메뉴 건너뛰기




Volumn 23, Issue 1, 2013, Pages 169-180

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

EID: 84871962210     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.139618.112     Document Type: Article
Times cited : (146)

References (58)
  • 2
    • 71749094924 scopus 로고    scopus 로고
    • Transposable elements in gene regulation and in the evolution of vertebrate genomes
    • Bourque G. 2009. Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opin Genet Dev 19: 607-612.
    • (2009) Curr Opin Genet Dev , vol.19 , pp. 607-612
    • Bourque, G.1
  • 4
    • 0014690698 scopus 로고
    • Gene regulation for higher cells: A theory
    • Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: A theory. Science 165: 349-357.
    • (1969) Science , vol.165 , pp. 349-357
    • Britten, R.J.1    Davidson, E.H.2
  • 5
    • 0029077187 scopus 로고
    • Mesoderm-specific B104 expression in the Drosophila embryo is mediated by internal cis-acting elements of thetransposon
    • Bronner G, Taubert H, Jackle H. 1995. Mesoderm-specific B104 expression in the Drosophila embryo is mediated by internal cis-acting elements of thetransposon. Chromosoma 103: 669-675.
    • (1995) Chromosoma , vol.103 , pp. 669-675
    • Bronner, G.1    Taubert, H.2    Jackle, H.3
  • 9
    • 70350232064 scopus 로고    scopus 로고
    • Endogenous retroviral LTRs as promoters for human genes: A critical assessment
    • Cohen CJ, Lock WM, Mager DL. 2009. Endogenous retroviral LTRs as promoters for human genes: A critical assessment. Gene 448: 105-114.
    • (2009) Gene , vol.448 , pp. 105-114
    • Cohen, C.J.1    Lock, W.M.2    Mager, D.L.3
  • 10
    • 0028618784 scopus 로고
    • Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis
    • Ding D, Lipshitz HD. 1994. Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis. Genet Res 64: 167-181.
    • (1994) Genet Res , vol.64 , pp. 167-181
    • Ding, D.1    Lipshitz, H.D.2
  • 13
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4    Gunter, C.5    Snyder, M.6
  • 16
    • 42349096534 scopus 로고    scopus 로고
    • Transposable elements and the evolution of regulatory networks
    • DOI 10.1038/nrg2337, PII NRG2337
    • Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405. (Pubitemid 351556062)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.5 , pp. 397-405
    • Feschotte, C.1
  • 17
    • 33747299885 scopus 로고    scopus 로고
    • Comparative genomics of Drosophila and human core promoters
    • doi: 10.1186/gb-2006-7-7-r53.
    • FitzGerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C. 2006. Comparative genomics of Drosophila and human core promoters. Genome Biol 7: R53. doi: 10.1186/gb-2006-7-7-r53.
    • (2006) Genome Biol , vol.7
    • FitzGerald, P.C.1    Sturgill, D.2    Shyakhtenko, A.3    Oliver, B.4    Vinson, C.5
  • 18
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant CE, Bailey TL, Noble WS. 2011. FIMO: Scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018.
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 20
    • 0027328728 scopus 로고
    • Determination of messenger RNA 5'-ends by reverse transcription of the cap structure
    • Hirzmann J, Luo D, Hahnen J, Hobom G. 1993. Determination of messenger-Rna 5′-ends by reverse transcription of the cap structure. Nucleic Acids Res 21: 3597-3598. (Pubitemid 23241512)
    • (1993) Nucleic Acids Research , vol.21 , Issue.15 , pp. 3597-3598
    • Hirzmann, J.1    Luo, D.2    Hahnen, J.3    Hobom, G.4
  • 22
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 24
    • 84871952979 scopus 로고    scopus 로고
    • Non-autonomous family of Helitrons: A consensus sequence
    • Kapitonov V, Jurka J. 2007. Non-autonomous family of Helitrons: A consensus sequence. Repbase 7: 313.
