Abstract
Chromatin immunoprecipitation, or ChIP, is a powerful experimental technique for probing protein-DNA interactions in vivo. This assay can be used to investigate the association of a protein of interest with specific target loci. Alternatively, it can be combined with high-throughput sequencing technology to identify genome-wide binding sites. Here, we describe a ChIP protocol that was optimized for low-abundance transcription factors in Arabidopsis, and provide guidance on how to adapt it for other types of plants and proteins.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Park PJ (2009) ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680
Huang W, Pérez-García P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336:75–79
Adams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA (2018) Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. New Phytol 220:893–907
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Koike N, Yoo S-H, Huang H-C, Kumar V, Lee C, Kim T-K, Takahashi JS (2012) Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338:349–354
Perales M, Mas P (2007) A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. Plant Cell 19:2111–2123
Hemmes H, Henriques R, Jang I-C, Kim S, Chua N-H (2012) Circadian clock regulates dynamic chromatin modifications associated with Arabidopsis CCA1/LHY and TOC1 transcriptional rhythms. Plant Cell Physiol 53:2016–2029
Song H-R, Noh Y-S (2012) Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci. Mol Cell 34:279–287
Malapeira J, Khaitova LC, Más P (2012) Ordered changes in histone modifications at the core of the Arabidopsis circadian clock. Proc Natl Acad Sci U S A 109:21540–21545
Baerenfaller K, Shu H, Hirsch-Hoffmann M, Fütterer J, Opitz L, Rehrauer H, Hennig L, Gruissem W (2016) Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis. Plant Cell Environ 39:2557–2569
Adams S, Manfield I, Stockley P, Carré IA (2015) Revised morning loops of the Arabidopsis circadian clock based on analyses of direct regulatory interactions. PLoS One 10:e0143943
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22:1813–1831
Gendrel A-V, Lippman Z, Yordan C, Colot V, Martienssem RA (2002) Dependence on heterochromatic Histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297:1871–1873
O’Neill LP, Turner BM (2003) Immunoprecipitation of native chromatin: NChIP. Methods 31:76–82
Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc 1:179–185
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013) Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol 9:e1003326
Acknowledgment
This work was supported by BBSRC grant BB/F022832/1 to IAC.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Adams, S., Carré, I.A. (2022). Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins. In: Staiger, D., Davis, S., Davis, A.M. (eds) Plant Circadian Networks. Methods in Molecular Biology, vol 2398. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1912-4_12
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1912-4_12
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1911-7
Online ISBN: 978-1-0716-1912-4
eBook Packages: Springer Protocols