PDF herunterladen
Plant Biol (Stuttg) 2007; 9(3): 435-441
DOI: 10.1055/s-2006-924633
Short Research Paper

Georg Thieme Verlag Stuttgart KG · New York

The Binding of Nuclear Factors to the as-1 Element in the CaMV 35S Promoter is Affected by Cytosine Methylation in Vitro

A. Kanazawa1 , M. O'Dell2 , R. P. Hellens3
  • 1Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Sapporo 060-8589, Japan
  • 2Department of Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
  • 3Gene Discovery and Functions Department, HortResearch, Private Bag 92 169, Auckland, New Zealand
Weitere Informationen

Publikationsverlauf

Received: June 27, 2006

Accepted: August 15, 2006

Publikationsdatum:
13. November 2006 (online)

  Lizenzen und Reprints

Abstract

Transcriptional gene silencing (TGS) is often associated with an increased level of cytosine methylation in the affected promoters. The effect of methylation of the cauliflower mosaic virus (CaMV) 35S promoter sequence on its binding to factors present in the nuclei was analyzed by electrophoretic mobility shift assays using extracts of petunia flowers. Specific DNA‐protein interactions were detected in the region of the CaMV 35S promoter that contains the as‐1 element and the region between - 345 and - 208. The binding of protein factor(s) to the as‐1 element was influenced by cytosine methylation, whereas the binding to the region between - 345 and - 208 was unaffected. The results suggest that cytosine methylation of the as-1 element potentially affects the activity of the CaMV 35S promoter.

Key words

Cauliflower mosaic virus 35S promoter - cytosine methylation - DNA-protein interaction - electrophoretic mobility shift assay - transcriptional gene silencing

