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Volumn 8, Issue 6, 2007, Pages 413-423

Genome-wide transcription and the implications for genomic organization

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 34249088350     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2083     Document Type: Review
Times cited : (600)

References (119)
  • 1
    • 54249116230 scopus 로고    scopus 로고
    • Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961). A seminal work on the regulation of gene expression; the first to suggest that RNA could have a role.
    • Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961). A seminal work on the regulation of gene expression; the first to suggest that RNA could have a role.
  • 2
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
    • Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93-102 (2005).
    • (2005) Trends Genet , vol.21 , pp. 93-102
    • Johnson, J.M.1    Edwards, S.2    Shoemaker, D.3    Schadt, E.E.4
  • 3
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149-1154 (2005).
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1
  • 4
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) project
    • ENCODE Project Consortium
    • ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306, 636-640 (2004).
    • (2004) Science , vol.306 , pp. 636-640
  • 5
    • 34249069108 scopus 로고    scopus 로고
    • The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome
    • ENCODE Project Consortium, in the press
    • ENCODE Project Consortium. The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature (in the press).
    • Nature
  • 6
    • 4344623260 scopus 로고    scopus 로고
    • Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    • Imanishi, T. et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, e162 (2004).
    • (2004) PLoS Biol , vol.2
    • Imanishi, T.1
  • 7
    • 24644519490 scopus 로고    scopus 로고
    • Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005). This reference provides an unparalleled insight into the complexity of the mouse transcriptome on the basis of sequencing of full-length cDNAs and cDNA tags.
    • Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005). This reference provides an unparalleled insight into the complexity of the mouse transcriptome on the basis of sequencing of full-length cDNAs and cDNA tags.
  • 8
    • 33745286231 scopus 로고    scopus 로고
    • TUF love for 'junk' DNA
    • Willingham, A. T. & Gingeras, T. R. TUF love for 'junk' DNA. Cell 125, 1215-1220 (2006).
    • (2006) Cell , vol.125 , pp. 1215-1220
    • Willingham, A.T.1    Gingeras, T.R.2
  • 9
    • 34249105047 scopus 로고    scopus 로고
    • Genome-wide RNA maps reveal interlaced transcript architecture, new classes of RNAs and possible function for pervasive transcription
    • in the press
    • Kapranov, P. et al. Genome-wide RNA maps reveal interlaced transcript architecture, new classes of RNAs and possible function for pervasive transcription. Science (in the press).
    • Science
    • Kapranov, P.1
  • 10
    • 24644472515 scopus 로고    scopus 로고
    • Antisense transcription in the mammalian transcriptome
    • Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566 (2005).
    • (2005) Science , vol.309 , pp. 1564-1566
    • Katayama, S.1
  • 11
    • 33749870103 scopus 로고    scopus 로고
    • A large quantity of novel human antisense transcripts detected by LongSAGE
    • Ge, X., Wu, Q., Jung, Y. C., Chen, J. & Wang, S. M. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics 22, 2475-2479 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2475-2479
    • Ge, X.1    Wu, Q.2    Jung, Y.C.3    Chen, J.4    Wang, S.M.5
  • 12
    • 33746785696 scopus 로고    scopus 로고
    • Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species
    • Zhang, Y., Liu, X. S., Liu, Q. R. & Wei, L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 34, 3465-3475 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. 3465-3475
    • Zhang, Y.1    Liu, X.S.2    Liu, Q.R.3    Wei, L.4
  • 13
    • 33744805985 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian promoter architecture and evolution
    • Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genet. 38, 626-635 (2006).
    • (2006) Nature Genet , vol.38 , pp. 626-635
    • Carninci, P.1
  • 14
    • 34250369629 scopus 로고    scopus 로고
    • Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • in the press
    • Denoeud, F. et al. Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. (in the press).
    • Genome Res
    • Denoeud, F.1
  • 15
    • 33749153857 scopus 로고    scopus 로고
    • Biological function of unannotated transcription during the early development of Drosophila melanogaster
    • Manak, J. R. et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genet. 38, 1151-1158 (2006).
    • (2006) Nature Genet , vol.38 , pp. 1151-1158
    • Manak, J.R.1
  • 16
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • Kapranov, P. et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15, 987-997 (2005).
