genome Res 2006;16:30-36.
    • (2006) Genome Res , vol.16 , pp. 30-36
    • Akiva, P.1    Toporik, A.2    Edelheit, S.3
  • 17
    • 0038688072 scopus 로고    scopus 로고
    • Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection
    • Numata K, Kanai A, Saito R, et al. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res 2003;13:1301-6.
    • (2003) Genome Res , vol.13 , pp. 1301-1306
    • Numata, K.1    Kanai, A.2    Saito, R.3
  • 18
    • 30044434769 scopus 로고    scopus 로고
    • Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
    • Ravasi T, Suzuki H, Pang KC, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 2006;16:11-19.
    • (2006) Genome Res , vol.16 , pp. 11-19
    • Ravasi, T.1    Suzuki, H.2    Pang, K.C.3
  • 19
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009;458:223-7.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3
  • 20
    • 0037012881 scopus 로고    scopus 로고
    • Large-scale transcriptional activity in chromosomes 21 and 22
    • Kapranov P, Cawley SE, Drenkow J, et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002;296:916-9.
    • (2002) Science , vol.296 , pp. 916-919
    • Kapranov, P.1    Cawley, S.E.2    Drenkow, J.3
  • 21
    • 12344302543 scopus 로고    scopus 로고
    • A comprehensive transcript index of the human genome generated using microarrays and computational approaches
    • Schadt EE, Edwards SW, Guha Thakurta D, et al. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004;5:R73.
    • (2004) Genome Biol , vol.5
    • Schadt, E.E.1    Edwards, S.W.2    Guha Thakurta, D.3
  • 22
    • 0037442493 scopus 로고    scopus 로고
    • The transcriptional activity of human Chromosome 22
    • Rinn JL, Euskirchen G, Bertone P, et al. The transcriptional activity of human Chromosome 22. Genes Dev 2003;17:529-40.
    • (2003) Genes Dev , vol.17 , pp. 529-540
    • Rinn, J.L.1    Euskirchen, G.2    Bertone, P.3
  • 23
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng J, Kapranov P, Drenkow J, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005;308:1149-54.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3
  • 24
    • 33750482555 scopus 로고    scopus 로고
    • Functionality of intergenic transcription: an evolutionary comparison
    • Khaitovich P, Kelso J, Franz H, et al. Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet 2006;2:e171.
    • (2006) PLoS Genet , vol.2
    • Khaitovich, P.1    Kelso, J.2    Franz, H.3
  • 25
    • 12144287461 scopus 로고    scopus 로고
    • Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    • Kampa D, Cheng J, Kapranov P, et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004;14:331-42.
    • (2004) Genome Res , vol.14 , pp. 331-342
    • Kampa, D.1    Cheng, J.2    Kapranov, P.3
  • 26
    • 22144467302 scopus 로고    scopus 로고
    • Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    • Royce TE, Rozowsky JS, Bertone P, et al. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005;21:466-75.
    • (2005) Trends Genet , vol.21 , pp. 466-475
    • Royce, T.E.1    Rozowsky, J.S.2    Bertone, P.3
  • 27
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 28
    • 46249103973 scopus 로고    scopus 로고
    • Stem cell transcriptome profiling via massive-scale mRNA sequencing
    • Cloonan N, Forrest ARR, Kolle G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 2008;5:613-9.
    • (2008) Nat Methods , vol.5 , pp. 613-619
    • Cloonan, N.1    Forrest, A.R.R.2    Kolle, G.3
  • 29
    • 46249096804 scopus 로고    scopus 로고
    • Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
    • Wilhelm BT, Marguerat S, Watt S, et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008;453:1239-43.
    • (2008) Nature , vol.453 , pp. 1239-1243
    • Wilhelm, B.T.1    Marguerat, S.2    Watt, S.3
  • 30
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8.
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3
  • 31
    • 47949084846 scopus 로고    scopus 로고
    • Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
    • Morin R, Bainbridge M, Fejes A, et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 2008;45:81-94.
    • (2008) BioTechniques , vol.45 , pp. 81-94
    • Morin, R.1    Bainbridge, M.2    Fejes, A.3
  • 32
    • 4344623260 scopus 로고    scopus 로고
    • Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    • Imanishi T, Itoh T, Suzuki Y, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004;2:e162.
    • (2004) PLoS Biol , vol.2
    • Imanishi, T.1    Itoh, T.2    Suzuki, Y.3
  • 33
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • Lister R, O'Malley RC, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008;133:523-36.
