Chromatin Immunoprecipitation (ChiP) Protocol for the Analysis of Gene Regulation by Histone Modifications in Agave angustifolia Haw

  • Rosa Us-Camas
  • Clelia De-la-PeñaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1815)


Chromatin is a dynamic entity that regulates different biological processes crucial for the proper functioning of the cell. Chromatin regulation depends largely on the interactions that occur between DNA with histones and nonhistone proteins. The chromatin immunoprecipitation assay (ChiP) is a widely used technique for the study of these DNA-histone and DNA-nonhistone interactions and their biological repercussions. Here we describe a ChiP protocol that allows in vivo analysis of the associations of histone modifications with genomic DNA in Agave angustifolia Haw. Although this protocol is established for A. angustifolia, it can be used in other species to obtain similar results. We also propose a strategy to shorten the times in some steps of the standard protocol.

Key words

Agave angustifolia ChiP H3K4me3 H3K27me3 LCYβ PEPCase RubS 



The work from CDLP laboratory was supported by a grant received from the National Council for Science and Technology (CONACyT, 1515).


  1. 1.
    Vaquero A, Loyola A, Reinberg D (2003) The constantly changing face of chromatin. Sci Aging Knowl Environ 2003:Re4. CrossRefGoogle Scholar
  2. 2.
    Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11:285–296. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10:645–652. CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Luger K, Mader AW, Richmond RK et al (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260. CrossRefPubMedGoogle Scholar
  5. 5.
    Cosgrove MS, Wolberger C (2005) How does the histone code work? Biochem Cell Biol 83:468–476. CrossRefPubMedGoogle Scholar
  6. 6.
    Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Zhang K, Sridhar VV, Zhu J et al (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 2:e1210. CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837. CrossRefPubMedGoogle Scholar
  9. 9.
    Huebert DJ, Kamal M, O’Donovan A, Bernstein BE (2006) Genome-wide analysis of histone modifications by ChIP-on-chip. Methods 40:365–369. CrossRefPubMedGoogle Scholar
  10. 10.
    Núñez Noriega L (2001) La producción de mezcal bacanora: una oportunidad económica para Sonora. Centro de Investigación en Alimentación y Desarrollo, Hermosillo, SonoraGoogle Scholar
  11. 11.
    Saleh A, Alvarez-Venegas R, Avramova Z (2008) An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 3:1018–1025. CrossRefPubMedGoogle Scholar
  12. 12.
    De-La-Peña C, Nic-Can G, Ojeda G et al (2012) KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp. BMC Plant Biol 12:203. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. CrossRefGoogle Scholar
  14. 14.
    Robert ML, Herrera-Herrera JL, Castillo E et al (2006) An efficient method for the micropropagation of Agave species. Methods Mol Biol 318:165–178. CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Unidad de Biotecnología, Centro de Investigación Científica de YucatánMéridaMexico

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