References

  • 1 Amedeo P., Habu Y., Afsar K., Mittelsten Scheid O., Paszkowski J.. Distribution of the plant gene MOM releases transcriptional silencing of methylated genes.  Nature. (2000);  405 203-206
    PubMedSuche in Google Scholar
  • 2 Ashraf S. I., Ip Y. T.. Transcription control: repression by local chromatin modification.  Current Biology. (1998);  8 R683-686
    CrossrefPubMedSuche in Google Scholar
  • 3 Baulcombe D.. RNA silencing in plants.  Nature. (2004);  431 356-363
    CrossrefPubMedSuche in Google Scholar
  • 4 Bednarik D. P., Duckett C., Kim S. U., Perez V. L., Griffis K., Guenthner P. C., Folks T. M.. DNA CpG methylation inhibits binding of NF-kappa B proteins to the HIV‐1 long terminal repeat cognate DNA motifs.  The New Biologist. (1991);  3 969-976
    PubMedSuche in Google Scholar
  • 5 Benfey P. N., Chua N.-H.. The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants.  Science. (1990);  250 959-966
    CrossrefPubMedSuche in Google Scholar
  • 6 Benfey P. N., Ren L., Chua N.-H.. Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development.  The EMBO Journal. (1990);  9 1677-1684
    PubMedSuche in Google Scholar
  • 7 Bird A.. DNA methylation patterns and epigenetic memory.  Genes and Development. (2002);  16 6-21
    CrossrefPubMedSuche in Google Scholar
  • 8 Bird A. P., Wolffe A. P.. Methylation-induced repression - belts, braces and chromatin.  Cell. (1999);  99 451-454
    CrossrefPubMedSuche in Google Scholar
  • 9 Bradford M. M.. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.  Analytical Biochemistry. (1976);  72 248-254
    PubMedSuche in Google Scholar
  • 10 Campanero M. R., Armstrong M. I., Flemington E. K.. CpG methylation as a mechanism for the regulation of E2F activity.  Proceedings of the National Academy of Sciences of the USA. (2000);  97 6481-6486
    CrossrefPubMedSuche in Google Scholar
  • 11 Diéguez M. J., Vaucheret H., Paszkowski J., Mittelsten Scheid O.. Cytosine methylation at CG and CNG sites is not a prerequisite for the initiation of transcriptional gene silencing in plants, but it is required for its maintenance.  Molecular and General Genetics. (1998);  259 207-215
    PubMedSuche in Google Scholar
  • 12 Fromm H., Katagiri F., Chua N. H.. The tobacco transcription activator TGA1a binds to a sequence in the 5′ upstream region of a gene encoding a TGA1a-related protein.  Molecular and General Genetics. (1991);  229 181-188
    PubMedSuche in Google Scholar
  • 13 Gälweiler L., Conlan R. S., Mader P., Palme K., Moore I.. The DNA-binding activity of Gal4 is inhibited by methylation of the Gal4 binding site in plant chromatin.  The Plant Journal. (2000);  23 143-157
    CrossrefPubMedSuche in Google Scholar
  • 14 He X., Fütterer J., Hohn T.. Sequence-specific and methylation-dependent and ‐independent binding of rice nuclear proteins to a rice tungro bacilliform virus vascular bundle expression element.  The Journal of Biological Chemistry. (2001);  276 2644-2651
    CrossrefPubMedSuche in Google Scholar
  • 15 Hermann R., Doerfler W.. Interference with protein binding at AP2 sites by sequence-specific methylation in the late E2A promoter of adenovirus type 2 DNA.  FEBS Letters. (1991);  281 191-195
    CrossrefPubMedSuche in Google Scholar
  • 16 Hershkovitz M., Gruenbaum Y., Renbaum P., Razin A., Loyter A.. Effect of CpG methylation on gene expression in transfected plant protoplasts.  Gene. (1990);  94 189-193
    CrossrefPubMedSuche in Google Scholar
  • 17 Holler M., Westin G., Jiricny J., Schaffner W.. Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated.  Genes and Development. (1988);  2 1127-1135
    PubMedSuche in Google Scholar
  • 18 Iguchi-Ariga S. M., Schaffner W.. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific binding as well as transcriptional activation.  Genes and Development. (1989);  3 612-619
    PubMedSuche in Google Scholar
  • 19 Inamdar N. M., Ehrlich K. C., Ehrlich M.. CpG methylation inhibits binding of several sequence-specific DNA-binding proteins from pea, wheat, soybean and cauliflower.  Plant Molecular Biology. (1991);  17 111-123
    CrossrefPubMedSuche in Google Scholar
  • 20 Jackson J. P., Lindroth A. M., Cao X., Jacobsen S. E.. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.  Nature. (2002);  416 556-560
    PubMedSuche in Google Scholar
  • 21 Jones L., Ratcliff F., Baulcombe D. C.. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance.  Current Biology. (2001);  11 747-757
    CrossrefPubMedSuche in Google Scholar
  • 22 Jorgensen R. A., Cluster P. D., English J., Que Q., Napoli C. A.. Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single-copy vs. complex T‐DNA sequences.  Plant Molecular Biology. (1996);  31 957-973
    CrossrefPubMedSuche in Google Scholar
  • 23 Kanazawa A., O'Dell M., Hellens R. P., Hitchin E., Metzlaff M.. Mini-scale method for nuclear run-on transcription assay in plants.  Plant Molecular Biology Reporter. (2000);  18 377-383
    PubMedSuche in Google Scholar
  • 24 Kapoor A., Agarwal M., Andreucci A., Zheng X., Gong Z., Hasegawa P. M., Bressan R. A., Zhu J.-K.. Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis.  Current Biology. (2005);  15 1912-1918
    CrossrefPubMedSuche in Google Scholar
  • 25 Kass S. U., Pruss D., Wolffe A. P.. How does DNA methylation repress transcription?.  Trends in Genetics. (1997);  13 444-449
    CrossrefPubMedSuche in Google Scholar