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3
  • 34
    • 20844463584 scopus 로고    scopus 로고
    • Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
    • Ng P, Wei C, Sung W, et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods 2005;2:105-111.
    • (2005) Nat. Methods , vol.2 , pp. 105-111
    • Ng, P.1    Wei, C.2    Sung, W.3
  • 35
    • 32544451144 scopus 로고    scopus 로고
    • Alternative trans-splicing: a novel mode of pre-mRNA processing
    • Horiuchi T, Aigaki T. Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol Cell 2006;98:135-40.
    • (2006) Biol Cell , vol.98 , pp. 135-140
    • Horiuchi, T.1    Aigaki, T.2
  • 36
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: an expanding universe
    • Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet 2009;10:94-108.
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 37
    • 22844440427 scopus 로고    scopus 로고
    • Identification of hundreds of conserved and nonconserved human microRNAs
    • Bentwich I, Avniel A, Karov Y, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005;37:766-70.
    • (2005) Nat Genet , vol.37 , pp. 766-770
    • Bentwich, I.1    Avniel, A.2    Karov, Y.3
  • 38
    • 33749377869 scopus 로고    scopus 로고
    • Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
    • Berezikov E, van Tetering G, Verheul M, et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 2006;16:1289-1298.
    • (2006) Genome Res , vol.16 , pp. 1289-1298
    • Berezikov, E.1    van Tetering, G.2    Verheul, M.3
  • 40
    • 38849167412 scopus 로고    scopus 로고
    • Biogenesis and germline functions of piRNAs
    • Klattenhoff C, Theurkauf W. Biogenesis and germline functions of piRNAs. Development 2008;135:3-9.
    • (2008) Development , vol.135 , pp. 3-9
    • Klattenhoff, C.1    Theurkauf, W.2
  • 41
    • 33745402414 scopus 로고    scopus 로고
    • A novel class of small RNAs bind to MILI protein in mouse testes
    • Aravi A, Gaidatzis D, Pfeffer S, et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006;442:203-7.
    • (2006) Nature , vol.442 , pp. 203-207
    • Aravi, A.1    Gaidatzis, D.2    Pfeffer, S.3
  • 42
    • 33947273235 scopus 로고    scopus 로고
    • Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
    • Brennecke J, Aravin AA, Stark A, et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007;128:1089-103.
    • (2007) Cell , vol.128 , pp. 1089-1103
    • Brennecke, J.1    Aravin, A.A.2    Stark, A.3
  • 43
    • 33745336617 scopus 로고    scopus 로고
    • A germline-specific class of small RNAs binds mammalian Piwi proteins
    • Girard A, Sachidanandam R, Hannon GJ, et al. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006;442:199-202.
    • (2006) Nature , vol.442 , pp. 199-202
    • Girard, A.1    Sachidanandam, R.2    Hannon, G.J.3
  • 44
    • 33746527679 scopus 로고    scopus 로고
    • Characterization of the piRNA complex from rat testes
    • Lau NC, Seto AG, Kim J, et al. Characterization of the piRNA complex from rat testes. Science 2006;313:363-7.
    • (2006) Science , vol.313 , pp. 363-367
    • Lau, N.C.1    Seto, A.G.2    Kim, J.3
  • 45
    • 66149084316 scopus 로고    scopus 로고
    • qiRNA is a new type of small interfering RNA induced by DNA damage
    • Lee H, Chang S, Choudhary S, et al. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 2009;459:274-7.
    • (2009) Nature , vol.459 , pp. 274-277
    • Lee, H.1    Chang, S.2    Choudhary, S.3
  • 46
    • 67651149479 scopus 로고    scopus 로고
    • MicroRNA-mediated gene silencing modulates the UV-induced DNA-damage response
    • Pothof J, Verkaik NS, van IJcken W, et al. MicroRNA-mediated gene silencing modulates the UV-induced DNA-damage response. EMBO J 2009;28:2090-9.
    • (2009) EMBO J , vol.28 , pp. 2090-2099
    • Pothof, J.1    Verkaik, N.S.2    van IJcken, W.3
  • 47
    • 67749143728 scopus 로고    scopus 로고
    • Modulation of microRNA processing by p53
    • Suzuki HI, Yamagata K, Sugimoto K, et al. Modulation of microRNA processing by p53. Nature 2009;460:529-33.
