Abstract
In vitro culture is one of the most studied techniques, and it is used to study many developmental processes, especially in forestry species, because of growth timing and easy manipulation. Epigenetics has been shown as an important influence on many research analyses such as cancer in mammals and developmental processes in plants such as flowering, but regarding in vitro culture, techniques to study DNA methylation or chromatin modifications were mainly limited to identify somaclonal variation of the micropropagated material. Because in vitro culture is not only a way to generate plant material but also a bunch of differentially induced developmental processes, an approach of techniques and some research carried out to study the different changes regarding DNA methylation and chromatin and translational modifications that take place during these processes is reviewed.
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References
Abarca D, Díaz-Sala C (2009) Reprogramming adult cells during organ regeneration in forest species. Plant Signal Behav 4:793–795
Bhalla P, Singh M (2006) Molecular control of stem cell maintenance in shoot apical meristem. Plant Cell Rep 25:249–256
Law RD, Suttle JC (2005) Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions. Plant Physiol Biochem 43:527–534
Pischke MS, Huttlin EL, Hegeman AD, Sussman MR (2006) A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol 140:1255
Grandbastien M (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181–187
Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43:179–188
Martienssen RA, Kloc A, Slotkin RK, Tanurdzic M (2008) Epigenetic inheritance and reprogramming in plants and fission yeast. In: Cold Spring Harbor Symp Quant Biol. Cold Spring Harbor Laboratory Press, pp 265–271
Costa S, Shaw P (2007) ‘Open minded’ cells: how cells can change fate. Trends Cell Biol 17:101–106
Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286:481
Li G, Hall TC, Holmes-Davis R (2002) Plant chromatin: development and gene control. Bioessays 24:234–243
Cedar H, Bergman Y (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10:295–304
Okitsu CY, Hsieh CL (2007) DNA methylation dictates histone H3K4 methylation. Mol Cell Biol 27:2746
Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20:244–251
Thomas AJ, Sherratt HSA (1956) The isolation of nucleic acid fractions from plant leaves and their purine and pyrimidine composition. Biochem J 62:1–4
Wyatt GR (1951) Recognition and estimation of 5-methylcytosine in nucleic acids. Biochem J 48:581
Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201
Gruenbaum Y, Naveh-Many T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292:860–862
Bowler C, Benvenuto G, Laflamme P et al (2004) Chromatin techniques for plant cells. Plant J 39:776–789
Fraga MF, Esteller M (2002) DNA methylation: a profile of methods and applications. Biotechniques 33:632–649
Fraga MF, Cañal MJ, Rodríguez R (2002) Phase change related epigenetic and physiological changes in Pinus radiata D. Don. Planta 215:672–676
Jaligot E, Rival A, Beule T et al (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19:684–690
Causevic A, Delaunay A, Ounnar S et al (2005) DNA methylating and demethylating treatments modify phenotype and cell wall differentiation state in sugarbeet cell lines. Plant Physiol Biochem 43:681–691
Fraga MF, Rodríguez R, Cañal MJ (2000) Rapid quantification of DNA methylation by high performance capillary electrophoresis. Electrophoresis 21:2990–2994
Hasbún R, Valledor L, Rodríguez JL et al (2008) HPCE quantification of 5-methyl-2′-deoxycytidine in genomic DNA: methodological optimization for chestnut and other woody species. Plant Physiol Biochem 46:815–822
Johnston JW, Harding K, Bremner DH et al (2005) HPLC analysis of plant DNA methylation: a study of critical methodological factors. Plant Physiol Biochem 43:844–853
Magaña AA, Wrobel K, Caudillo YA et al (2008) High-performance liquid chromatography determination of 5-methyl-2′-deoxycytidine, 2′-deoxycytidine, and other deoxynucleosides and nucleosides in DNA digests. Anal Biochem 374:378–385
Valledor L, Meijón M, Hasbún R et al (2009) Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability. J Plant Physiol 167:351–357
Fraga MF, Cañal MJ, Aragones A, Rodriguez R (2002) Factors involved in Pinus radiata D. Don. micrografting. Ann For Sci 59:155–161
Hasbún R, Valledor L, Berdasco M et al (2007) Dynamics of DNA methylation during chestnut trees development, Application to breeding programs. Act Hort 760:563
Viejo M, Rodríguez R, Valledor L et al (2010) DNA methylation during sexual embryogenesis and implications on the induction of somatic embryogenesis in Castanea sativa Miller. Sex Plant Reprod 23:315–323
Baurens FC, Nicolleau J, Legavre T et al (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
