Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/22402
標題: 冰花Ppc1基因在生長發育過程與鹽逆境處理下啟動子甲基化變化之研究
Changes in promoter methylation pattern of ice plant Ppc1 gene during development and under salt stress
作者: 李俊毅
Lee, Jun-Yi
關鍵字: ice plant;冰花;Ppc1;methylation;promoter;stress;Ppc1;甲基化;啟動子;逆境
出版社: 生命科學系所
引用: Adams, P., Nelson, D., Yamada, S., Chmara, W., Jensen, R.G., Bohnert, H.J., and Griffiths, H. (1998). Growth development of Mesembryanthemum crystallinum (Aizoaceae). New Phytol. 138, 171-190. Adams, P., Vernon, D.M., Thomas, J.C., Bohnert, H.J., and Jenson R.G. (1992). Distinct cellular and organismic responses to salt strss. Plant Cell Physiol. 33, 1215-1223. Angell, S.M., and Baulcombe, D.C. (1997). Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. EMBO J. 16, 3675-3684. Antequera, F., and Bird, A. (1993). Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA 90, 11995-11999. Bednarik, D.P., Duckett, C., Kim, S.U., Perez, V.L., Griffis, K., Guenthner, P.C., and Folks, T.M. (1991). DNA CpG methylation inhibits binding of NF-kappa B proteins to the HIV-1 long terminal repeat cognate DNA motifs. New Biol. 3, 969-976. Bender, J. (2004). DNA methylation and epigenetics. Annu. Rev. Plant Physiol. Plant Mol. Biol. 55, 41-68. Berg, A., Meza, T.J., Mahic´, M., Thorstensen, T., Kristiansen, K., and Aalen, R.B. (2003). Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development. Nucleic Acid Res. 31, 5291-5304. Bird, A. (1992). The essentials of DNA methylation. Cell 70, 5-8. Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21 Bird, A., Taggart, M., Frommer, M., Miller, O.J., and Macleod. D. (1985). A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40, 91-99. Bird, A.P. (1996). The relationship of DNA methylation to cancer. Cancer Surv. 28, 87-101 Bird, A.P., Taggart, H., Nicholls, R.D., and Higgs, D.R. (1987). Non-methylated CpG -rich islands at the human alpha-globin locus: implications for evolution of the alpha-globin pseudogene. EMBO J. 6, 999-1004. Bird, A.P., amd Wolffe, A.P. (1999). Methylation-induced repression—belts, braces, and chromatin. Cell 99, 451-454. Bohnert H.J. and Cushman, J. (2000). The ice plant cometh: lessons in abiotic strss tolerance. J. Plant Growth Regul. 19, 334-346. Bohnert, H.J., and Cushman, J.C. (2001). The ice plant cometh: lessons in abiotic stress tolerance. J. Plant Growth Regul. 19, 334-34 Burn, J.E., Bagnall, D.J., Metzger, J.D., Dennis, E.S., and Peacock, W.J. (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl Acad. Sci. USA 90, 287-291. Campanero, M.R., Armstrong, M.I., and Flemington, E.K. (2000). CpG methylation as a mechanism for the regulation of E2F activity. Proc. Natl. Acad. Sci. USA 97, 6481-6486. Chan, S.W., Henderson, I.R., and Jacobsen, S.E. (2005). Gardening the genome: DNA methylation Arabidopsis thaliana. Nat Rev Genet. 6, 351-360. Clark, S.J., Harrison, J., Paul, C.L., and Frommer, M. (1994). High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990-2997. Comb, M., and Goodman, H.M. (1990). CpG methylation inhibits preenkephalin gene expression and binding of the transcription factor AP-2. Nucleic Acids Res. 18, 3975-3982. Costello, J.F., Plass, C. (2002). Methylation matters. J. Med Genet. 