    • (2009) Nature , vol.460 , pp. 529-533
    • Suzuki, H.I.1    Yamagata, K.2    Sugimoto, K.3
  • 48
    • 67649979858 scopus 로고    scopus 로고
    • The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells
    • Kato M, Paranjape T, Ullrich R, et al. The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells. Oncogene 2009;28:2419-24.
    • (2009) Oncogene , vol.28 , pp. 2419-2424
    • Kato, M.1    Paranjape, T.2    Ullrich, R.3
  • 49
    • 34250160256 scopus 로고    scopus 로고
    • RNA maps reveal new RNA classes and a possible function for pervasive transcription
    • Kapranov P, Cheng J, Dike S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007;316:1484-8.
    • (2007) Science , vol.316 , pp. 1484-1488
    • Kapranov, P.1    Cheng, J.2    Dike, S.3
  • 50
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008;322:1845-8.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 51
    • 57849123049 scopus 로고    scopus 로고
    • RNA exosome depletion reveals transcription upstream of active human promoters
    • Preker P, Nielsen J, Kammler S, et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008;322:1851-4.
    • (2008) Science , vol.322 , pp. 1851-1854
    • Preker, P.1    Nielsen, J.2    Kammler, S.3
  • 52
    • 60549115605 scopus 로고    scopus 로고
    • Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
    • Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project
    • Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 2009;457:1028-32.
    • (2009) Nature , vol.457 , pp. 1028-1032
  • 53
    • 67349157682 scopus 로고    scopus 로고
    • Tiny RNAs associated with transcription start sites in animals
    • Taft RJ, Glazov EA, Cloonan N, et al. Tiny RNAs associated with transcription start sites in animals. Nat Genet 2009;41:572-8.
    • (2009) Nat Genet , vol.41 , pp. 572-578
    • Taft, R.J.1    Glazov, E.A.2    Cloonan, N.3
  • 54
    • 57849140661 scopus 로고    scopus 로고
    • Divergent transcription from active promoters
    • Seila AC, Calabrese JM, Levine SS, et al. Divergent transcription from active promoters. Science 2008;322:1849-51.
    • (2008) Science , vol.322 , pp. 1849-1851
    • Seila, A.C.1    Calabrese, J.M.2    Levine, S.S.3
  • 55
    • 37349038984 scopus 로고    scopus 로고
    • Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
    • Chekanova JA, Gregory BD, Reverdatto SV, et al. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 2007;131:1340-53.
    • (2007) Cell , vol.131 , pp. 1340-1353
    • Chekanova, J.A.1    Gregory, B.D.2    Reverdatto, S.V.3
  • 56
    • 60549108380 scopus 로고    scopus 로고
    • Bidirectional promoters generate pervasive transcription in yeast
    • Xu Z, Wei W, Gagneur J, et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009;457:1033-7.
    • (2009) Nature , vol.457 , pp. 1033-1037
    • Xu, Z.1    Wei, W.2    Gagneur, J.3
  • 57
    • 60549114880 scopus 로고    scopus 로고
    • Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    • Neil H, Malabat C, d'Aubenton-Carafa Y, et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009;457:1038-42.
    • (2009) Nature , vol.457 , pp. 1038-1042
    • Neil, H.1    Malabat, C.2    d'Aubenton-Carafa, Y.3
  • 58
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • Shiraki T, Kondo S, Katayama S, et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad Sci USA 2003;100:15776-81.
    • (2003) Proc. Natl Acad Sci USA , vol.100 , pp. 15776-15781
    • Shiraki, T.1    Kondo, S.2    Katayama, S.3
  • 59
    • 33744805985 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian promoter architecture and evolution
    • Carninci P, Sandelin A, Lenhard B, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006;38:626-35.
    • (2006) Nat Genet , vol.38 , pp. 626-635
    • Carninci, P.1    Sandelin, A.2    Lenhard, B.3
  • 60
    • 23844519339 scopus 로고    scopus 로고
    • A high-resolution map of active promoters in the human genome
    • Kim TH, Barrera LO, Zheng M, et al. A high-resolution map of active promoters in the human genome. Nature 2005;436:876-80.
    • (2005) Nature , vol.436 , pp. 876-880
    • Kim, T.H.1    Barrera, L.O.2    Zheng, M.3
  • 61
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, et al. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007;130:77-88.
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3
  • 62
    • 36549013619 scopus 로고    scopus 로고
    • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    • Zeitlinger J, Stark A, Kellis M, et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 2007;39:1512-6.