Marum LM, Hasbún R, Rodriguez R et al (2008) Epigenetic Studies in Embryogenic Culture of Pinus pinaster. In: Laamanen J, Uosukainen M, Häggman H et al (eds) Cryoperservation of crop species in Europe. COST Action 871, Oulu, Finland, p 69
Bionti MB, Cozza R, Chiappetta A et al (2002) Distinct nuclear organization, DNA methylation pattern and cytokinin distribution mark juvenile, juvenile-like and adult vegetative apical meristems in peach (Prunus persica (L.) Batsch). J Exp Bot 53:1047–1054
Fraga MF, Rodríguez R, Cañal MJ (2002) Genomic DNA methylation-demethylation during ageing-reinvigoration of Pinus radiata. Tree Physiol 22:813–816
Monteuuis O, Doulbeau S, Verdeil JL (2008) DNA methylation in different origin clonal offspring from a mature Sequoiadendron giganteum genotype. Trees Struct Funct 22:779–784
Zluvova J, Janousek B, Vyskot B (2001) Immunoshistochemical study of DNA methylation dynamics during plant development. J Exp Bot 52:2265–2273
Meijon M, Feito I, Valledor L et al (2010) Dynamics of DNA methylation and Histone H 4 acetylation during floral bud differentiation in azalea. BMC Plant Biol 10:10
Meijón M, Rodríguez R, Jesús Cañal M, Feito I (2009) Improvement of compactness and floral quality in azalea by means of application of plant growth regulators. Sci Hortic 119:169–176
Zhao Y, Zhou Y, Grout BWW (2008) Alterations in flower and seed morphologies and meiotic chromosome behaviors of micropropagated rhubarb (Rheum rhaponticum L.) PC49′. Sci Hortic 116:162–168
Santamaría ME, Hasbún R, Valera MJ et al (2009) Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. J Plant Physiol 166:1360–1369
Bordallo PN, Silva DH, Maria J et al (2004) Somaclonal variation on in vitro callus culture potato cultivars. Hortic Bras 22:300–304
Côte FX, Teisson C, Perrier X (2001) Somaclonal variation rate evolution in plant tissue culture: contribution to understanding through a statistical approach. In Vitro Cell Dev Biol Plant 37:539–542
Huang THM, Perry MR, Laux DE (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8:459
He X, Chang S, Zhang J et al (2008) Methy cancer: the database of human DNA methylation and cancer. Nucleic Acids Res 36:D836–D841
Schumacher A, Kapranov P, Kaminsky Z et al (2006) Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 34:528–542
Jaligot E, Beulé T, Rival A (2002) Methylation-sensitive RFLPs: characterisation of two oil palm markers showing somaclonal variation-associated polymorphism. Theor Appl Genet 104:1263–1269
Gonzalgo ML, Liang G, Spruck CH et al (1997) Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res 57:594
Park SY, Murthy HN, Chakrabarthy D, Paek KY (2009) Detection of epigenetic variation in tissue-culture-derived plants of Doritaenopsis by methylation-sensitive amplification polymorphism (MSAP) analysis. In Vitro Cell Dev Biol Plant 45:104–108
Causevic A, Gentil MV, Delaunay A et al (2006) Relationship between DNA methylation and histone acetylation levels, cell redox and cell differentiation states in sugarbeet lines. Planta 224:812–827
Oh TJ, Cullis MA, Kunert K et al (2007) Genomic changes associated with somaclonal variation in banana (Musa spp.). Physiol Plant 129:766–774
Rauch T, Pfeifer GP (2005) Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85:1172–1180
Weber M, Davies JJ, Wittig D et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862
Rauch TA, Pfeifer GP (2010) DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). Methods 52:213–217
Weng YI, Huang TH, Yan PS (2009) Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. Methods Mol Biol 590:165
Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532
Clark SJ, Frommer M (1995) Deamination with NaHSO3 in DNA methylation studies, DNA and nucleoprotein structure in vivo. Springer Verlag, Heidelberg, Germany, pp 123–135
Gonzalgo ML, Liang G (2007) Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) for quantitative measurement of DNA methylation. Nat Protoc 2:1931–1936
Gitan RS, Shi H, Chen CM et al (2002) Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12:158
Herman J, Graff J, Myöhänen S et al (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93:9821–9826
Eads CA, Danenberg KD, Kawakami K et al (2000) MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28:E32
Afonina I, Zivarts M, Kutyavin I et al (1997) Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder. Nucleic Acids Res 25:2657
Zeschnigk M, Böhringer S, Price EA et al (2004) A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus. Nucleic Acids Res 32:e125
Frommer M, McDonald LE, Millar DS et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827–1831
Tusnády GE, Simon I, Váradi A, Tamás A (2005) BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Res 33:e9
Berdasco M, Alcázar R, García-Ortiz MV et al (2008) Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS One 3:e3306. doi:10.1371/journal.pone.0003306
Ngezahayo F, Xu C, Wang H et al (2009) Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Biol 9:91
Dupont J, Tost T, Jammes H, Gut IG (2004) De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal Biochem 333:119–127
