메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes

Author keywords

Arabidopsis; Cis element; Gene expression; Inter motif distance; Promoter regulation; Rice; Sorghum; Soybean; Spacer; Stress

Indexed keywords

ADENINE; CYTOSINE; GUANINE; JASMONIC ACID; SPACER DNA; THYMINE;

EID: 84875297643     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-203     Document Type: Article
Times cited : (33)

References (50)
  • 1
    • 0025369859 scopus 로고
    • Activator and targets
    • 10.1038/346329a0, 2142753
    • Ptashne M, Gann AA. Activator and targets. Nature 1990, 346:329-333. 10.1038/346329a0, 2142753.
    • (1990) Nature , vol.346 , pp. 329-333
    • Ptashne, M.1    Gann, A.A.2
  • 2
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • 10.1093/bioinformatics/16.1.16, 10812473
    • Stormo GD. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23. 10.1093/bioinformatics/16.1.16, 10812473.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 3
    • 0035477093 scopus 로고    scopus 로고
    • Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
    • 10.1101/gad.924301, 312797, 11581157
    • Butler JE, Kadonanhga JT. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 2001, 15:2515-2519. 10.1101/gad.924301, 312797, 11581157.
    • (2001) Genes Dev , vol.15 , pp. 2515-2519
    • Butler, J.E.1    Kadonanhga, J.T.2
  • 4
    • 33645748095 scopus 로고    scopus 로고
    • What are DNA sequence motifs?
    • 10.1038/nbt0406-423, 16601727
    • D'haeseleer P. What are DNA sequence motifs?. Nat Biotechnol 2006, 24(4):423-425. 10.1038/nbt0406-423, 16601727.
    • (2006) Nat Biotechnol , vol.24 , Issue.4 , pp. 423-425
    • D'haeseleer, P.1
  • 5
    • 0030927867 scopus 로고    scopus 로고
    • Searching for regulatory elements in human noncoding sequences
    • 10.1016/S0959-440X(97)80058-9, 9204283
    • Duret L, Bucher P. Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol 1997, 7:399-406. 10.1016/S0959-440X(97)80058-9, 9204283.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 399-406
    • Duret, L.1    Bucher, P.2
  • 7
    • 0029864497 scopus 로고    scopus 로고
    • Combinations of closely situated cis-acting elements determine tissue-specific patterns and anterior extent of early Hoxc8 expression
    • 10.1073/pnas.93.22.12364, 37997, 8901587
    • Shashikant CS, Ruddle FH. Combinations of closely situated cis-acting elements determine tissue-specific patterns and anterior extent of early Hoxc8 expression. Proc Natl Acad Sci U S A 1996, 93(22):12364-12369. 10.1073/pnas.93.22.12364, 37997, 8901587.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , Issue.22 , pp. 12364-12369
    • Shashikant, C.S.1    Ruddle, F.H.2
  • 8
    • 0037035388 scopus 로고    scopus 로고
    • Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model
    • 10.1098/rspb.2002.1968, 1690979, 12028779
    • Carter AJ, Wagner GP. Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model. Proc Biol Sci 2002, 269(1494):953-960. 10.1098/rspb.2002.1968, 1690979, 12028779.
    • (2002) Proc Biol Sci , vol.269 , Issue.1494 , pp. 953-960
    • Carter, A.J.1    Wagner, G.P.2
  • 9
    • 34250896139 scopus 로고    scopus 로고
    • Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    • 10.1093/nar/gkm201, 1904283, 17452354
    • Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 2007, 35(10):3203-3213. 10.1093/nar/gkm201, 1904283, 17452354.
    • (2007) Nucleic Acids Res , vol.35 , Issue.10 , pp. 3203-3213
    • Vardhanabhuti, S.1    Wang, J.2    Hannenhalli, S.3
  • 10
    • 0023942147 scopus 로고
    • The SV40 enhancer contains two distinct levels of organization
    • 10.1038/333040a0, 2834649
    • Ondek B, Gloss L, Herr W. The SV40 enhancer contains two distinct levels of organization. Nature 1988, 333(6168):40-45. 10.1038/333040a0, 2834649.