    • (2007) Nat Genet , vol.39 , pp. 1512-1516
    • Zeitlinger, J.1    Stark, A.2    Kellis, M.3
  • 63
    • 36549061004 scopus 로고    scopus 로고
    • RNA polymerase is poised for activation across the genome
    • Muse GW, Gilchrist DA, Nechaev S, et al. RNA polymerase is poised for activation across the genome. Nat Genet 2007;39:1507-11.
    • (2007) Nat Genet , vol.39 , pp. 1507-1511
    • Muse, G.W.1    Gilchrist, D.A.2    Nechaev, S.3
  • 64
    • 33644784770 scopus 로고    scopus 로고
    • Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae
    • Davis CA, Ares M. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2006;103:3262-7.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 3262-3267
    • Davis, C.A.1    Ares, M.2
  • 65
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • Yuan G, Liu Y, Dion MF, et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005;309:626-30.
    • (2005) Science , vol.309 , pp. 626-630
    • Yuan, G.1    Liu, Y.2    Dion, M.F.3
  • 66
    • 43749099875 scopus 로고    scopus 로고
    • Nucleosome organization in the Drosophila genome
    • Mavrich TN, Jiang C, Ioshikhes IP, et al. Nucleosome organization in the Drosophila genome. Nature 2008;453:358-62.
    • (2008) Nature , vol.453 , pp. 358-362
    • Mavrich, T.N.1    Jiang, C.2    Ioshikhes, I.P.3
  • 67
    • 46449103738 scopus 로고    scopus 로고
    • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    • Valouev A, Ichikawa J, Tonthat T, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18:1051-63.
    • (2008) Genome Res , vol.18 , pp. 1051-1063
    • Valouev, A.1    Ichikawa, J.2    Tonthat, T.3
  • 68
    • 33846862405 scopus 로고    scopus 로고
    • High-throughput mapping of the chromatin structure of human promoters
    • Ozsolak F, Song JS, Liu XS, et al. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 2007;25:244-8.
    • (2007) Nat Biotechnol , vol.25 , pp. 244-248
    • Ozsolak, F.1    Song, J.S.2    Liu, X.S.3
  • 69
    • 0033538531 scopus 로고    scopus 로고
    • Fundamentally different logic of gene regulation in eukaryotes and prokaryotes
    • Struhl K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 1999;98:1-4.
    • (1999) Cell , vol.98 , pp. 1-4
    • Struhl, K.1
  • 70
    • 56849114880 scopus 로고    scopus 로고
    • Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome
    • Cheung V, Chua G, Batada NN, et al. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol 2008;6:e277.
    • (2008) PLoS Biol , vol.6
    • Cheung, V.1    Chua, G.2    Batada, N.N.3
  • 71
    • 33846984935 scopus 로고    scopus 로고
    • Transcriptional noise and the fidelity of initiation by RNA polymerase II
    • Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 2007;14:103-5.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 103-105
    • Struhl, K.1
  • 72
    • 17644382616 scopus 로고    scopus 로고
    • Waste not, want not-transcript excess in multicellular eukaryotes
    • Brosius J. Waste not, want not-transcript excess in multicellular eukaryotes. Trends Genet 2005;21:287-288.
    • (2005) Trends Genet , vol.21 , pp. 287-288
    • Brosius, J.1
  • 73
    • 34547147926 scopus 로고    scopus 로고
    • Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae
    • Dobi KC, Winston F. Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol 2007;27:5575-86.
    • (2007) Mol Cell Biol , vol.27 , pp. 5575-5586
    • Dobi, K.C.1    Winston, F.2
  • 74
    • 0025852478 scopus 로고
    • Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation
    • Rice GA, Kane CM, Chamberlin MJ. Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation. Proc Natl Acad Sci USA 1991;88:4245-9.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 4245-4249
    • Rice, G.A.1    Kane, C.M.2    Chamberlin, M.J.3
  • 76
    • 43049152845 scopus 로고    scopus 로고
    • Poised RNA polymerase II gives pause for thought
    • Margaritis T, Holstege FCP. Poised RNA polymerase II gives pause for thought. Cell 2008;133:581-4.
    • (2008) Cell , vol.133 , pp. 581-584
    • Margaritis, T.1    Holstege, F.C.P.2
  • 77
    • 41349094797 scopus 로고    scopus 로고
    • Transcription regulation through promoter-proximal pausing of RNA polymerase II
    • Core LJ, Lis JT. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 2008;319:1791-2.