    • (2007) Repbase , vol.7 , pp. 313
    • Kapitonov, V.1    Jurka, J.2
  • 26
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • DOI 10.1038/nrg2083, PII NRG2083
    • Kapranov P, Willingham AT, Gingeras TR. 2007b. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423. (Pubitemid 46789245)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.6 , pp. 413-423
    • Kapranov, P.1    Willingham, A.T.2    Gingeras, T.R.3
  • 28
    • 0030857802 scopus 로고    scopus 로고
    • Twist-mediated activation of the NK-4 homeobox gene in the visceral mesoderm of Drosophila requires two distinct clusters of E-box regulatory elements
    • DOI 10.1074/jbc.272.28.17531
    • Lee YM, Park T, Schulz RA, Kim Y. 1997. Twist-mediated activation of the NK-4 homeobox gene in the visceral mesoderm of Drosophila requires two distinct clusters of E-box regulatory elements. J Biol Chem 272: 17531-17541. (Pubitemid 27311186)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.28 , pp. 17531-17541
    • Lee, Y.M.1    Park, T.2    Schulz, R.A.3    Kim, Y.4
  • 30
    • 28044446960 scopus 로고    scopus 로고
    • Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome
    • doi: 10.1186/1741-7007-3-24
    • Lipatov M, Lenkov K, Petrov DA, Bergman CM. 2005. Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol 3: 24. doi: 10.1186/1741-7007-3-24.
    • (2005) BMC Biol , vol.3 , pp. 24
    • Lipatov, M.1    Lenkov, K.2    Petrov, D.A.3    Bergman, C.M.4
  • 32
    • 80055010534 scopus 로고    scopus 로고
    • Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
    • Lynch VJ, Leclerc RD, May G, Wagner GP. 2011. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43: 1154-1158.
    • (2011) Nat Genet , vol.43 , pp. 1154-1158
    • Lynch, V.J.1    Leclerc, R.D.2    May, G.3    Wagner, G.P.4
  • 34
    • 84863537088 scopus 로고    scopus 로고
    • Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    • Marbach D, Roy S, Ay F,Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. 2012. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res 22: 1334-1349.
    • (2012) Genome Res , vol.22 , pp. 1334-1349
    • Marbach, D.1    Roy, S.2    Ay, F.3    Meyer, P.E.4    Candeias, R.5    Kahveci, T.6    Bristow, C.A.7    Kellis, M.8
  • 36
    • 0028822316 scopus 로고
    • Dorsal-ventral patterning genes restrict NK-2 homeobox gene expression to the ventral half of the central nervous system of Drosophila embryos
    • Mellerick DM, Nirenberg M. 1995. Dorsal-ventral patterning genes restrict NK-2 homeobox gene expression to the ventral half of the central nervous system of Drosophila embryos. Dev Biol 171: 306-316.
    • (1995) Dev Biol , vol.171 , pp. 306-316
    • Mellerick, D.M.1    Nirenberg, M.2
  • 37
    • 0028230861 scopus 로고
    • Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain
    • Mozer BA, Benzer S. 1994. Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain. Development 120: 1049-1058. (Pubitemid 24150032)
    • (1994) Development , vol.120 , Issue.5 , pp. 1049-1058
    • Mozer, B.A.1    Benzer, S.2
  • 40
  • 41
    • 0036251775 scopus 로고    scopus 로고
    • Many human genes are transcribed from the antisense promoter of L1 retrotransposon
    • DOI 10.1006/geno.2002.6758
    • Nigumann P, Redik K, Matlik K, Speek M. 2002. Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 79: 628-634. (Pubitemid 34499478)
    • (2002) Genomics , vol.79 , Issue.5 , pp. 628-634
    • Nigumann, P.1    Redik, K.2    Matlik, K.3    Speek, M.4
  • 42
    • 0023282178 scopus 로고
    • Developmental expression of Drosophila melanogaster retrovirus-like transposable elements
    • Parkhurst SM, Corces VG. 1987. Developmental expression of Drosophila melanogaster retrovirus-like transposable elements. EMBO J 6: 419-424.