38, 285-303. Cross, S.H., and Bird, A.P. (1995). CpG islands and genes. Curr. Opin. Genet. Dev. 5, 309-314. Cushman, J.C., Meyer, G., Michalowski, C.B., Schmitt, J.M., and Bohnert, H.J. (1989). Salt stress leads to differential expression of two isogenes of phosphoenolpyruvate carboxylase during Crassulacean acid metabolism induction in the common ice plant. Plant Cell 1, 715-725. Cushman, J.C., Vernon, D.M., and Bohnert, H.J. (1993). ABA and the transcriptional control of CAM induction during salt stress in the common ice plant. In DPS Verma, ed, Control of Plant Gene Expression. CRC Press, Boca Raton, FL, pp 287-300 Dalmay, T., Hamilton, A., Rudd, S., Susan, A., and Baulcombe. D.C. (2000). An RNA-Dependent RNA polymerase gene in Arabidopsis Is Required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101, 543-553. Douglas, U.K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685. Dyachenko, O.V., Zakharchenko, N.S., Shevchuk, T.V., Bohnert, H.J., Cushman, J.C., and Buryanov, Y.I. (2006). Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochemistry (Mosc.) 71, 461-465. Ehrich, M., and Wang, R.Y. (1981). 5-Methylcytosine in eukaryotic DNA. Science 212, 1350-1357. Finnegan, E.J., and Kovac, K.A. (2000). Plant DNA methyltransferases. Plant Mol. Biol. 43, 189-201. Finnegan, E.J., Kovac, K.A., Jaligot, E., Sheldon, C., Peacock, W.J., and Dennis, E.S. (2005). The downregulation of FLOWERING LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms. Plant J. 44, 420-432. Fujimori, S., Washio, T., and Tomita, M. (2005). GC-compositional strand bias around transcription start sites in plant and fungi. BMC Genomics 6, 26-37. Gardiner-Garden, M., and Frommer, M. (1987). CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282. Gruenbaum, Y., Stein, H., Cedar, H., and Razin, A. (1981). Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 124, 67-71. Gupta, S.K., Ku, M.SB., Lin, J.H., Zhang, D., Edwards, C.E. (1994). Light/dark modulation of phosphoenolpyruvate carboxylase in C3 and C4 species. Photo Res. 42, 133-143. Hagen, G., and Guilfoyle. T.J. (1985). Rapid induction of selective transcription by auxins. Mol. Cell Biol. 5, 1197-1203. Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D., and Baylin, S.B. (1996). Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA. 93, 9821-9826. Hofner, R., Vazquez-Moreno, L., Winter, K., Bohnert, H.J., and Schmitt, J.M. (1987). Induction of Crassulacean Acid Metabolism in Mesembryanthemum crystallinum by High Salinity: Mass Increase and de Novo Synthesis of PEP-Carboxylase. Plant Physiol. 83, 915-919. Holtum, J.A.M., and Winter, K. (1982). Activity of enzymes of carbon metabolism during the induction of Crassulacean acid metabolism in Mesembryanthemum crystallinum L. Planta 155, 8-16. Huang, T.H., Perry, M.R., and Laux, D.E. (1999). Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8, 459-470. Ingelbrechit, I., Houdt, H.V., Montagu, M.V., and Depicker, A. (1994). Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. Proc. Natl. Acad. Sci. USA 91,7347-7351. Iguchi-Ariga, S.M., and Schaffner, W. (1989). CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev. 3, 612-619. Ito, M., Koike, A., Koizumi, N., and Sano, H. (2003). Methylated DNA-binding proteins from Arabidopsis. Plant Physiol. 133, 1747-1754. Jaenisch, R., and Jahner, D. (1984). Methylation, expression and chromosomal position of genes in mammals. Biochem. Biophys. Acts 782, 1-9. Jullien, P.E., Kinoshita, T., Ohad, M., Berger, F. (2006). Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18, 1360-1372. Latzko, E., and Kelly, G.L. (1983). The many-faceted function of phosphoenolpyruvate carboxylase in C3 plants. Physiologie VeÂgeÂtale 21, 805-815. Mette, M.F., Aufsatz, W., van der Winden, J., Matzke, M.A., and Matzke, A.J.M. (2000). Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194-5201. Michalowski, C.B., Olson, S.W., Piepenbrock, M., Schmitt, J.M., and Bohnert, H.J. (1989). Time Course of mRNA Induction Elicited by Salt Stress in the Common Ice Plant (Mesembryanthemum crystallinum). Plant Physiol. 