    • (2008) Science , vol.319 , pp. 1791-1792
    • Core, L.J.1    Lis, J.T.2
  • 78
    • 24644472515 scopus 로고    scopus 로고
    • Antisense transcription in the mammalian transcriptome
    • Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcription in the mammalian transcriptome. Science 2005;309:1564-6.
    • (2005) Science , vol.309 , pp. 1564-1566
    • Katayama, S.1    Tomaru, Y.2    Kasukawa, T.3
  • 80
    • 0036307006 scopus 로고    scopus 로고
    • Overlapping antisense transcription in the human genome
    • Fahey ME, Moore TF, Higgins DG. Overlapping antisense transcription in the human genome. Comp. Funct Genomics 2002;3:244-53.
    • (2002) Comp. Funct Genomics , vol.3 , pp. 244-253
    • Fahey, M.E.1    Moore, T.F.2    Higgins, D.G.3
  • 81
    • 0036468258 scopus 로고    scopus 로고
    • Antisense transcripts in the human genome
    • Lehner B, Williams G, Campbell RD, et al. Antisense transcripts in the human genome. Trends Genet 2002;18:63-5.
    • (2002) Trends Genet , vol.18 , pp. 63-65
    • Lehner, B.1    Williams, G.2    Campbell, R.D.3
  • 82
    • 0037158780 scopus 로고    scopus 로고
    • Computational discovery of sense-antisense transcription in the human and mouse genomes
    • Shendure J, Church GM. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol 2002;3:RESEARCH0044.
    • (2002) Genome Biol , vol.3
    • Shendure, J.1    Church, G.M.2
  • 83
    • 12244275645 scopus 로고    scopus 로고
    • Widespread occurrence of antisense transcription in the human genome
    • Yelin R, Dahary D, Sorek R, et al. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 2003;21:379-86.
    • (2003) Nat Biotechnol , vol.21 , pp. 379-386
    • Yelin, R.1    Dahary, D.2    Sorek, R.3
  • 84
    • 0037673656 scopus 로고    scopus 로고
    • Antisense transcripts with FANTOM2 clone set and their implications for gene regulation
    • Kiyosawa H, Yamanaka I, Osato N, et al. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res 2003;13:1324-34.
    • (2003) Genome Res , vol.13 , pp. 1324-1334
    • Kiyosawa, H.1    Yamanaka, I.2    Osato, N.3
  • 85
    • 36148972085 scopus 로고    scopus 로고
    • Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    • Perocchi F, Xu Z, Clauder-Münster S, et al. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 2007;35: e128.
    • (2007) Nucleic Acids Res , vol.35
    • Perocchi, F.1    Xu, Z.2    Clauder-Münster, S.3
  • 86
    • 57849105533 scopus 로고    scopus 로고
    • The antisense transcriptomes of human cells
    • He Y, Vogelstein B, Velculescu VE, et al. The antisense transcriptomes of human cells. Science 2008;322:1855-7.
    • (2008) Science , vol.322 , pp. 1855-1857
    • He, Y.1    Vogelstein, B.2    Velculescu, V.E.3
  • 87
    • 62649085538 scopus 로고    scopus 로고
    • The DNA-encoded nucleosome organization of a eukaryotic genome
    • Kaplan N, Moore IK, Fondufe-Mittendorf Y, et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009;458:362-6.
    • (2009) Nature , vol.458 , pp. 362-366
    • Kaplan, N.1    Moore, I.K.2    Fondufe-Mittendorf, Y.3
  • 88
    • 34248162440 scopus 로고    scopus 로고
    • Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    • Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 2007;17:556-65.
    • (2007) Genome Res , vol.17 , pp. 556-565
    • Ponjavic, J.1    Ponting, C.P.2    Lunter, G.3
  • 89
    • 33646474262 scopus 로고    scopus 로고
    • Clusters of internally primed transcripts reveal novel long noncoding RNAs
    • Furuno M, Pang KC, Ninomiya N, et al. Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2006;2:e37.
    • (2006) PLoS Genet , vol.2
    • Furuno, M.1    Pang, K.C.2    Ninomiya, N.3
  • 90
    • 34250729138 scopus 로고    scopus 로고
    • Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    • Rinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007;129:1311-23.
    • (2007) Cell , vol.129 , pp. 1311-1323
    • Rinn, J.L.1    Kertesz, M.2    Wang, J.K.3
  • 91
    • 46649093597 scopus 로고    scopus 로고
    • Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
    • Wang X, Arai S, Song X, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008;454:126-30.