    • (1987) EMBO J , vol.6 , pp. 419-424
    • Parkhurst, S.M.1    Corces, V.G.2
  • 45
    • 78149276744 scopus 로고    scopus 로고
    • Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn
    • doi: 10.2202/1544-6115.1585
    • Phipson B, Smyth GK. 2010. Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn. Stat Appl Genet Mol Biol 9: Article39. doi: 10.2202/1544-6115.1585.
    • (2010) Stat Appl Genet Mol Biol , vol.9
    • Phipson, B.1    Smyth, G.K.2
  • 47
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 48
    • 68049107475 scopus 로고    scopus 로고
    • Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
    • doi: 10.1186/gb-2009-10-7-r73
    • Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. 2009. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 10: R73. doi: 10.1186/gb-2009-10-7-r73.
    • (2009) Genome Biol , vol.10
    • Rach, E.A.1    Yuan, H.Y.2    Majoros, W.H.3    Tomancak, P.4    Ohler, U.5
  • 50
    • 0040891824 scopus 로고
    • Differential regulation of the two transcripts from the Drosophila gap segmentation gene hunchback
    • Schroder C, Tautz D, Seifert E, Jackle H. 1988. Differential regulation of the two transcripts from the Drosophila gap segmentation gene hunchback. EMBO J 7: 2881-2887.
    • (1988) EMBO J , vol.7 , pp. 2881-2887
    • Schroder, C.1    Tautz, D.2    Seifert, E.3    Jackle, H.4
  • 54
    • 0029936218 scopus 로고    scopus 로고
    • Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster
    • Udomkit A, Forbes S, McLean C, Arkhipova I, Finnegan DJ. 1996. Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster. EMBO J 15: 3174-3181. (Pubitemid 26187764)
    • (1996) EMBO Journal , vol.15 , Issue.12 , pp. 3174-3181
    • Udomkit, A.1    Forbes, S.2    McLean, C.3    Arkhipova, I.4    Finnegan, D.J.5
  • 55
    • 0141561907 scopus 로고    scopus 로고
    • Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions
    • DOI 10.1016/j.tig.2003.08.004
    • van de Lagemaat LN, Landry JR, Mager DL, Medstrand P. 2003. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19: 530-536. (Pubitemid 37204911)
    • (2003) Trends in Genetics , vol.19 , Issue.10 , pp. 530-536
    • Van De, L.L.N.1    Landry, J.-R.2    Mager, D.L.3    Medstrand, P.4
  • 56
    • 0031468348 scopus 로고    scopus 로고
    • Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development
    • Yin Z, Xu XL, Frasch M. 1997. Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development. Development 124: 4971-4982. (Pubitemid 28025123)
    • (1997) Development , vol.124 , Issue.24 , pp. 4971-4982
    • Yin, Z.1    Xu, X.-L.2    Frasch, M.3
  • 57
    • 0035498955 scopus 로고    scopus 로고
    • biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila
    • Zaffran S, Kuchler A, Lee HH, Frasch M. 2001. biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila. Genes Dev 15: 2900-2915. (Pubitemid 33042059)
    • (2001) Genes and Development , vol.15 , Issue.21 , pp. 2900-2915
    • Zaffran, S.1    Kuchler, A.2    Lee, H.-H.3    Frasch, M.4
  • 58
    • 0024652566 scopus 로고
    • Substrate specificity of T4 RNA-ligase. The effect of the nucleotide composition of substrates and the size of phosphate donor on the effectiveness of intermolecular ligation
    • Zhenodarova SM, Kliagina VP, Maistrenko FG, Pustoshilova NM, Smolianinova OA. 1989. Substrate specificity of T4 RNA-ligase. The effect of the nucleotide composition of substrates and the size of phosphate donor on the effectiveness of intermolecular ligation. Bioorg Khim 15: 478-483.
    • (1989) Bioorg Khim , vol.15 , pp. 478-483
    • Zhenodarova, S.M.1    Kliagina, V.P.2    Maistrenko, F.G.3    Pustoshilova, N.M.4    Smolianinova, O.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.