Involvement of DNA methylation in tree development and micropropagation
Tóm tắt
Từ khóa
Tài liệu tham khảo
Altman A, Loberant B (2000) Micropropagation of plants: principles and practices. In: Tj R (ed) Encyclopedia of Cell Technology, vol 1. John Wiley & Sons, Inc., New York, pp 916–929
Alvarez-Venegas R, Avramova Z (2005) Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants. NAR 33:5199–5207
Anderson J, Chao W, Horvath D. (2001) A current review on the regulation of dormancy in vegetative buds. Weed Sci 49:581–589
Arnholdt-Schmitt B, Herterich S, Neumann K (1995) Physiological aspects of genome variavility in tissue culture. I. growth phase-dependent differential DNA methylation of the carrot genome (Daucus carota L.) during primary culture. TAG 91:809–815
Baurens FC, Nicolleau J, Legavre T, Verdeil JL, Monteuuis O (2004) Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker. Tree Physiol 24:401–407
Bonga JM, von Aderkas P (1993) Rejuvenation of tissues from mature conifers and its implications for propagation in vitro. In: Ahuja MR, Libby WJ (eds) Clonal forestry I, genetics and biotechnology. Springer-Verlag, Berlin, Heidelberg, pp 182–199
Brar DS, Jain SM (1998) Somaclonal variation: mechanisms and applications in crop improvement. In: Jain SM, Brar DS, Ahloowalia BS (eds) Somaclonal variation and induced mutations in crop improvement. Kluwer Academic Publishers, Boston, USA, pp17–37
Burn JE, Bagnall DJ, Metzger JD, Dennis ES, Peacock WJ (1993) DNA methylation, vernalization and the initiation of flowering. PNAS 90(1):287–291
Causevic A, Delaunay A, Ounnar S, Righezza M, Delmotte F, Brignolas F, Hagège D, Maury S (2005) DNA methylation and demethylating treatments modify phenotype and cell wall differentiation state in sugarbeet cell lines. Plant Physiol Biochem 43:681–691
Charbit E, Legavre T, Lardet L, Bourgeois E, Ferrière N, Carron MP (2004) Identification of differentially expressed cDNA sequences and histological characteristics of Hevea brasiliensis calli in relation to their embryogenic and regenerative capacities. Plant Cell Rep 22:539–548
de Diego JG, Rodríguez FD, Rodríguez Lorenzo JL, Cervantes E, Grappin P (2006) cDNA-AFLP analysis of seed germination in Arabidopsis thaliana identifies transposons and new genomic sequences . J Plant Physiol 163:452–462
de Keukeleire P, Maes T, Sauer M, Zethof J, Van Montagu M, Gerats T (2001) Analysis by Transposon Display of the behavior of the dTph1 element family during ontogeny and inbreeding of Petunia hybrida. Mol Genet Genomics 265:72–81
Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998) DNA methylation in plants. Annu Rev Plant Physiol Plant Mol Biol 49:223–247
Finnegan J, Kovak KA, Jaligot E, Sheldon CC, Peacock WJ, Dennis ES (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(20):420–432
Finnegan EJ, Peacock WJ, Dennis ES (2000) DNA methylation, a key regulator of plant development and other processes. Curr Opin Gen Dev 10:217–223
Fraga M, Cañal M, Rodriguez R (2002a) Phase-change related epigenetic and physiological changes in Pinus radiata D. Don Planta 215:672–678
Fraga MF, Esteller M (2002) DNA Methylation: A profile of methods and applications. BioTechniques 33(3):632–649
Fraga MF, Rodriguez R, Cañal MJ (2002c) Genomic DNA methylation–demethylation during aging and reinvigoration of Pinus radiata. Tree Physiol 22:813–816
Fraga MF, Uriol E, Diego LB, Berdasco M, Esteller M, Cañal MJ, Rodríguez R (2002b) High-performance capillary electrophoretic method for the quantification of 5-methyl 2′-deoxycytidine in genomic DNA: Application to plant, animal and human cancer tissues. Electrophoresis 23:1677–1681
Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. PNAS 89:1827–1831
Galaud JP, Gaspa T, Boyer N (1993a) Effect of anti-DNA methylation drugs on growth, level of methylated DNA, peroxidase activity and ethylene production of Bryonia dioica internodes. Physiologia plantarum 87:528–534