    • (1988) Nature , vol.333 , Issue.6168 , pp. 40-45
    • Ondek, B.1    Gloss, L.2    Herr, W.3
  • 11
    • 0023988470 scopus 로고
    • Constraints on spacing between transcription factor binding sites in a simple adenovirus promoter
    • 10.1101/gad.2.4.403, 2836264
    • Wu L, Berk A. Constraints on spacing between transcription factor binding sites in a simple adenovirus promoter. Genes Dev 1988, 2(4):403-411. 10.1101/gad.2.4.403, 2836264.
    • (1988) Genes Dev , vol.2 , Issue.4 , pp. 403-411
    • Wu, L.1    Berk, A.2
  • 12
    • 0025375525 scopus 로고
    • Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter
    • 551874, 2347304
    • Donald RG, Cashmore AR. Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J 1990, 9(6):1717-1726. 551874, 2347304.
    • (1990) EMBO J , vol.9 , Issue.6 , pp. 1717-1726
    • Donald, R.G.1    Cashmore, A.R.2
  • 13
    • 0026903278 scopus 로고
    • Functional elements of the Arabidopsis Adh promoter include the G-box
    • 10.1007/BF00027081, 1643286
    • McKendree WL, Ferl RJ. Functional elements of the Arabidopsis Adh promoter include the G-box. Plant Mol Biol 1992, 19(5):859-862. 10.1007/BF00027081, 1643286.
    • (1992) Plant Mol Biol , vol.19 , Issue.5 , pp. 859-862
    • McKendree, W.L.1    Ferl, R.J.2
  • 14
    • 0027567217 scopus 로고
    • Identification of a methyl jasmonate-responsive domain in the soybean vspB promoter
    • 160266, 8467221
    • Mason HS, DeWald DB, Mullet JE. Identification of a methyl jasmonate-responsive domain in the soybean vspB promoter. Plant Cell 1993, 5(3):241-251. 160266, 8467221.
    • (1993) Plant Cell , vol.5 , Issue.3 , pp. 241-251
    • Mason, H.S.1    DeWald, D.B.2    Mullet, J.E.3
  • 15
    • 0029853633 scopus 로고    scopus 로고
    • Activation of the CaMV as-1 cis-element by salicylic acid: differential DNA-binding of a factor related to TGA1a
    • 452312, 8896461
    • Jupin I, Chua NH. Activation of the CaMV as-1 cis-element by salicylic acid: differential DNA-binding of a factor related to TGA1a. EMBO J 1996, 15(20):5679-5689. 452312, 8896461.
    • (1996) EMBO J , vol.15 , Issue.20 , pp. 5679-5689
    • Jupin, I.1    Chua, N.H.2
  • 16
    • 0025706143 scopus 로고
    • A plant leucine zipper protein that recognizes an abscisic acid response element
    • 10.1126/science.2145628, 2145628
    • Guiltinan MJ, Marcotte WR, Quatrano RS. A plant leucine zipper protein that recognizes an abscisic acid response element. Science 1990, 250(4978):267-271. 10.1126/science.2145628, 2145628.
    • (1990) Science , vol.250 , Issue.4978 , pp. 267-271
    • Guiltinan, M.J.1    Marcotte, W.R.2    Quatrano, R.S.3
  • 17
    • 0027444711 scopus 로고
    • Hormone response complex in a novel abscisic acid and cycloheximide-inducible barley gene
    • Shen Q, Uknes SJ, Ho TH. Hormone response complex in a novel abscisic acid and cycloheximide-inducible barley gene. J Biol Chem 1993, 268(31):23652-23660.
    • (1993) J Biol Chem , vol.268 , Issue.31 , pp. 23652-23660
    • Shen, Q.1    Uknes, S.J.2    Ho, T.H.3
  • 18
    • 0032104856 scopus 로고    scopus 로고
    • Regulation of abscisic acid-induced transcription
    • 10.1023/A:1006058700720, 9617810
    • Busk PK, Pages M. Regulation of abscisic acid-induced transcription. Plant Mol Biol 1998, 37:425-435. 10.1023/A:1006058700720, 9617810.
    • (1998) Plant Mol Biol , vol.37 , pp. 425-435
    • Busk, P.K.1    Pages, M.2
  • 19
    • 0028425477 scopus 로고
    • Soybean GH3 promoter contains multiple auxin-inducible elements
    • 160465, 8038604
    • Liu B, Ulmasov T, Shi X, Hagen G, Guilfoyle TJ. Soybean GH3 promoter contains multiple auxin-inducible elements. Plant Cell 1994, 6:645-657. 160465, 8038604.
