Abstract
Gene activity is regulated via chromatin dynamics in eukaryotes. In plants, alterations of histone modifications are correlated with gene regulation for development, vernalization, and abiotic stress responses. Using ChIP, ChIP-on-chip, and ChIP-seq analyses, the direct binding regions of transcription factors and alterations of histone modifications can be identified on a genome-wide level. We have established reliable and reproducible ChIP and ChIP-on-chip methods that have been optimized for the Arabidopsis model system. These methods are not only useful for identifying the direct binding of transcription factors and chromatin status but also for scanning the regulatory network in Arabidopsis.
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
Wolffe AP (1998) Packaging principle: how DNA methylation and histone acetylation control the transcriptional activity of chromatin. J Exp Zool 282:239–244
Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:683–692
Kurdistani SK, Grunstein M (2003) Histone acetylation and deacetylation in yeast. Nat Rev Mol Cell Biol 4:276–284
Nightingale KP, O’Neill LP, Turner BM (2006) Histone modifications: signaling receptors and potential elements of a heritable epigenetic code. Curr Opin Genet Dev 16:125–136
Kouzarides T (2007) Chromatin modification and their function. Cell 128:693–705
Bhaumik SR, Smith E, Shilatifard A (2007) Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 14:1008–1016
Bártová E et al (2008) Histone modifications and nuclear architecture: a review. J Histochem Cytochem 56:711–721
Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10:645–652
To TK et al (2011) Arabidopsis HDA6 is required for freezing tolerance. Biochem Biophys Res Commun 406:414–419
Sokol A et al (2007) Up-regulation of stress-inducible genes in tobacco anad Arabidopsis cells in response to abiotic stresses and ABA treatment correlates with dynamic changes in histone H3 and H4 modifications. Planta 227: 245–254
Kim JM et al (2008) Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol 49:1580–1588
Kim JM et al (2010) Chromatin regulation function in plant abiotic stress responses. Plant Cell Environ 33:604–611
Kwon CS et al (2009) Histone occupancy-dependent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J 60:112–121
Katou Y et al (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424:1078–1083
Cawley S et al (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499–509
Katou Y et al (2006) Genomic approach for the understanding of dynamic aspect of chromosome behavior. Methods Enzymol 409:389–410
Lee TL, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1:729–748
Zhang X et al (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201
Zilberman D et al (2006) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61–69
Zhang X et al (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14:869–871
Lee J et al (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19:731–749
Morohashi K, Grotewold E (2009) A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet 5:e1000396
Bolstad BM et al (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193
Liu CL, Schreiber SL, Bernstein BE (2003) Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4:19
Matsui A et al (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using tiling array. Plant Cell Physiol 49:1135–1149
Acknowledgements
This research was supported by The Grant-in-Aid for Scientific Research (Priority Areas no. 20127033 and 23012036; Innovative Areas 23119522) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan (to MS) and grants from the RIKEN Plant Science Center (to MS).
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
Kim, JM. et al. (2014). Highly Reproducible ChIP-on-Chip Analysis to Identify Genome-Wide Protein Binding and Chromatin Status in Arabidopsis thaliana . In: Sanchez-Serrano, J., Salinas, J. (eds) Arabidopsis Protocols. Methods in Molecular Biology, vol 1062. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-580-4_22
Download citation
DOI: https://doi.org/10.1007/978-1-62703-580-4_22
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-579-8
Online ISBN: 978-1-62703-580-4
eBook Packages: Springer Protocols