Galaud JP, Gaspa T, Boyer N (1993b) Inhibition of internode growth due to mechanical stress in Bryonia dioica: relationship between changes in DNA methylation and ethylene metabolism. Physiologia plantarum 87:25–30
Gerger RK, Peacock WJ, Dennis ES, Finnegan EJ (2003) Opposing effects of reduced DNA methylation on flowering time in Arabidopsis thaliana. Planta 2003(3):461–466
Goodrich J, Tweedie S (2002) Remembrance of things past: Chromatin remodelling in plan development. Ann Rev Cell Dev Biol 18:707–746
Grandbastien M (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci Rev 3:181–187
Grant-Downton RT, Dickinson HG (2005) Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. Ann Bot 96:1143–1164
Grant-Downton RT, Dickinson HG (2006) Epigenetics and its implications for plant biology 2. The ‘epigenetic epiphany’: epigenetics, evolution and beyond. Ann Bot 97:11–27
Hasbún R, Valledor L, Berdasco M, Santamaría E, Cañal MJ, Rodríguez R, Rios D, Sánchez M (2005) In vitro proliferation and Genome DNA methylation in adult chesnuts. Act Hort 693:333–339
Hasbún R, Valledor L, Berdasco M, Santamaría E, Cañal MJ, Rodríguez R, (2007) Dynamics of DNA methylation during chestnut trees development, Application to breeding programs. Act Hort (in press)
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. PNAS 93:7783–7788
Horvath D, Chao W, Anderson J, Foley M. (2003) Knowing when to grow: signal transduction processes regulating dormancy in vegetative buds. Trends Plant Sci 8:534–540
Jaligot E, Rival A, Beulé T, Dussert S, Verdeil JL (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19:684–690
Johnston JW, Harding K, Bremner DH, Souch G, Green J, Lynch PT, Grout B, Benson EE (2005) HPLC analysis of plant DNA methylation: a study of critical methodological factors. Plant Physiol Biochem 43:844–853
Jones L, Ratcliff F, Baulcombe DC (2001) RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol 11:747–757
Joyce SM, Cassells AC (2002) Variation in potato microplant morphology in vitro and DNA methylation. Plant Cell Tissue Organ Cult 70:125–137
Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43:179–188
Kaeppler SM, Phillips RL (1993) Tissue culture-induced DNA methylation variation in maize. PNAS 90:8773–8776
Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution in wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. PNAS 97:6603–6607
Karp A (1994) Origins, causes, and uses of variation in plant tissue cultures. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 139–151
Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33:102–106
Kovarìk A, Matyásek R, Leitch B, Gazdová B, Fulnecek J, Bezdek M (1997) Variability in CpNpG methylation in higher plant genomes. Gene 204:308–315
Kubis SE, Castilho AMF, Vershinin AV, Heslop-Harrison JS (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52:69–79
Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak GS, Hao·Bao L (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. TAG 109:200–209
Maekawa M, Hase Y, Shikazono N, Tanaka A (2003) Induction of somatic instability in stable yellow leaf Mutant of rice by ion beam irradiation. Nucl Instr and Meth in Phys Res B 206:579–585
Meijón M (2005) Desarrollo vegetativo y floral en azalea. Marcadores moleculares y fisiológicos de calidad de planta. Dissertation, University of Oviedo
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation Abolishing full DNA methylation in Arabidopsis. Nature 411:212–214
Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marín MI, Martínez-Macias MI, Ariza RR, Roldán Arjona T (2006) Demeter and Repressor Of Silencing 1 encode 5-methylcytosine-DNA glycosylases. PNAS 103:6853–6858
Nakabayashi K, Okamoto M, Koshiba T,Kamiya Y,Nambara E (2005) Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J 41(5):697–709
Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. PNAS 91:5222–5226
Portis E, Acquadro A, Lanteri S (2004) Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 166(1):169–178