    • (2005) Genome Res , vol.15 , pp. 987-997
    • Kapranov, P.1
  • 17
    • 30044445670 scopus 로고    scopus 로고
    • Tandem chimerism as a means to increase protein complexity in the human genome
    • Parra, G. et al. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res. 16, 37-44 (2006).
    • (2006) Genome Res , vol.16 , pp. 37-44
    • Parra, G.1
  • 19
    • 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 98, 135-140 (2006).
    • (2006) Biol. Cell , vol.98 , pp. 135-140
    • Horiuchi, T.1    Aigaki, T.2
  • 20
    • 0036123757 scopus 로고    scopus 로고
    • Intergenic mRNAs. Minor gene products or tools of diversity?
    • Finta, C., Warner, S. C. & Zaphiropoulos, P. G. Intergenic mRNAs. Minor gene products or tools of diversity? Histol. Histopathol. 17, 677-682 (2002).
    • (2002) Histol. Histopathol , vol.17 , pp. 677-682
    • Finta, C.1    Warner, S.C.2    Zaphiropoulos, P.G.3
  • 21
    • 17644392110 scopus 로고    scopus 로고
    • High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene
    • Chen, C. et al. High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene. Nucleic Acids Res. 33, 2332-2342 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 2332-2342
    • Chen, C.1
  • 22
    • 0037014661 scopus 로고    scopus 로고
    • Naturally occurring heterologous trans-splicing of adenovirus RNA with host cellular transcripts during infection
    • Kikumori, T., Cote, G. J. & Gagel, R. F. Naturally occurring heterologous trans-splicing of adenovirus RNA with host cellular transcripts during infection. FEBS Lett. 522, 41-46 (2002).
    • (2002) FEBS Lett , vol.522 , pp. 41-46
    • Kikumori, T.1    Cote, G.J.2    Gagel, R.F.3
  • 23
    • 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. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004).
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1
  • 24
    • 0142027777 scopus 로고    scopus 로고
    • Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, 12247-12252 (2003). References 23 and 24 represent the first reports of the unbiased profiling of transcription factor binding sites and provide the first comprehensive evidence for the utilization of promoters in non-canonical genomic locations.
    • Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, 12247-12252 (2003). References 23 and 24 represent the first reports of the unbiased profiling of transcription factor binding sites and provide the first comprehensive evidence for the utilization of promoters in non-canonical genomic locations.
  • 25
    • 0347135948 scopus 로고    scopus 로고
    • An abundance of bidirectional promoters in the human genome
    • Trinklein, N. D. et al. An abundance of bidirectional promoters in the human genome. Genome Res. 14, 62-66 (2004).
    • (2004) Genome Res , vol.14 , pp. 62-66
    • Trinklein, N.D.1
  • 26
    • 0033926304 scopus 로고    scopus 로고
    • Stability and evolution of overlapping genes
    • Krakauer, D. C. Stability and evolution of overlapping genes. Evolution 54, 731-739 (2000).
    • (2000) Evolution , vol.54 , pp. 731-739
    • Krakauer, D.C.1
  • 27
    • 0034221653 scopus 로고    scopus 로고
    • Overlapping genes in bacterial and bacteriophage genomes
    • Shcherbakov, D. V. & Garber, M. B. Overlapping genes in bacterial and bacteriophage genomes. Mol. Biol. (Mosk) 34, 572-583 (2000).
    • (2000) Mol. Biol. (Mosk) , vol.34 , pp. 572-583
    • Shcherbakov, D.V.1    Garber, M.B.2
  • 28
    • 19844379515 scopus 로고    scopus 로고
    • Genome-wide assembly and analysis of alternative transcripts in mouse
    • Sharov, A. A., Dudekula, D. B. & Ko, M. S. Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res. 15, 748-754 (2005).
    • (2005) Genome Res , vol.15 , pp. 748-754
    • Sharov, A.A.1    Dudekula, D.B.2    Ko, M.S.3
  • 29
    • 0038349624 scopus 로고    scopus 로고
    • Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
    • Zavolan, M. et al. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 13, 1290-1300 (2003).
    • (2003) Genome Res , vol.13 , pp. 1290-1300
    • Zavolan, M.1
  • 30
    • 0014690698 scopus 로고
    • Gene regulation for higher cells: A theory
    • Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349-357 (1969).