89, 811-816. Meyer, P., Niedenhof, I., and ten Lohuis, M. (1994). Evidence for cytosine methylation of non symmetrical sequence in plants. EMBO J. 13, 2084-2088. Meza, T.J., Kamfjord, D., Hakelien, A-M., Evans, I., Godager, L.H., Mandal, A., Jakobsen, K.S., and Aalen, R.B. (2001). The frequency of silencing in Arabidopsis thaliana varies highly between progeny of siblings and can be influenced by environmental factors. Transgenic Res. 10, 53-67. Nakano, Y., Steward, N., Kusano, T., and Sano, H. (2000). A tobacco NtMET1 encoding a DNA methyltransferase: molecular characterization and abnormal phenotypes of antisense transgenic tobacco plants. Plant Cell Physiol. 41, 448-457. Nan, X., Ng, H.H., Johnson, C.A., Laherty, C.D., Turner, B.M., Eisenman, R. N., and Bird, A. (1998). Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386-390. Ng, H.H., and Bird, A. (1999). DNA methylation and chromatin modification. Curr. Opin. Genet. Dev. 9, 158-163. Ordway, J.M., and Curran, T. (2002). Methylation matters: modeling a manageable genome. Cell Growth Differ. 13, 149-162. Ostrem, J.A. Olson, S.W. Schmitt, J.M., and Bohnert, H.J. (1987). Salt Stress increases the level of translatable mRNA for phosphoenolpyruvate carboxylase in Mesembryanthemum crystallinum. Plant Physiol. 84, 1270-1275. Peng, M., Cui, Y., Bi, Y-M., and Rothstein, S.J. (2006). AtMBD9: a protein with a methyl-CpG-binding domain regulated flowering time and shoot branching in Arabidopsis. Plant J. 46, 282-296. Prendergast, G.C., Lawe, D., and Ziff, E.B. (1991). Association of Myn, the murine homolog of max, with c-Myc stimulates methylation-sensitive DNA binding and ras cotransformation. Cell 65, 395-407. Razin, A., and Cedar, H. (1991). DNA methylation and gene expression. Microbiol. Rev. 55, 451-458. Ruiz-Garica. L., Cervera, M.T., Martinez-Zapater, J.M. (2005). DNA methylation increase throughout Arabidopsis development. Planta 222, 301-306. Sado, T., and Ferguson-Smith, A.C. (2005). Imprinted X inactivation and reprogramming in the preimplantation mouse embryo. Hum. Mol. Genet. 14 (suppl_1), R59-R64. Scebba, F., Bernacchia, G., De Bastiani, M., Evangelista, M., Cantoni, R.M., Cella, R., Locci, M.T., and Pitto, L. (2003). Arabidopsis MBD proteins show different binding specificities and nuclear localization. Plant Mol. Biol. 53, 715-731. Schaeffer, H.J., Forsthoefel, N.R., and Cushman, J.C. (1995). Identification of enhancer and silencer regions involved in salt-responsive expression of Crassulacean acid metabolism (CAM) genes in the facultative halophyte Mesembryanthemum crystallinum. Plant Mol Biol. 28, 205-218. Singal, R., and Ginder, G.D. (1999). DNA methylation. Blood 93, 4059-4070. Shapiro, R., Braverman, B., Louis, J.B., and Servis, R.E. (1973). Nucleic acid reactivity and conformation. II. Reaction of cytosine and uracil with sodium bisulfite. J. Biol. Chem. 248, 4060-4064. Springer, N.M., and Kaeppler, S.M. (2005). Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiol. 138, 92-104 Stam, M. Viterbo, A., Mol, J.N.M., and Kooter, J.M. (1998). Position-Dependent Methylation and Transcriptional Silencing of Transgenes in Inverted T-DNA Repeats: Implications for Posttranscriptional Silencing of Homologous Host Genes in Plants. Mol. Cell Biol. 11, 6165-6177. Steward, N., Ito, M., Yamaguchi, Y., Koizumi, N., and Sano, H. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741-37746. Tariq, M., and Paszkowski, J. (2004). DNA and histone methylation in plant. Trends Genet. 20, 244-251. Tate, P.H., and Bird, A.P. (1993). Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3, 226-231. Tchurikov, N. A. (2005). Molecular mechanisms of epigenetics. Biochemistry (Mosc) 70, 406-423. Teixeira, S.M.R., and daRocha W.D. (2003). Control of gene expression and genetic manipulation in the trypanosomatidae. Genet. Mol. Res. 2, 148-158. Thomashow, M.F. (1998). Role of cold-responsive genes in plant freezing tolerance. Plant Physiol. 118, 1-8. Toyota, M., Ho, C., Ahuja, N., Jair, K.W., Li, Q., Ohe-Toyota, M., Baylin, S.B., and Issa, J.P. (1999). Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res. 59, 2307-2312. Vaucheret, H., Beclin, C., and Fagard, M. (2001). Post-transcriptional gene silencing in plants. J. Cell Sci. 114, 3083-3091. Vaucheret, H., and Fagard, M. (2001). Transcriptional gene silencing in plant: targets, inducers and regulators. Trends Genet. 17, 29-35. Wada, Y., Miyamoto, K., Kusano, T., Sano, H. (2004). Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol. Genet. Genomics 271, 658-666. Wasseneggers, M., Heimes, S., and Sanger, H.L. (1994). An infectious viroid RNA replicon evolved from an in vitro-generated non-infectious viroid deletion mutant via a complementary deletion in vivo. EMBO J. 13, 6172-6177. Warnevke, P.M., Mann, J.R., Frommer, M., and Clark, S.J. (1998). Bisulfite sequencing in preimplantation embryos: DNA methylation profile of the upstream region of the mouse imprinted H19 gene. Genomics 51, 182-190. Xiong, Z., and Larid, P.W. (1997). COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acid Res. 25, 2532-2534. Yoder, J.A., Walsh, C.P., and Bestor, T.H. (1997). Cytosine methylation and the ecology of intragenomics parasites. Trends Genet. 13, 335-340. Zemach, A., and Grafi, G. (2003). Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J. 34, 565-572.
摘要: 
耐鹽植物冰花(Mesembryanthemum crystallinum L.)由於在生長發育過程中,鹽誘導光合作用形式的轉換(C3 to Crassulacean Acid Metabolism)及耐鹽機制的啟動均牽涉到許多基因表現層次的變化,因此被視為研究高等植物耐鹽機制的模式植物。在CAM型光合作用中把無機碳轉成有機酸的第一個酵素為PEPC (phosphoenolpyruvate carboxylase),已知在鹽逆境誘導光合作用形式轉換過程中此酵素活性的升高原因之一是由於Ppc1基因表現增加。在真核生物基因組中,調節基因表現的重要機制之ㄧ為DNA甲基化。本論文利用亞硫酸鈉定序及南方墨點等方法來確認冰花在生長發育及鹽逆境處理下Ppc1基因轉錄起始點附近是否有甲基化改變。結果指出經亞硫酸鈉定序並結合南方墨點法發現在Ppc1基因啟動子上特定抑制子結合區域經光合作用轉換後甲基化程度提高,推測Ppc1啟動子藉由特定序列的甲基化來干擾與抑制子的結合;進一步分析發現在Ppc1基因5’UTR位置,其特定序列的DNA甲基化程度下降,推測去甲基化增加Ppc1基因表現之程度。兩者雖然甲基化程度變化不同,但均可使得基因表現增加。根據以上結果推測,鹽逆境下Ppc1基因藉由特定序列的甲基化來干擾與抑制子結合以及降低5’UTR甲基化程度來啟動基因表現。

The facultative halophyte Mesembryanthemum crystallinum L. (ice plant) is a well-established model for studying plant salt stress. A large number of genes are expressed during switching from C3 to Crassulacean Acid Metabolism (CAM) photosynthesis and the induction of salt-tolerant mechanism, therefore ice plant is suggested as a model for studying salt tolerance in higher plants. Phosphoenolpyruvate carboxylase (PEPC) is the first enzyme in the CAM-photosynthesis. The amounts of the PEPC and the corresponding mRNA sharply increased in ice plant under salt stress. One of the main factors that contribute to the induction of PEPC is the increase in the transcription of the Ppc1 gene. Enzymatic methylation of DNA is a major way to regulate gene expression in eukaryotes. In this thesis, the possible influence in Ppc1 expression by DNA methylation was examined. Bisulfite sequencing and Southern blotting were used to identity the changes in DNA methylation pattern of Ppc1 gene in salt-induced transition from C3 to CAM. The results showed the methylation status of certain cytosines was changed, either becoming methylated or demethylated in the region around the transcription start sites of Ppc1. The significance of this finding related to the salt-induced Ppc1 expression is discussed.
URI: http://hdl.handle.net/11455/22402
其他識別: U0005-2408200617443900
Appears in Collections:生命科學系所

Show full item record
 

Google ScholarTM

Check


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.