Xiao W, Oefner PJ (2001) Denaturing high performance liquid chromatography: a review. Hum Mutat 17:439–474
Deng D, Deng G, Smith MF et al (2002) Simultaneous detection of CpG methylation and single nucleotide polymorphism by denaturing high performance liquid chromatography. Nucleic Acids Res 30:e13
Wagner D (2003) Chromatin regulation of plant development. Curr Opin Plant Biol 6:20–28
Jarillo JA, Piñeiro M, Cubas P, Martínez-Zapater JM (2009) Chromatin remodeling in plant development. Int J Dev Biol 53:1581–1596
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Freitas MA, Sklenar AR, Parthun MR (2004) Application of mass spectrometry to the identification and quantification of histone post translational modifications. J Cell Biochem 92:691–700
Valledor L, Meijón M, Hasbún R et al (2010) Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability. J Plant Physiol 167:351–357
Garcia BA, Shabanowitz J, Hunt DF (2007) Characterization of histones and their post-translational modifications by mass spectrometry. Curr Opin Chem Biol 11:66–73
Gurley LR, Valdez JG, Prentice DA, Spall WD (1983) Histone fractionation by high-performance liquid chromatography. Anal Biochem 129:132–144
Olsen JV, Mann M (2004) Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci USA 101:13417
Siuti N, Kelleher NL (2007) Decoding protein modifications using top-down mass spectrometry. Nat Methods 4:817–821
Thiede B, Höhenwarter W, Krah A et al (2005) Peptide mass fingerprinting. Methods 35:237–247
Saleh A, Alvarez-Venegas R, Yilmaz M et al (2008) The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell 20:568
Haring M, Offermann S, Danker T et al (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:11
Reimer J, Turck F (2010) Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part A: ChIP-chip molecular methods. In: Kovalchuk I, Zemp F (eds) Plant epigenetics: methods and protocols. Springer, Hatfeld, pp 139–160
Ricardi MM, González RM, Iusem ND (2010) Protocol: fine-tuning of a Chromatin Immunoprecipitation(ChIP) protocol in tomato. Plant Methods 6:11
Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7:81–102
Roh T, Ngau WC, Cui K et al (2004) High-resolution genome-wide mapping of histone modifications. Nat Biotechnol 22:1013–1016
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484
Impey S, McCorkle SR, Cha-Molstad H et al (2004) Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 119:1041–1054
Marinescu VD, Kohane IS, Kim TK et al (2006) START: an automated tool for serial analysis of chromatin occupancy data. Bioinformatics 22:999
Ng P, Wei CL, Sung WK et al (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2:105–111
Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9:179–191
Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83:349–360
Charron JBF, He H, Elling AA, Deng XW (2009) Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21:3732–3748
Park PJ (2009) ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680
Rhodes D, Giraldo R (1995) Telomere structure and function. Curr Opin Struct Biol 5:311–322
Rossetti L, Cacchione S, Fua M, Savino M (1998) Nucleosome assembly on telomeric sequences. Biochemistry 37:6727–6737
Jiang C, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161–172
Tirosh I, Barkai N (2008) Two strategies for gene regulation by promoter nucleosomes. Genome Res 18:1084
Pecinka A, Dinh HQ, Baubec T et al (2010) Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22:3118–3129
Kumar SV, Wigge PA (2010) H2A. Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140:136–147
Dennis JH, Fan HY, Reynolds SM et al (2007) Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res 17:928
Mukhopadhyay A, Deplancke B, Walhout AJM et al (2008) Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc 3:698–709
Valouev A, Johnson DS, Sundquist A et al (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5:829–834
Kim VN (2005) Small RNAs: classification, biogenesis, and function. Mol Cells 19:1–15
Reinhart BJ, Weinstein EG, Rhoades MW et al (2004) MicroRNAs in plants. Genes Dev 16:1616–1626
Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31–S36
Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019
Rhoades MW, Reinhart BJ, Lim LP et al (2002) Prediction of plant microRNA targets. Cell 110:513–520
Tanurdzic M, Vaughn MW, Jiang H et al (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 6:e302
Yakovlev IA, Fossdal CG, Johnsen Ø (2010) MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. New Phytol 187:1154–1169
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Rodríguez, J.L. et al. (2012). Basic Procedures for Epigenetic Analysis in Plant Cell and Tissue Culture. In: Loyola-Vargas, V., Ochoa-Alejo, N. (eds) Plant Cell Culture Protocols. Methods in Molecular Biology, vol 877. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-818-4_25
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