    • (1969) Science , vol.165 , pp. 349-357
    • Britten, R.J.1    Davidson, E.H.2
  • 31
    • 33746018653 scopus 로고    scopus 로고
    • Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript
    • Gupta, A., Gartner, J. J., Sethupathy, P., Hatzigeorgiou, A. G. & Fraser, N. W. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442, 82-85 (2006).
    • (2006) Nature , vol.442 , pp. 82-85
    • Gupta, A.1    Gartner, J.J.2    Sethupathy, P.3    Hatzigeorgiou, A.G.4    Fraser, N.W.5
  • 32
    • 24644446398 scopus 로고    scopus 로고
    • Ribo-gnome: The big world of small RNAs
    • Zamore, P. D. & Haley, B. Ribo-gnome: the big world of small RNAs. Science 309, 1519-1524 (2005).
    • (2005) Science , vol.309 , pp. 1519-1524
    • Zamore, P.D.1    Haley, B.2
  • 33
  • 36
    • 33748303049 scopus 로고    scopus 로고
    • Non-coding-RNA regulators of RNA polymerase II transcription
    • Goodrich, J. A. & Kugel, J. F. Non-coding-RNA regulators of RNA polymerase II transcription. Nature Rev. Mol. Cell Biol. 7, 612-616 (2006).
    • (2006) Nature Rev. Mol. Cell Biol , vol.7 , pp. 612-616
    • Goodrich, J.A.1    Kugel, J.F.2
  • 37
    • 33846169089 scopus 로고    scopus 로고
    • Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21, 11-42 (2007). A comprehensive review of ncRNAs.
    • Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21, 11-42 (2007). A comprehensive review of ncRNAs.
  • 38
    • 1842584883 scopus 로고    scopus 로고
    • RNA regulation: A new genetics?
    • Mattick, J. S. RNA regulation: a new genetics? Nature Rev. Genet. 5, 316-323 (2004).
    • (2004) Nature Rev. Genet , vol.5 , pp. 316-323
    • Mattick, J.S.1
  • 39
    • 0028631058 scopus 로고
    • Introns: Evolution and function
    • Mattick, J. S. Introns: evolution and function. Curr. Opin. Genet. Dev. 4, 823-831 (1994).
    • (1994) Curr. Opin. Genet. Dev , vol.4 , pp. 823-831
    • Mattick, J.S.1
  • 40
    • 0035195942 scopus 로고    scopus 로고
    • Non-coding RNAs: The architects of eukaryotic complexity
    • 986-991
    • Mattick, J. S. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986-991 (2001).
    • (2001) EMBO Rep , vol.2
    • Mattick, J.S.1
  • 41
    • 0141867857 scopus 로고    scopus 로고
    • Mattick, J. S. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25, 930-939 (2003). References 38-41 review the concept of RNA as a carrier of information in the cell.
    • Mattick, J. S. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25, 930-939 (2003). References 38-41 review the concept of RNA as a carrier of information in the cell.
  • 42
    • 33344477448 scopus 로고    scopus 로고
    • Genomics of microRNA
    • Kim, V. N. & Nam, J. W. Genomics of microRNA. Trends Genet. 22, 165-173 (2006).
    • (2006) Trends Genet , vol.22 , pp. 165-173
    • Kim, V.N.1    Nam, J.W.2
  • 43
    • 0037133942 scopus 로고    scopus 로고
    • Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions
    • Kiss, T. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145-148 (2002).
    • (2002) Cell , vol.109 , pp. 145-148
    • Kiss, T.1
  • 44
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 45
    • 0036591884 scopus 로고    scopus 로고
    • Biogenesis of small nucleolar ribonucleoproteins
    • Filipowicz, W. & Pogacic, V. Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 14, 319-327 (2002).
    • (2002) Curr. Opin. Cell Biol , vol.14 , pp. 319-327
    • Filipowicz, W.1    Pogacic, V.2
  • 46
    • 23644457818 scopus 로고    scopus 로고
    • Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs
    • Huang, Z. P. et al. Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs. RNA 11, 1303-1316 (2005).
    • (2005) RNA , vol.11 , pp. 1303-1316
    • Huang, Z.P.1
  • 47
    • 6344281172 scopus 로고    scopus 로고
    • Identification of mammalian microRNA host genes and transcription units
    • Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902-1910 (2004).
