Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato

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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 chromat...

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Autores principales: Ricardi, M.M., González, R.M., Iusem, N.D.
Formato: Artículo publishedVersion
Publicado: 2010
Materias:
Arabidopsis
Lycopersicon esculentum
Solanum
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_17464811_v6_n1_p_Ricardi
https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_17464811_v6_n1_p_Ricardi_oai
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Repositorio Digital de la Universidad de Buenos Aires (UBA) de Universidad de Buenos Aires
id I28-R145-paper_17464811_v6_n1_p_Ricardi_oai
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spelling I28-R145-paper_17464811_v6_n1_p_Ricardi_oai2024-08-16 Ricardi, M.M. González, R.M. Iusem, N.D. 2010 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. Fil:Ricardi, M.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:González, R.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Iusem, N.D. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. application/pdf http://hdl.handle.net/20.500.12110/paper_17464811_v6_n1_p_Ricardi info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar Plant Methods 2010;6(1) Arabidopsis Lycopersicon esculentum Solanum Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_17464811_v6_n1_p_Ricardi_oai
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-145
collection Repositorio Digital de la Universidad de Buenos Aires (UBA)
topic Arabidopsis
Lycopersicon esculentum
Solanum
spellingShingle Arabidopsis
Lycopersicon esculentum
Solanum
Ricardi, M.M.
González, R.M.
Iusem, N.D.
Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
topic_facet Arabidopsis
Lycopersicon esculentum
Solanum
description 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.
format Artículo
Artículo
publishedVersion
author Ricardi, M.M.
González, R.M.
Iusem, N.D.
author_facet Ricardi, M.M.
González, R.M.
Iusem, N.D.
author_sort Ricardi, M.M.
title Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
title_short Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
title_full Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
title_fullStr Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
title_full_unstemmed Protocol: Fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
title_sort protocol: fine-tuning of a chromatin immunoprecipitation (chip) protocol in tomato
publishDate 2010
url http://hdl.handle.net/20.500.12110/paper_17464811_v6_n1_p_Ricardi
https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_17464811_v6_n1_p_Ricardi_oai
work_keys_str_mv AT ricardimm protocolfinetuningofachromatinimmunoprecipitationchipprotocolintomato
AT gonzalezrm protocolfinetuningofachromatinimmunoprecipitationchipprotocolintomato
AT iusemnd protocolfinetuningofachromatinimmunoprecipitationchipprotocolintomato
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