    • (1994) Plant Cell , vol.6 , pp. 645-657
    • Liu, B.1    Ulmasov, T.2    Shi, X.3    Hagen, G.4    Guilfoyle, T.J.5
  • 20
    • 0035077752 scopus 로고    scopus 로고
    • Designing of an artificial expression cassette for high level expression of transgenes in plants
    • Sawant SV, Singh PK, Madanala R, Tuli R. Designing of an artificial expression cassette for high level expression of transgenes in plants. Theor Appl Genet 2001, 102:635-644.
    • (2001) Theor Appl Genet , vol.102 , pp. 635-644
    • Sawant, S.V.1    Singh, P.K.2    Madanala, R.3    Tuli, R.4
  • 21
    • 23944495876 scopus 로고    scopus 로고
    • A variety of synergistic and antagonistic interactions mediated by cis acting DNA motifs regulate gene expression in plant cells and modulate stability of the transcription complex formed on basal promoter
    • 10.1093/jxb/eri227, 16014367
    • Sawant SV, Kiran K, Mehrotra R, Chaturvedi CP, Ansari SA, Singh P, Lodhi N. A variety of synergistic and antagonistic interactions mediated by cis acting DNA motifs regulate gene expression in plant cells and modulate stability of the transcription complex formed on basal promoter. J Exp Bot 2005, 56:2345-2353. 10.1093/jxb/eri227, 16014367.
    • (2005) J Exp Bot , vol.56 , pp. 2345-2353
    • Sawant, S.V.1    Kiran, K.2    Mehrotra, R.3    Chaturvedi, C.P.4    Ansari, S.A.5    Singh, P.6    Lodhi, N.7
  • 22
    • 34948879269 scopus 로고    scopus 로고
    • Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice
    • 10.1186/1471-2164-8-260, 2000901, 17672917
    • Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 2007, 8:260. 10.1186/1471-2164-8-260, 2000901, 17672917.
    • (2007) BMC Genomics , vol.8 , pp. 260
    • Gómez-Porras, J.L.1    Riaño-Pachón, D.M.2    Dreyer, I.3    Mayer, J.E.4    Mueller-Roeber, B.5
  • 23
    • 77955053116 scopus 로고    scopus 로고
    • Promoter activation by ACGT in response to salicylic and abscisic acids is differentially regulated by the spacing between two copies of the motif
    • 10.1016/j.jplph.2010.04.005, 20554077
    • Mehrotra R, Mehrotra S. Promoter activation by ACGT in response to salicylic and abscisic acids is differentially regulated by the spacing between two copies of the motif. J Plant Physiol 2010, 167:1214-1218. 10.1016/j.jplph.2010.04.005, 20554077.
    • (2010) J Plant Physiol , vol.167 , pp. 1214-1218
    • Mehrotra, R.1    Mehrotra, S.2
  • 24
    • 25144478364 scopus 로고    scopus 로고
    • Effect of copy number and spacing of the ACGT and GT cis elements on transient expression of minimal promoter in plants
    • 10.1007/BF02715844, 16131718
    • Mehrotra R, Kiran K, Chaturvedi CP, Ansari SA, Lodhi N, Sawant S, Tuli R. Effect of copy number and spacing of the ACGT and GT cis elements on transient expression of minimal promoter in plants. J Genet 2005, 84:183-187. 10.1007/BF02715844, 16131718.
    • (2005) J Genet , vol.84 , pp. 183-187
    • Mehrotra, R.1    Kiran, K.2    Chaturvedi, C.P.3    Ansari, S.A.4    Lodhi, N.5    Sawant, S.6    Tuli, R.7
  • 25
    • 0024740034 scopus 로고
    • Abscisic acid-responsive sequences from the Em gene of wheat
    • 159833, 2562556
    • Marcotte WR, Russel SH, Quatrano RS. Abscisic acid-responsive sequences from the Em gene of wheat. Plant Cell 1989, 1:969-976. 159833, 2562556.
    • (1989) Plant Cell , vol.1 , pp. 969-976
    • Marcotte, W.R.1    Russel, S.H.2    Quatrano, R.S.3
  • 26
    • 0025098288 scopus 로고
    • Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene
    • USA, 10.1073/pnas.87.4.1406, 53484, 2137613
    • Mundy J, Yamaguchi-Shinozaki K, Chua N-H. Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene. Proc Natl Acad Sci 1990, 87:1406-1410. USA, 10.1073/pnas.87.4.1406, 53484, 2137613.