    • (2004) Genome Res , vol.14 , pp. 1902-1910
    • Rodriguez, A.1    Griffiths-Jones, S.2    Ashurst, J.L.3    Bradley, A.4
  • 48
    • 13944260434 scopus 로고    scopus 로고
    • Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    • Baskerville, S. & Bartel, D. P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241-247 (2005).
    • (2005) RNA , vol.11 , pp. 241-247
    • Baskerville, S.1    Bartel, D.P.2
  • 49
    • 33745175558 scopus 로고    scopus 로고
    • Profiling Caenorhabditis elegans noncoding RNA expression with a combined microarray
    • He, H. et al. Profiling Caenorhabditis elegans noncoding RNA expression with a combined microarray. Nucleic Acids Res. 34, 2976-2983 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. 2976-2983
    • He, H.1
  • 50
    • 20944450160 scopus 로고    scopus 로고
    • Combinatorial microRNA target predictions
    • Krek, A. et al. Combinatorial microRNA target predictions. Nature Genet. 37, 495-500 (2005).
    • (2005) Nature Genet , vol.37 , pp. 495-500
    • Krek, A.1
  • 51
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 53
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434, 338-345 (2005).
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1
  • 54
    • 13944282215 scopus 로고    scopus 로고
    • Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    • Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773 (2005).
    • (2005) Nature , vol.433 , pp. 769-773
    • Lim, L.P.1
  • 55
    • 29144505309 scopus 로고    scopus 로고
    • The widespread impact of mammalian MicroRNAs on mRNA repression and evolution
    • Farh, K. K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310, 1817-1821 (2005).
    • (2005) Science , vol.310 , pp. 1817-1821
    • Farh, K.K.1
  • 56
    • 33748675254 scopus 로고    scopus 로고
    • An RNA gene expressed during cortical development evolved rapidly in humans
    • Pollard, K. S. et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443, 167-172 (2006).
    • (2006) Nature , vol.443 , pp. 167-172
    • Pollard, K.S.1
  • 57
    • 33846950027 scopus 로고    scopus 로고
    • A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas
    • Lin, R., Maeda, S., Liu, C., Karin, M. & Edgington, T. S. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26, 851-858 (2006).
    • (2006) Oncogene , vol.26 , pp. 851-858
    • Lin, R.1    Maeda, S.2    Liu, C.3    Karin, M.4    Edgington, T.S.5
  • 58
    • 33645823589 scopus 로고    scopus 로고
    • A noncoding RNA is a potential marker of cell fate during mammary gland development
    • Ginger, M. R. et al. A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc. Natl Acad. Sci. USA 103, 5781-5786 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 5781-5786
    • Ginger, M.R.1
  • 59
    • 24644481406 scopus 로고    scopus 로고
    • Willingham, A. T. et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309, 1570-1573 (2005). An example of the use of high-throughput technologies to elucidate the function of human ncRNAs.
    • Willingham, A. T. et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309, 1570-1573 (2005). An example of the use of high-throughput technologies to elucidate the function of human ncRNAs.
  • 60
    • 33644514069 scopus 로고    scopus 로고
    • Noncoding RNAs of trithorax response elements recruit Drosophila ASH1 to Ultrabithorax
    • Sanchez-Elsner, T., Gou, D., Kremmer, E. & Sauer, F. Noncoding RNAs of trithorax response elements recruit Drosophila ASH1 to Ultrabithorax. Science 311, 1118-1123 (2006).
    • (2006) Science , vol.311 , pp. 1118-1123
    • Sanchez-Elsner, T.1    Gou, D.2    Kremmer, E.3    Sauer, F.4
  • 61
    • 29444448047 scopus 로고    scopus 로고
    • On a chromosome far, far away: LCRs and gene expression
    • Dean, A. On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22, 38-45 (2006).
    • (2006) Trends Genet , vol.22 , pp. 38-45
    • Dean, A.1
  • 63
    • 33645460549 scopus 로고    scopus 로고
    • How imprinting centres work
    • Lewis, A. & Reik, W. How imprinting centres work. Cytogenet. Genome Res. 113, 81-89 (2006).
