Abstract
Histone modifications play an essential role in chromatin-associated processes including gene regulation and epigenetic inheritance. It is therefore very important to quantitatively analyze histone modifications at both the single gene and whole genome level. Here, we describe a robust chromatin immunoprecipitation (ChIP) method for Arabidopsis, which could be adapted for other plant species. This method is compatible with multiple downstream applications including qPCR, tilling arrays, and high-throughput sequencing.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11:285–296
Turner BM (2007) Defining an epigenetic code. Nat Cell Biol 9:2–6
Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1:e67
Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167
De Lucia F, Crevillen P, Jones AM, Greb T, Dean C (2008) A PHD-Polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci U S A 105:16831–16836
Haring M, Offermann S, Danker T, Horst I, Peterhansel C, Stam M (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:e11
Ricardi M, Gonzalez R, Iusem N (2010) Protocol: fine-tuning of a chromatin immunoprecipitation (ChIP) protocol in tomato. Plant Methods 6:e11
Nelson JD, Denisenko O, Sova P, Bomsztyk K (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res 34:e2
Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung M-S, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SCR, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18:91–93
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Delta][Delta]CT method. Methods 25:402–408
Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5:e129
Finnegan EJ, Dennis ES (2007) Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr Biol 17:1978–1983
Yu X, Michaels SD (2010) The Arabidopsis Paf1c complex component CDC73 Participates in the modification of FLOWERING LOCUS C chromatin. Plant Physiol 153:1074–1084
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res 17:877–885
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Song, J., Rutjens, B., Dean, C. (2014). Detecting Histone Modifications in Plants. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 1112. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-773-0_11
Download citation
DOI: https://doi.org/10.1007/978-1-62703-773-0_11
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-772-3
Online ISBN: 978-1-62703-773-0
eBook Packages: Springer Protocols