    • (1990) Proc Natl Acad Sci , vol.87 , pp. 1406-1410
    • Mundy, J.1    Yamaguchi-Shinozaki, K.2    Chua, N.-H.3
  • 27
    • 0029311280 scopus 로고
    • Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1: analysis of cis-acting prmoter elements required for regulation by abscisic acid and VP1
    • 10.1046/j.1365-313X.1995.07060913.x, 7599651
    • Hattori T, Terada T, Hamasuna S. Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1: analysis of cis-acting prmoter elements required for regulation by abscisic acid and VP1. Plant J 1995, 7:913-925. 10.1046/j.1365-313X.1995.07060913.x, 7599651.
    • (1995) Plant J , vol.7 , pp. 913-925
    • Hattori, T.1    Terada, T.2    Hamasuna, S.3
  • 28
    • 0030267663 scopus 로고    scopus 로고
    • The rab76B promoter of rice contains two distinct abscisic acid-responsive elements
    • Ono A, Izawa T, Chua NH, Shimamoto K. The rab76B promoter of rice contains two distinct abscisic acid-responsive elements. Plant Physiol 1996, 11(2):483-491.
    • (1996) Plant Physiol , vol.11 , Issue.2 , pp. 483-491
    • Ono, A.1    Izawa, T.2    Chua, N.H.3    Shimamoto, K.4
  • 29
    • 0030199209 scopus 로고    scopus 로고
    • Modular nature of abscisic acid (ABA) response complexes: composite promoter units that Are necessary and sufficient for ABA lnduction of gene expression in barley
    • 161185, 8768371
    • Shen Q, Zhang P, Ho TH. Modular nature of abscisic acid (ABA) response complexes: composite promoter units that Are necessary and sufficient for ABA lnduction of gene expression in barley. Plant Cell 1996, 8:1107-1119. 161185, 8768371.
    • (1996) Plant Cell , vol.8 , pp. 1107-1119
    • Shen, Q.1    Zhang, P.2    Ho, T.H.3
  • 34
    • 0032918558 scopus 로고    scopus 로고
    • Plant cis-acting regulatory DNA elements (PLACE) database
    • 10.1093/nar/27.1.297, 148163, 9847208
    • Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res 1999, 27(1):297-300. 10.1093/nar/27.1.297, 148163, 9847208.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 297-300
    • Higo, K.1    Ugawa, Y.2    Iwamoto, M.3    Korenaga, T.4
  • 35
    • 84856621471 scopus 로고    scopus 로고
    • High GC content: critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana
    • 10.6026/97320630004151, 2825596, 20198191
    • Mishra AK, Agarwal S, Jain CK, Rani V. High GC content: critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana. Bioinformation 2009, 4(4):151-154. 10.6026/97320630004151, 2825596, 20198191.
    • (2009) Bioinformation , vol.4 , Issue.4 , pp. 151-154
    • Mishra, A.K.1    Agarwal, S.2    Jain, C.K.3    Rani, V.4
  • 40
    • 0025389088 scopus 로고
    • A DNA-binding protein factor recognizes two binding domains within the octopine synthase enhancer element
    • 159878, 2152113
    • Tokuhisa JG, Singh K, Dennis ES, Peacock WJ. A DNA-binding protein factor recognizes two binding domains within the octopine synthase enhancer element. Plant Cell 1990, 2(3):215-224. 159878, 2152113.
    • (1990) Plant Cell , vol.2 , Issue.3 , pp. 215-224
    • Tokuhisa, J.G.1    Singh, K.2    Dennis, E.S.3    Peacock, W.J.4
  • 41
    • 0031310825 scopus 로고    scopus 로고
    • The mechanism of transcriptional synergy of an in vitro assembled interferon- β enhanceosome
    • 10.1016/S1097-2765(00)80013-1, 9659909
    • Kim TK, Maniatis T. The mechanism of transcriptional synergy of an in vitro assembled interferon- β enhanceosome. Mol Cell 1997, 1(1):119-129. 10.1016/S1097-2765(00)80013-1, 9659909.