    • (2006) Cytogenet. Genome Res , vol.113 , pp. 81-89
    • Lewis, A.1    Reik, W.2
  • 64
    • 22144442010 scopus 로고    scopus 로고
    • Globalisation reaches gene regulation: The case for vertebrate limb development
    • Zuniga, A. Globalisation reaches gene regulation: the case for vertebrate limb development. Curr. Opin. Genet. Dev. 15, 403-409 (2005).
    • (2005) Curr. Opin. Genet. Dev , vol.15 , pp. 403-409
    • Zuniga, A.1
  • 65
    • 21744448354 scopus 로고    scopus 로고
    • The HS2 enhancer of the β-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter
    • Ling, J., Baibakov, B., Pi, W., Emerson, B. M. & Tuan, D. The HS2 enhancer of the β-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter. J. Mol. Biol. 350, 883-896 (2005).
    • (2005) J. Mol. Biol , vol.350 , pp. 883-896
    • Ling, J.1    Baibakov, B.2    Pi, W.3    Emerson, B.M.4    Tuan, D.5
  • 66
    • 0037320461 scopus 로고    scopus 로고
    • Chromatin remodeling and extragenic transcription at the MHC class II locus control region
    • Masternak, K., Peyraud, N., Krawczyk, M., Barras, E. & Reith, W. Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nature Immunol. 4, 132-137 (2003).
    • (2003) Nature Immunol , vol.4 , pp. 132-137
    • Masternak, K.1    Peyraud, N.2    Krawczyk, M.3    Barras, E.4    Reith, W.5
  • 67
    • 0030826364 scopus 로고    scopus 로고
    • Intergenic transcription and transinduction of the human β-globin locus
    • Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev. 11, 2494-2509 (1997).
    • (1997) Genes Dev , vol.11 , pp. 2494-2509
    • Ashe, H.L.1    Monks, J.2    Wijgerde, M.3    Fraser, P.4    Proudfoot, N.J.5
  • 68
    • 17444410031 scopus 로고    scopus 로고
    • The influence of non-coding RNAs on allele-specific gene expression in mammals
    • O'Neill, M. J. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol. Genet. 14, R113-R120 (2005).
    • (2005) Hum. Mol. Genet , vol.14
    • O'Neill, M.J.1
  • 69
    • 0037075032 scopus 로고    scopus 로고
    • The non-coding Air RNA is required for silencing autosomal imprinted genes
    • Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813 (2002).
    • (2002) Nature , vol.415 , pp. 810-813
    • Sleutels, F.1    Zwart, R.2    Barlow, D.P.3
  • 70
    • 33646598385 scopus 로고    scopus 로고
    • Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes
    • Mancini-Dinardo, D., Steele, S. J., Levorse, J. M., Ingram, R. S. & Tilghman, S. M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 20, 1268-1282 (2006).
    • (2006) Genes Dev , vol.20 , pp. 1268-1282
    • Mancini-Dinardo, D.1    Steele, S.J.2    Levorse, J.M.3    Ingram, R.S.4    Tilghman, S.M.5
  • 71
    • 33746423865 scopus 로고    scopus 로고
    • Locus control region transcription plays an active role in long-range gene activation
    • Ho, Y., Elefant, F., Liebhaber, S. A. & Cooke, N. E. Locus control region transcription plays an active role in long-range gene activation. Mol. Cell 23, 365-675 (2006).
    • (2006) Mol. Cell , vol.23 , pp. 365-675
    • Ho, Y.1    Elefant, F.2    Liebhaber, S.A.3    Cooke, N.E.4
  • 72
    • 10944220506 scopus 로고    scopus 로고
    • Ling, J. et al. HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J. Biol. Chem. 279, 51704-51713 (2004). References 69-72 show that long-range transcription is required for gene activation and silencing.
    • Ling, J. et al. HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J. Biol. Chem. 279, 51704-51713 (2004). References 69-72 show that long-range transcription is required for gene activation and silencing.
  • 73
    • 33646589016 scopus 로고    scopus 로고
    • Imprinting mechanisms - it only takes two
    • Pauler, F. M. & Barlow, D. P. Imprinting mechanisms - it only takes two. Genes Dev. 20, 1203-1206 (2006).
    • (2006) Genes Dev , vol.20 , pp. 1203-1206
    • Pauler, F.M.1    Barlow, D.P.2
  • 74
    • 8744308029 scopus 로고    scopus 로고
    • Properties of overlapping genes are conserved across microbial genomes
    • Johnson, Z. I. & Chisholm, S. W. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 14, 2268-2272 (2004).
