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Abstract:

Background: Searching thoroughly for plant cis-elements corresponding to transcription factors is worthwhile to reveal novel gene activation cascades. At the same time, a great deal of research is currently focused on epigenetic events in plants. A widely used method serving both purposes is chromatin immunoprecipitation, which was developed for Arabidopsis and other plants but is not yet operational for tomato (Solanum lycopersicum), a model plant species for a group of economically important crops.Results: We developed a chromatin immunoprecipitation protocol suitable for tomato by adjusting the parameters to optimise in vivo crosslinking, purification of nuclei, chromatin extraction, DNA shearing and precipitate analysis using real-time PCR. Results were obtained with two different antibodies, five control loci and two normalisation criteria.Conclusion: Here we provide a chromatin immunoprecipitation procedure for tomato leaves that could be combined with high-throughput sequencing to generate a detailed map of epigenetic modifications or genome-wide nucleosome positioning data. © 2010 Ricardi et al; licensee BioMed Central Ltd.

Registro:

Documento: Artículo
Título:Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
Autor:Ricardi, M.M.; González, R.M.; Iusem, N.D.
Filiación:Departamento de Fisiología, Biología Molecular y Celular, IFIByNE-CONICET. Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
Palabras clave:Arabidopsis; Lycopersicon esculentum; Solanum
Año:2010
Volumen:6
Número:1
DOI: http://dx.doi.org/10.1186/1746-4811-6-11
Título revista:Plant Methods
Título revista abreviado:Plant Methods
ISSN:17464811
PDF:https://bibliotecadigital.exactas.uba.ar/download/paper/paper_17464811_v6_n1_p_Ricardi.pdf
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17464811_v6_n1_p_Ricardi

Referencias:

  • Priest, H.D., Filichkin, S.A., Mockler, T.C., Cis-regulatory elements in plant cell signaling (2009) Curr Opin Plant Biol, 12, pp. 643-649. , 10.1016/j.pbi.2009.07.016, 19717332
  • Takeda, S., Paszkowski, J., DNA methylation and epigenetic inheritance during plant gametogenesis (2006) Chromosoma, 115, pp. 27-35. , 10.1007/s00412-005-0031-7, 16249938
  • Turck, F., Roudier, F., Farrona, S., Martin-Magniette, M.L., Guillaume, E., Buisine, N., Gagnot, S., Colot, V., Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27 (2007) PLoS Genet, 3, pp. e86. , 10.1371/journal.pgen.0030086, 1885283,1885283, 17542647
  • Barone, A., Di Matteo, A., Carputo, D., Frusciante, L., High-throughput genomics enhances tomato breeding efficiency (2009) Curr Genomics, 10, pp. 1-9. , 10.2174/138920209787581226, 2699839, 19721805
  • Hoeven, R., Ronning, C., Giovannoni, J., Martin, G., Tanksley, S., Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing (2002) Plant Cell, 14, pp. 1441-1456. , 10.1105/tpc.010478, 150698, 12119366
  • Fridman, E., Zamir, D., Functional divergence of a syntenic invertase gene family in tomato, potato, and Arabidopsis (2003) Plant Physiol, 131, pp. 603-609. , 10.1104/pp.014431, 166836, 12586884
  • Leseberg, C.H., Eissler, C.L., Wang, X., Johns, M.A., Duvall, M.R., Mao, L., Interaction study of MADS-domain proteins in tomato (2008) J Exp Bot, 59, pp. 2253-2265. , 10.1093/jxb/ern094, 18487636
  • Caramelo, J.J., Iusem, N.D., When cells lose water: Lessons from biophysics and molecular biology (2009) Prog Biophys Mol Biol, 99, pp. 1-6. , 10.1016/j.pbiomolbio.2008.10.001, 18977383
  • Haring, M., Offermann, S., Danker, T., Horst, I., Peterhansel, C., Stam, M., Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization (2007) Plant Methods, 3, p. 11. , 10.1186/1746-4811-3-11, 2077865, 17892552
  • Das, P.M., Ramachandran, K., vanWert, J., Singal, R., Chromatin immunoprecipitation assay (2004) Biotechniques, 37, pp. 961-969
  • Bowler, C., Benvenuto, G., Laflamme, P., Molino, D., Probst, A.V., Tariq, M., Paszkowski, J., Chromatin techniques for plant cells (2004) Plant J, 39, pp. 776-789. , 10.1111/j.1365-313X.2004.02169.x, 15315638
  • Conconi, A., Ryan, C.A., DNase I and micrococcal nuclease analysis of the tomato proteinase inhibitor I gene in chromatin (1993) J Biol Chem, 268, pp. 430-435
  • Schumacher, J., Sanger, H.L., Riesner, D., Subcellular localization of viroids in highly purified nuclei from tomato leaf tissue (1983) EMBO J, 2, pp. 1549-1555. , 555321, 11892810
  • O'Neill, L.P., Turner, B.M., Immunoprecipitation of native chromatin: NChIP (2003) Methods, 31, pp. 76-82. , 10.1016/S1046-2023(03)00090-2, 12893176
  • Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Zhao, K., High-resolution profiling of histone methylations in the human genome (2007) Cell, 129, pp. 823-837. , 10.1016/j.cell.2007.05.009, 17512414
  • Mathieu, O., Probst, A.V., Paszkowski, J., Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis (2005) EMBO J, 24, pp. 2783-2791. , 10.1038/sj.emboj.7600743, 1182238, 16001083
  • Larionov, A., Krause, A., Miller, W., A standard curve based method for relative real time PCR data processing (2005) BMC Bioinformatics, 6, p. 62. , 10.1186/1471-2105-6-62, 1274258, 15780134
  • Pokalsky, A.R., Hiatt, W.R., Ridge, N., Rasmussen, R., Houck, C.M., Shewmaker, C.K., Structure and expression of elongation factor 1 alpha in tomato (1989) Nucleic Acids Res, 17, pp. 4661-4673. , 10.1093/nar/17.12.4661, 318023, 2748335
  • Tam, S.M., Causse, M., Garchery, C., Burck, H., Mhiri, C., Grandbastien, M.A., The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species (2007) J Evol Biol, 20, pp. 1056-1072. , 10.1111/j.1420-9101.2007.01293.x, 17465916
  • Schones, D.E., Cui, K., Cuddapah, S., Roh, T.Y., Barski, A., Wang, Z., Wei, G., Zhao, K., Dynamic regulation of nucleosome positioning in the human genome (2008) Cell, 132, pp. 887-898. , 10.1016/j.cell.2008.02.022, 18329373

Citas:

---------- APA ----------
Ricardi, M.M., González, R.M. & Iusem, N.D. (2010) . Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato. Plant Methods, 6(1).
http://dx.doi.org/10.1186/1746-4811-6-11
---------- CHICAGO ----------
Ricardi, M.M., González, R.M., Iusem, N.D. "Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato" . Plant Methods 6, no. 1 (2010).
http://dx.doi.org/10.1186/1746-4811-6-11
---------- MLA ----------
Ricardi, M.M., González, R.M., Iusem, N.D. "Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato" . Plant Methods, vol. 6, no. 1, 2010.
http://dx.doi.org/10.1186/1746-4811-6-11
---------- VANCOUVER ----------
Ricardi, M.M., González, R.M., Iusem, N.D. Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato. Plant Methods. 2010;6(1).
http://dx.doi.org/10.1186/1746-4811-6-11