    • (2008) Nature , vol.454 , pp. 126-130
    • Wang, X.1    Arai, S.2    Song, X.3
  • 92
    • 33744804277 scopus 로고    scopus 로고
    • The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator
    • Feng J, Bi C, Clark BS, et al. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 2006;20:1470-84.
    • (2006) Genes Dev , vol.20 , pp. 1470-1484
    • Feng, J.1    Bi, C.2    Clark, B.S.3
  • 93
    • 24644481406 scopus 로고    scopus 로고
    • A strategy for probing the function of noncoding RNAs finds a repressor of NFAT
    • Willingham AT, Orth AP, Batalov S, et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005;309:1570-73.
    • (2005) Science , vol.309 , pp. 1570-1573
    • Willingham, A.T.1    Orth, A.P.2    Batalov, S.3
  • 94
    • 33645324024 scopus 로고    scopus 로고
    • RNA-mediated response to heat shock in mammalian cells
    • Shamovsky I, Ivannikov M, Kandel ES, et al. RNA-mediated response to heat shock in mammalian cells. Nature 2006;440:556-60.
    • (2006) Nature , vol.440 , pp. 556-560
    • Shamovsky, I.1    Ivannikov, M.2    Kandel, E.S.3
  • 95
    • 64349116887 scopus 로고    scopus 로고
    • Missing lincs in the transcriptome
    • Gingeras T. Missing lincs in the transcriptome. Nat Biotechnol 2009;27:346-7.
    • (2009) Nat Biotechnol , vol.27 , pp. 346-347
    • Gingeras, T.1
  • 96
    • 16544380610 scopus 로고    scopus 로고
    • Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs
    • following 757; discussion following 757
    • Wang J, Zhang J, Zheng H, et al. Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature 2004;431:1p following 757; discussion following 757.
    • (2004) Nature , vol.431 , pp. 1
    • Wang, J.1    Zhang, J.2    Zheng, H.3
  • 97
    • 29444457713 scopus 로고    scopus 로고
    • Rapid evolution of non-coding RNAs: lack of conservation does not mean lack of function
    • Pang KC, Frith MC, Mattick JS. Rapid evolution of non-coding RNAs: lack of conservation does not mean lack of function. Trends Genet 2006;22:1-5.
    • (2006) Trends Genet , vol.22 , pp. 1-5
    • Pang, K.C.1    Frith, M.C.2    Mattick, J.S.3
  • 98
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone P, Stolc V, Royce TE, et al. Global identification of human transcribed sequences with genome tiling arrays. Science 2004;306:2242-6.
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1    Stolc, V.2    Royce, T.E.3
  • 99
    • 33947604744 scopus 로고    scopus 로고
    • Comparative analysis of cis-encoded antisense RNAs in eukaryotes
    • Numata K, Okada Y, Saito R, et al. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 2007;392:134-41.
    • (2007) Gene , vol.392 , pp. 134-141
    • Numata, K.1    Okada, Y.2    Saito, R.3
  • 100
    • 34250212945 scopus 로고    scopus 로고
    • Sense-antisense pairs in mammals: functional and evolutionary considerations
    • Galante PAF, Vidal DO, de Souza JE, et al. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol 2007;8:R40.
    • (2007) Genome Biol , vol.8
    • Galante, P.A.F.1    Vidal, D.O.2    de Souza, J.E.3
  • 101
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955-64.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 102
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe TM, Eddy SR. A computational screen for methylation guide snoRNAs in yeast. Science 1999;283:1168-71.
    • (1999) Science , vol.283 , pp. 1168-1171
    • Lowe, T.M.1    Eddy, S.R.2
  • 103
    • 4043120552 scopus 로고    scopus 로고
    • Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome
    • Schattner P, Decatur WA, Davis CA, et al. Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 2004;32:4281-96.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4281-4296
    • Schattner, P.1    Decatur, W.A.2    Davis, C.A.3
  • 104
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res 1994;22:2079-88.
    • (1994) Nucleic Acids Res , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 105
    • 16344363338 scopus 로고    scopus 로고
    • Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
    • Havgaard JH, Lyngsø RB, Stormo GD, et al. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 2005;21:1815-24.