  • 26 Katagiri F., Lam E., Chua N.-H.. Two tobacco DNA-binding proteins with homology to the nuclear factor CREB.  Nature. (1989);  340 727-730
    PubMedSuche in Google Scholar
  • 27 Krawczyk S., Thurow C., Niggeweg R., Gatz C.. Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential.  Nucleic Acids Research. (2002);  30 775-781
    CrossrefPubMedSuche in Google Scholar
  • 28 Kunze R.. The maize transposable element Activator (Ac). Saedler, H. and Gierl, A., eds. Transposable Elements. Berlin, Heidelberg; Springer-Verlag (1996): 161-194
    Suche in Google Scholar
  • 29 Lam E., Benfey P. N., Gilmartin P. M., Fang R.-X., Chua N.-H.. Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants.  Proceedings of the National Academy of Sciences of the USA. (1989);  86 7890-7894
    CrossrefPubMedSuche in Google Scholar
  • 30 Matzke M. A., Birchler J. A.. RNAi-mediated pathways in the nucleus.  Nature Reviews Genetics. (2005);  6 24-35
    CrossrefPubMedSuche in Google Scholar
  • 31 Metzlaff M., O'Dell M., Cluster P. D., Fravell R. B.. RNA-mediated degradation and chalcone synthase A silencing in petunia.  Cell. (1997);  88 845-854
    CrossrefPubMedSuche in Google Scholar
  • 32 Meyer P., Niedenhof I., ten Lohuis M.. Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida.  The EMBO Journal. (1994);  13 2084-2088
    PubMedSuche in Google Scholar
  • 33 Montminy M. R., Sevarino K. A., Wagner J. A., Mandel G., Goodman R. H.. Identification of a cyclic-AMP-responsive element within the rat somatostatin gene.  Proceedings of the National Academy of Sciences of the USA. (1986);  83 6682-6686
    CrossrefPubMedSuche in Google Scholar
  • 34 Muskens M. W. M., Vissers A. P. A., Mol J. N. M., Kooter J. M.. Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing.  Plant Molecular Biology. (2000);  43 243-260
    CrossrefPubMedSuche in Google Scholar
  • 35 Napoli C., Lemieux C., Jorgensen R.. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans.  Plant Cell. (1990);  2 279-289
    CrossrefPubMedSuche in Google Scholar
  • 36 Niggeweg R., Thurow C., Weigel R., Pfitzner U., Gatz C.. Tobacco TGA factors differ with respect to interaction with NPR1, activation potential and DNA-binding properties.  Plant Molecular Biology. (2000);  42 775-788
    CrossrefPubMedSuche in Google Scholar
  • 37 O'Dell M., Metzlaff M., Fravell R. B.. Post-transcriptional gene silencing of chalcone synthase in transgenic petunias, cytosine methylation and epigenetic variation.  The Plant Journal. (1999);  18 33-42
    CrossrefPubMedSuche in Google Scholar
  • 38 Otagaki S., Arai M., Takahashi A., Goto K., Hong J.-S., Masuta C., Kanazawa A.. Rapid induction of transcriptional and post-transcriptional gene silencing using a novel Cucumber mosaic virus vector.  Plant Biotechnology. (2006);  23 259-265
    PubMedSuche in Google Scholar
  • 39 Park Y.-D., Papp I., Moscone E. A., Iglesias V. A., Vaucheret H., Matzke A. J. M., Matzke M. A.. Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity.  The Plant Journal. (1996);  9 183-194
    CrossrefPubMedSuche in Google Scholar
  • 40 Pradhan S., Urwin N. A. R., Jenkins G. I., Adams R. L. P.. Effect of CWG methylation of expression of plant genes.  Biochemical Journal. (1999);  341 473-476
    CrossrefPubMedSuche in Google Scholar
  • 41 Razin A., Kafri T.. DNA methylation from embryo to adult.  Progress in Nucleic Acid Research and Molecular Biology. (1994);  48 53-81
    PubMedSuche in Google Scholar
  • 42 Rossi V., Motto M., Pellegrini L.. Analysis of the methylation pattern of the maize opaque-2 (O2) promoter and in vitro binding studies indicate that the O2 b-Zip protein and other endosperm factors can bind to methylated target sequences.  The Journal of Biological Chemistry. (1997);  272 13758-13765
    CrossrefPubMedSuche in Google Scholar
  • 43 Scebba F., Bernacchia G., De Bastiani M., Evangelista M., Cantoni R. M., Cella R., Locci M. T., Pitto L.. Arabidopsis MBD proteins show different binding specificities and nuclear localization.  Plant Molecular Biology. (2003);  53 755-771
    CrossrefPubMedSuche in Google Scholar
  • 44 Sijen T., Vijn I., Rebocho A., van Blokland R., Roelofs D., Mol J. N. M., Kooter J. M.. Transcriptional and posttranscriptional gene silencing are mechanistically related.  Current Biology. (2001);  11 436-440
    CrossrefPubMedSuche in Google Scholar
  • 45 Staiger D., Kaulen H., Schell J.. A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein.  Proceedings of the National Academy of Sciences of the USA. (1989);  86 6930-6934
    CrossrefPubMedSuche in Google Scholar
  • 46 Sturaro M., Viotti A.. Methylation of the Opaque2 box in zein genes is parent-dependent and affects O2 DNA binding activity in vitro.  Plant Molecular Biology. (2001);  46 549-560
    CrossrefPubMedSuche in Google Scholar
  • 47 Weber H., Graessmann A.. Biological activity of hemimethylated and single-stranded DNA after direct gene transfer into tobacco protoplasts.  FEBS Letters. (1989);  253 163-166
    CrossrefPubMedSuche in Google Scholar
  • 48 Xiang C., Miao Z., Lam E.. DNA-binding properties, genomic organization and expression pattern of TGA6, a new member of the TGA family of bZIP transcription factors in Arabidopsis thaliana.  Plant Molecular Biology. (1997);  34 403-415
    CrossrefPubMedSuche in Google Scholar

A. Kanazawa

Graduate School of Agriculture
Hokkaido University

Kita 9, Nishi 9

Sapporo 060-8589

Japan

eMail: kanazawa@res.agr.hokudai.ac.jp

Editor: M. Koornneef