Rabinowicz PD, Palmer LE, May BP, Hemann MT, Lowe SW, McCombie WR, Martienssen RA (2003) Genes and transposons are differentially methylated in pants, but not in mammals. Genome Res 13:2658–2664
Ramchandani S, Bhattacharya SK, Cervoni M, Szyf M (1999) DNA methylation is a reversible biological signal. PNAS 96:6107–6112
Rey M, Diaz-Sala C, Rodríguez R (1994) Effect of repeated severe pruning on endogenous polyamine content in hazelnut trees. Physiologia Plantarum 92(3):487–492
Reyes Rosa JC, Gruissem HW (2002) Chromatin-Remodeling and Memory Factors. New Regulators of Plant Development. Plant Physiol 130(3):1090–1101
Richards EJ, Elgin SC (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108:489–500
Rodríguez R, Fraga MF, Pacheco J, Cañal MJ (1998) Envejecimiento vegetal. Una barrera a la propagación vegetativa. Alternativas In: Ríos DG, Olate MS (eds)
Rohde A, Prensen E, De Rycke R, Engler G, Van Montagu M, Boerjan W (2002) PtABI3 impinges on the growth and differentiation of embryonic leaves during bud set in poplar. Plant Cell 14:1885–1901
Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273:654–657
Ruiz-García L, Cervera M, Martínez-Zapater J (2005) DNA methylation increases throughout Arabidopsis development. Planta 222:201–206
Russo VEA, Martienssen RA, Riggs AD (1996) Epigenetic mechanisms of gene regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Salajova T, Salaj J, Kormutak A, (1999) Initiation of embryogenic tissues and plantlet regeneration from somatic embryos of Pinus nigra Arn. Plant Sci 145:33–40
Saze H, Scheid OM, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Gen 34:65–69
Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J, Nilsson P, Bhalerao R (2004) Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J 40:173–187
Shapiro R, Servis RE, Welcher M (1970) Reactions of uracil and cytosine derivatives with sodium bisulfite:a specific deamination method. J Am Chem Soc 92:422–424
Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards A, Peacock WJ, Dennis ES (1999) The FLF Mads Box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458
Shimizu-Sato S, Mori H (2001) Control of outgrowth and dormancy in axillary buds. Plant Physiol 127:1405–1413
Shiraishi M, Hayatsu H (2004) High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of dna methylation. DNA Res 11:409–415
Singer T, Yordan C, Martienssen RA (2001) Robertson’s mutator transposons in A. thaliana are regulated by the chromatin-re-modelling gene Decrease in DNA Methylation (DDM1). Genes Dev 15:591–602
Smulders MJM, Rus-Kortekaas W, Vosman B (1995) Tissue culture-induced DNA methylation polymorphisms in repetitive DNA of tomato calli and regenerated plants. TAG 91:1257–1264
Steimer A, Schob H, Grossniklaus U (2004) Epigenetic control of plant development: new layers of complexity. Curr Opin Plant Biol 7:11–19
Sung S, Amasino R (2004) Vernalization and epigenetics: how plants remember winter. Curr Opin Plant Biol 7:4–10
Valledor L (2005) Monitorización epigenética de la producción comercial de cuatro clones de Pinus radiata D. Don mediante estaquillado y macroinjerto. Dissertation, University of Oviedo
Vlasova TI, Demidenko ZN, Kirnos MD, Vanyushin BF (1995) In vitro DNA methylation by wheat nuclear cytosine DNA methytransferase: effect of phytohormones. Gene 157:279–281
von Aderkas P, Bonga J (2000) Influencing micropropagation and somatic embrygenesis in mature trees by manipulation of phase change, stress and culture environment. Tree Physiol 20:921–928
Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926–1928
Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR, Clarka SJ (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods 27:101–107
Whitelaw E, Martin DIK (2001) Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nat Genet 27:361–365
Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532–2534
Yang I, Park IY, Jang S-M, Shi LH, Ku H-K, Park S-R (2006) Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR. Nucl Acids Res 34(e61):61–69
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201