    • (2005) Bioinformatics , vol.21 , pp. 1815-1824
    • Havgaard, J.H.1    Lyngsø, R.B.2    Stormo, G.D.3
  • 106
    • 33745590704 scopus 로고    scopus 로고
    • Thousands of corresponding human and mouse genomic regions unalign-able in primary sequence contain common RNA structure
    • Torarinsson E, Sawera M, Havgaard JH, et al. Thousands of corresponding human and mouse genomic regions unalign-able in primary sequence contain common RNA structure. Genome Res 2006;16:885-9.
    • (2006) Genome Res , vol.16 , pp. 885-889
    • Torarinsson, E.1    Sawera, M.2    Havgaard, J.H.3
  • 107
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001;2:8.
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 108
    • 25444452651 scopus 로고    scopus 로고
    • A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
    • Babak T, Blencowe BJ, Hughes TR. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005;6:104.
    • (2005) BMC Genomics , vol.6 , pp. 104
    • Babak, T.1    Blencowe, B.J.2    Hughes, T.R.3
  • 109
    • 39049142999 scopus 로고    scopus 로고
    • Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
    • Torarinsson E, Yao Z, Wiklund ED, et al. Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res 2008;18:242-51.
    • (2008) Genome Res , vol.18 , pp. 242-251
    • Torarinsson, E.1    Yao, Z.2    Wiklund, E.D.3
  • 110
    • 2942560254 scopus 로고    scopus 로고
    • Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
    • Martens JA, Laprade L, Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004;429:571-74.
    • (2004) Nature , vol.429 , pp. 571-574
    • Martens, J.A.1    Laprade, L.2    Winston, F.3
  • 111
    • 27744533201 scopus 로고    scopus 로고
    • Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae
    • Martens JA, Wu PJ, Winston F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 2005;19:2695-704.
    • (2005) Genes Dev , vol.19 , pp. 2695-2704
    • Martens, J.A.1    Wu, P.J.2    Winston, F.3
  • 112
    • 33846930357 scopus 로고    scopus 로고
    • Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
    • Martianov I, Ramadass A, Serra Barros A, et al. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007;445:666-70.
    • (2007) Nature , vol.445 , pp. 666-670
    • Martianov, I.1    Ramadass, A.2    Serra Barros, A.3
  • 113
    • 47349099971 scopus 로고    scopus 로고
    • Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation
    • Kuehner JN, Brow DA. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol Cell 2008;31:201-211.
    • (2008) Mol Cell , vol.31 , pp. 201-211
    • Kuehner, J.N.1    Brow, D.A.2
  • 114
    • 50249183162 scopus 로고    scopus 로고
    • Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae
    • Thiebaut M, Colin J, Neil H, et al. Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. Mol Cell 2008;31:671-82.
    • (2008) Mol Cell , vol.31 , pp. 671-682
    • Thiebaut, M.1    Colin, J.2    Neil, H.3
  • 115
    • 55549098872 scopus 로고    scopus 로고
    • Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
    • Hirota K, Miyoshi T, Kugou K, et al. Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 2008;456:130-4.
    • (2008) Nature , vol.456 , pp. 130-134
    • Hirota, K.1    Miyoshi, T.2    Kugou, K.3
  • 116
    • 43449096915 scopus 로고    scopus 로고
    • Chromatin decouples promoter threshold from dynamic range
    • Lam FH, Steger DJ, O'Shea EK. Chromatin decouples promoter threshold from dynamic range. Nature 2008;453:246-50.
    • (2008) Nature , vol.453 , pp. 246-250
    • Lam, F.H.1    Steger, D.J.2    O'Shea, E.K.3
  • 117
    • 38049155825 scopus 로고    scopus 로고
    • Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
    • Yu W, Gius D, Onyango P, et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008;451:202-6.
    • (2008) Nature , vol.451 , pp. 202-206
    • Yu, W.1    Gius, D.2    Onyango, P.3
  • 118
    • 41149112564 scopus 로고    scopus 로고
    • A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition
    • Beltran M, Puig I, Peña C, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008;22:756-69.
    • (2008) Genes Dev , vol.22 , pp. 756-769
    • Beltran, M.1    Puig, I.2    Peña, C.3
  • 119
    • 0032813924 scopus 로고    scopus 로고
    • LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using mono-chromosomal hybrids
    • Mitsuya K, Meguro M, Lee MP, et al. LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using mono-chromosomal hybrids. Hum Mol Genet 1999;8:1209-17.