    • (2004) Genome Res , vol.14 , pp. 2268-2272
    • Johnson, Z.I.1    Chisholm, S.W.2
  • 75
    • 19444386412 scopus 로고    scopus 로고
    • Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts
    • Chen, J., Sun, M., Hurst, L. D., Carmichael, G. G. & Rowley, J. D. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet. 21, 326-329 (2005).
    • (2005) Trends Genet , vol.21 , pp. 326-329
    • Chen, J.1    Sun, M.2    Hurst, L.D.3    Carmichael, G.G.4    Rowley, J.D.5
  • 76
    • 0037173089 scopus 로고    scopus 로고
    • Transcriptional collision between convergent genes in budding yeast
    • Prescott, E. M. & Proudfoot, N. J. Transcriptional collision between convergent genes in budding yeast. Proc. Natl Acad. Sci. USA 99, 8796-8801 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8796-8801
    • Prescott, E.M.1    Proudfoot, N.J.2
  • 77
    • 24644488895 scopus 로고    scopus 로고
    • Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation
    • Jen, C. H., Michalopoulos, I., Westhead, D. R. & Meyer, P. Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol. 6, R51 (2005).
    • (2005) Genome Biol , vol.6
    • Jen, C.H.1    Michalopoulos, I.2    Westhead, D.R.3    Meyer, P.4
  • 78
    • 0031816558 scopus 로고    scopus 로고
    • Antisense WT1 transcription parallels sense mRNA and protein expression in fetal kidney and can elevate protein levels in vitro
    • Moorwood, K. et al. Antisense WT1 transcription parallels sense mRNA and protein expression in fetal kidney and can elevate protein levels in vitro. J. Pathol. 185, 352-359 (1998).
    • (1998) J. Pathol , vol.185 , pp. 352-359
    • Moorwood, K.1
  • 79
    • 0017798436 scopus 로고
    • Evolution of overlapping genes
    • Miyata, T. & Yasunaga, T. Evolution of overlapping genes. Nature 272, 532-535 (1978).
    • (1978) Nature , vol.272 , pp. 532-535
    • Miyata, T.1    Yasunaga, T.2
  • 80
    • 5444230036 scopus 로고    scopus 로고
    • Shirasawa, S. et al. SNPs in the promoter of a B cellspecific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum. Mol. Genet. 13, 2221-2231 (2004). An example of an intronic SNP that causes predisposition to a disease by influencing the levels of an antisense transcript.
    • Shirasawa, S. et al. SNPs in the promoter of a B cellspecific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum. Mol. Genet. 13, 2221-2231 (2004). An example of an intronic SNP that causes predisposition to a disease by influencing the levels of an antisense transcript.
  • 81
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 82
    • 0016283394 scopus 로고
    • The metabolism of a poly(A) minus mRNA fraction in HeLa cells
    • Milcarek, C., Price, R. & Penman, S. The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 3, 1-10 (1974).
    • (1974) Cell , vol.3 , pp. 1-10
    • Milcarek, C.1    Price, R.2    Penman, S.3
  • 83
    • 0016826992 scopus 로고
    • Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos
    • Hough, B. R., Smith, M. J., Britten, R. J. & Davidson, E. H. Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos. Cell 5, 291-299 (1975).
    • (1975) Cell , vol.5 , pp. 291-299
    • Hough, B.R.1    Smith, M.J.2    Britten, R.J.3    Davidson, E.H.4
  • 84
    • 0019332437 scopus 로고
    • Sequence complexity of nuclear and messenger RNA in HeLa cells
    • Holland, C. A., Mayrand, S. & Pederson, T. Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138, 755-778 (1980).
    • (1980) J. Mol. Biol , vol.138 , pp. 755-778
    • Holland, C.A.1    Mayrand, S.2    Pederson, T.3
  • 85
    • 0019323954 scopus 로고
    • Satellite DNA is transcribed on lampbrush chromosomes
    • Varley, J. M., Macgregor, H. C. & Erba, H. P. Satellite DNA is transcribed on lampbrush chromosomes. Nature 283, 686-688 (1980).