    • (1997) Mol Cell , vol.1 , Issue.1 , pp. 119-129
    • Kim, T.K.1    Maniatis, T.2
  • 42
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: from enhancer binding to developmental control
    • 10.1038/nrg3207, 22868264
    • Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 2012, 13(9):613-626. 10.1038/nrg3207, 22868264.
    • (2012) Nat Rev Genet , vol.13 , Issue.9 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.2
  • 43
    • 0034633775 scopus 로고    scopus 로고
    • Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions
    • 10.1073/pnas.190309197, 17252, 11005831
    • Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc Natl Acad Sci U S A 2000, 97(21):11632-11637. 10.1073/pnas.190309197, 17252, 11005831.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , Issue.21 , pp. 11632-11637
    • Uno, Y.1    Furihata, T.2    Abe, H.3    Yoshida, R.4    Shinozaki, K.5    Yamaguchi-Shinozaki, K.6
  • 44
    • 84859302633 scopus 로고    scopus 로고
    • Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice
    • 10.1104/pp.111.190389, 3320183, 22301130
    • Ning T, Hua Z, Xianghua L, Jinghua X, Xiong L. Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol 2012, 158(4):1755-1768. 10.1104/pp.111.190389, 3320183, 22301130.
    • (2012) Plant Physiol , vol.158 , Issue.4 , pp. 1755-1768
    • Ning, T.1    Hua, Z.2    Xianghua, L.3    Jinghua, X.4    Xiong, L.5
  • 47
    • 0036008353 scopus 로고    scopus 로고
    • Experimentally determined sequence requirement of ACGT-containing abscisic acid response element
    • 10.1093/pcp/pcf014, 11828032
    • Hattori T, Totsuka M. Experimentally determined sequence requirement of ACGT-containing abscisic acid response element. Plant Cell Physiol 2002, 43(1):136-140. 10.1093/pcp/pcf014, 11828032.
    • (2002) Plant Cell Physiol , vol.43 , Issue.1 , pp. 136-140
    • Hattori, T.1    Totsuka, M.2
  • 48
    • 0036464537 scopus 로고    scopus 로고
    • Analysis of the spacing between the two palindromes of activation sequences-1 with respect to binding to different TGA factors and transcriptional activation potential
    • 10.1093/nar/30.3.775, 100291, 11809891
    • Krawczyk S, Thurow C, Niggeweg R, Gatz C. Analysis of the spacing between the two palindromes of activation sequences-1 with respect to binding to different TGA factors and transcriptional activation potential. Nucleic Acids Res 2002, 30:775-781. 10.1093/nar/30.3.775, 100291, 11809891.
    • (2002) Nucleic Acids Res , vol.30 , pp. 775-781
    • Krawczyk, S.1    Thurow, C.2    Niggeweg, R.3    Gatz, C.4
  • 49
    • 0024670927 scopus 로고
    • Saturation mutagenesis of the octopine synthase enhancer: correlation of mutant phenotypes with binding of a nuclear protein factor
    • 10.1073/pnas.86.10.3733, 287214, 2726750
    • Singh K, Tokuhisa JG, Dennis ES, Peacock WJ. Saturation mutagenesis of the octopine synthase enhancer: correlation of mutant phenotypes with binding of a nuclear protein factor. Proc Natl Acad Sci U S A 1989, 86(10):3733-3737. 10.1073/pnas.86.10.3733, 287214, 2726750.
    • (1989) Proc Natl Acad Sci U S A , vol.86 , Issue.10 , pp. 3733-3737
    • Singh, K.1    Tokuhisa, J.G.2    Dennis, E.S.3    Peacock, W.J.4
  • 50
    • 79952697620 scopus 로고    scopus 로고
    • Designer promoter: an artwork of cis engineering
    • 10.1007/s11103-011-9755-3, 21327513
    • Mehrotra R, Gupta G, Sethi R, Bhalothia P, Kumar N, Mehrotra S. Designer promoter: an artwork of cis engineering. Plant Mol Biol 2011, 75(6):527-536. 10.1007/s11103-011-9755-3, 21327513.
    • (2011) Plant Mol Biol , vol.75 , Issue.6 , pp. 527-536
    • Mehrotra, R.1    Gupta, G.2    Sethi, R.3    Bhalothia, P.4    Kumar, N.5    Mehrotra, S.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.