    • (1999) Hum Mol Genet , vol.8 , pp. 1209-1217
    • Mitsuya, K.1    Meguro, M.2    Lee, M.P.3
  • 120
    • 4444237596 scopus 로고    scopus 로고
    • Post-transcriptional regulation of endothelial nitric-oxide synthase by an overlapping antisense mRNA transcript
    • Robb GB, Carson AR, Tai SC, et al. Post-transcriptional regulation of endothelial nitric-oxide synthase by an overlapping antisense mRNA transcript. J Biol Chem 2004;279:37982-96.
    • (2004) J Biol Chem , vol.279 , pp. 37982-37996
    • Robb, G.B.1    Carson, A.R.2    Tai, S.C.3
  • 121
    • 33750814968 scopus 로고    scopus 로고
    • Antisense transcription controls cell fate in Saccharomyces cerevisiae
    • Hongay CF, Grisafi PL, Galitski T, et al. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006;127:735-45.
    • (2006) Cell , vol.127 , pp. 735-745
    • Hongay, C.F.1    Grisafi, P.L.2    Galitski, T.3
  • 122
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley S, Bekiranov S, Ng HH, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004;116:499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3
  • 123
    • 38649114329 scopus 로고    scopus 로고
    • Specific expression of long noncoding RNAs in the mouse brain
    • Mercer TR, Dinger ME, Sunkin SM, et al. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 2008;105:716-21.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 716-721
    • Mercer, T.R.1    Dinger, M.E.2    Sunkin, S.M.3
  • 124
    • 48249088866 scopus 로고    scopus 로고
    • Molecular biology. RNA interference in the nucleus
    • Meister G. Molecular biology. RNA interference in the nucleus. Science 2008;321:496-7.
    • (2008) Science , vol.321 , pp. 496-497
    • Meister, G.1
  • 125
    • 15544363403 scopus 로고    scopus 로고
    • Specific and potent RNAi in the nucleus of human cells
    • Robb GB, Brown KM, Khurana J, et al. Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol 2005;12:133-7.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 133-137
    • Robb, G.B.1    Brown, K.M.2    Khurana, J.3
  • 126
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2004;2: E79.
    • (2004) PLoS Biol , vol.2
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 127
    • 2442425954 scopus 로고    scopus 로고
    • Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation
    • Gilbert C, Kristjuhan A, Winkler GS, et al. Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. Mol Cell 2004;14:457-64.
    • (2004) Mol Cell , vol.14 , pp. 457-464
    • Gilbert, C.1    Kristjuhan, A.2    Winkler, G.S.3
  • 128
    • 7244259100 scopus 로고    scopus 로고
    • Megabase deletions of gene deserts result in viable mice
    • Nóbrega MA, Zhu Y, Plajzer-Frick I, et al. Megabase deletions of gene deserts result in viable mice. Nature 2004;431:988-93.
    • (2004) Nature , vol.431 , pp. 988-993
    • Nóbrega, M.A.1    Zhu, Y.2    Plajzer-Frick, I.3
  • 129
    • 7444233156 scopus 로고    scopus 로고
    • A gene expression map for the euchromatic genome of Drosophila melanogaster
    • Stolc V, Gauhar Z, Mason C, et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 2004;306:655-60.
    • (2004) Science , vol.306 , pp. 655-660
    • Stolc, V.1    Gauhar, Z.2    Mason, C.3
  • 130
    • 29444438757 scopus 로고    scopus 로고
    • Genome-wide transcription analyses in rice using tiling microarrays
    • Li L, Wang X, Stolc V, et al. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 2006;38:124-9.
    • (2006) Nat Genet , vol.38 , pp. 124-129
    • Li, L.1    Wang, X.2    Stolc, V.3
  • 131
    • 34948911591 scopus 로고    scopus 로고
    • Mapping the C. elegans non-coding transcriptome with a whole-genome tiling micro-array
    • He H, Wang J, Liu T, et al. Mapping the C. elegans non-coding transcriptome with a whole-genome tiling micro-array. Genome Res 2007;17:1471-7.
    • (2007) Genome Res , vol.17 , pp. 1471-1477
    • He, H.1    Wang, J.2    Liu, T.3
  • 132
    • 47649124124 scopus 로고    scopus 로고
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • Sultan M, Schulz MH, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008;321:956-60.
    • (2008) Science , vol.321 , pp. 956-960
    • Sultan, M.1    Schulz, M.H.2    Richard, H.3
  • 133
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang ET, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008;456:470-6.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3
  • 134
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008;40:1413-15.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3


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