    • (1980) Nature , vol.283 , pp. 686-688
    • Varley, J.M.1    Macgregor, H.C.2    Erba, H.P.3
  • 86
    • 0019524412 scopus 로고    scopus 로고
    • Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C. & Darnell, J. E. Jr. Large heterogeneous nuclear ribonucleic acid has three times as many 5′ caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1, 179-187 (1981). References 82-86 provide the first indications that a large fraction of the eukaryotic genome is transcribed, and that non-polyadenylated RNA is prevalent.
    • Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C. & Darnell, J. E. Jr. Large heterogeneous nuclear ribonucleic acid has three times as many 5′ caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1, 179-187 (1981). References 82-86 provide the first indications that a large fraction of the eukaryotic genome is transcribed, and that non-polyadenylated RNA is prevalent.
  • 87
    • 0033664358 scopus 로고    scopus 로고
    • RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
    • Selinger, D. W. et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol. 18, 1262-1268 (2000).
    • (2000) Nature Biotechnol , vol.18 , pp. 1262-1268
    • Selinger, D.W.1
  • 88
    • 0242300620 scopus 로고    scopus 로고
    • Empirical analysis of transcriptional activity in the Arabidopsis genome
    • Yamada, K. et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846 (2003).
    • (2003) Science , vol.302 , pp. 842-846
    • Yamada, K.1
  • 89
    • 7444233156 scopus 로고    scopus 로고
    • A gene expression map for the euchromatic genome of Drosophila melanogaster
    • Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655-660 (2004).
    • (2004) Science , vol.306 , pp. 655-660
    • Stolc, V.1
  • 90
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242-2246 (2004).
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1
  • 91
    • 29444438757 scopus 로고    scopus 로고
    • Genome-wide transcription analyses in rice using tiling microarrays
    • Li, L. et al. Genome-wide transcription analyses in rice using tiling microarrays. Nature Genet. 38, 124-129 (2006).
    • (2006) Nature Genet , vol.38 , pp. 124-129
    • Li, L.1
  • 92
    • 33751011601 scopus 로고    scopus 로고
    • The transcriptome of the sea urchin embryo
    • Samanta, M. P. et al. The transcriptome of the sea urchin embryo. Science 314, 960-962 (2006).
    • (2006) Science , vol.314 , pp. 960-962
    • Samanta, M.P.1
  • 93
    • 33645785104 scopus 로고    scopus 로고
    • A high-resolution map of transcription in the yeast genome
    • David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA 103, 5320-5325 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 5320-5325
    • David, L.1
  • 94
    • 0037012881 scopus 로고    scopus 로고
    • Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002). The first unbiased high-resolution microarraybased study of the genomics era, showing that the transcriptional complexity of human cytosolic polyadenylated RNA is up to an order of magnitude more complex that can be explained by exons of known genes.
    • Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002). The first unbiased high-resolution microarraybased study of the genomics era, showing that the transcriptional complexity of human cytosolic polyadenylated RNA is up to an order of magnitude more complex that can be explained by exons of known genes.
  • 95
    • 0037442493 scopus 로고    scopus 로고
    • The transcriptional activity of human Chromosome 22
    • Rinn, J. L. et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17, 529-540 (2003).
    • (2003) Genes Dev , vol.17 , pp. 529-540
    • Rinn, J.L.1
  • 96
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA 100, 15776-15781 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 15776-15781
    • Shiraki, T.1
  • 97
    • 20844463584 scopus 로고    scopus 로고
    • Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
    • Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105-111 (2005).
    • (2005) Nature Methods , vol.2 , pp. 105-111
    • Ng, P.1
  • 98
    • 0037126025 scopus 로고    scopus 로고
    • Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags
    • Chen, J. et al. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl Acad. Sci. USA 99, 12257-12262 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 12257-12262
    • Chen, J.1
  • 99
    • 0036246030 scopus 로고    scopus 로고
    • Using the transcriptome to annotate the genome
    • Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508-512 (2002).
    • (2002) Nature Biotechnol , vol.20 , pp. 508-512
    • Saha, S.1
  • 100
    • 0037737975 scopus 로고    scopus 로고
    • Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818 (2003).
    • Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818 (2003).
  • 101
    • 30044435097 scopus 로고    scopus 로고
    • Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
    • Deng, W. et al. Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res. 16, 20-29 (2006).
    • (2006) Genome Res , vol.16 , pp. 20-29
    • Deng, W.1
  • 102
    • 33845436047 scopus 로고    scopus 로고
    • Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    • Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193-1207 (2006).
    • (2006) Cell , vol.127 , pp. 1193-1207
    • Ruby, J.G.1
  • 103
    • 24644490196 scopus 로고    scopus 로고
    • Elucidation of the small RNA component of the transcriptome
    • Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science 309, 1567-1569 (2005).
    • (2005) Science , vol.309 , pp. 1567-1569
    • Lu, C.1
  • 104
    • 33745402414 scopus 로고    scopus 로고
    • A novel class of small RNAs bind to MILI protein in mouse testes
    • Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203-207 (2006).
    • (2006) Nature , vol.442 , pp. 203-207
    • Aravin, A.1
  • 105
    • 33745336617 scopus 로고    scopus 로고
    • Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199-202 (2006).
    • Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199-202 (2006).
  • 106
    • 33745621037 scopus 로고    scopus 로고
    • A novel class of small RNAs in mouse spermatogenic cells
    • Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev. 20, 1709-1714 (2006).
    • (2006) Genes Dev , vol.20 , pp. 1709-1714
    • Grivna, S.T.1    Beyret, E.2    Wang, Z.3    Lin, H.4
  • 107
    • 33746527679 scopus 로고    scopus 로고
    • Characterization of the piRNA complex from rat testes
    • Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363-367 (2006).
    • (2006) Science , vol.313 , pp. 363-367
    • Lau, N.C.1
  • 108
    • 33745599586 scopus 로고    scopus 로고
    • Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
    • Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20, 1732-1743 (2006).
    • (2006) Genes Dev , vol.20 , pp. 1732-1743
    • Watanabe, T.1
  • 109
    • 22244475458 scopus 로고    scopus 로고
    • An atlas of human gene expression from massively parallel signature sequencing (MPSS)
    • Jongeneel, C. V. et al. An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 15, 1007-1014 (2005).
    • (2005) Genome Res , vol.15 , pp. 1007-1014
    • Jongeneel, C.V.1
  • 110
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573 (2002).
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1
  • 111
    • 23844519339 scopus 로고    scopus 로고
    • A high-resolution map of active promoters in the human genome
    • Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876-880 (2005).
    • (2005) Nature , vol.436 , pp. 876-880
    • Kim, T.H.1
  • 112
    • 30344478870 scopus 로고    scopus 로고
    • A global map of p53 transcriptionfactor binding sites in the human genome
    • Wei, C. L. et al. A global map of p53 transcriptionfactor binding sites in the human genome. Cell 124, 207-219 (2006).
    • (2006) Cell , vol.124 , pp. 207-219
    • Wei, C.L.1
  • 114
    • 28844463698 scopus 로고    scopus 로고
    • Emerging technologies in DNA sequencing
    • Metzker, M. L. Emerging technologies in DNA sequencing. Genome Res. 15, 1767-1776 (2005).
    • (2005) Genome Res , vol.15 , pp. 1767-1776
    • Metzker, M.L.1
  • 115
    • 33644875376 scopus 로고    scopus 로고
    • Microarray expression technology: From start to finish
    • Elvidge, G. Microarray expression technology: from start to finish. Pharmacogenomics 7, 123-134 (2006).
    • (2006) Pharmacogenomics , vol.7 , pp. 123-134
    • Elvidge, G.1
  • 116
    • 3242766188 scopus 로고    scopus 로고
    • Beyond expression profiling: Next generation uses of high density oligonucleotide arrays
    • Kapranov, P., Sementchenko, V. I. & Gingeras, T. R. Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief. Funct. Genomic. Proteomic. 2, 47-56 (2003).
    • (2003) Brief. Funct. Genomic. Proteomic , vol.2 , pp. 47-56
    • Kapranov, P.1    Sementchenko, V.I.2    Gingeras, T.R.3
  • 117
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler, T. C. et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15 (2005).
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1
  • 118
    • 0037250168 scopus 로고    scopus 로고
    • The UCSC Genome Browser Database
    • Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54 (2003).
    • (2003) Nucleic Acids Res , vol.31 , pp. 51-54
    • Karolchik, D.1
  • 119
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
    • (2002) Genome Res , vol.12 , pp. 996-1006
    • Kent, W.J.1


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