Abstract
Covalent histone modifications and their effects on chromatin state and accessibility play a key role in the regulation of gene expression in eukaryotes. To gain insights into their functions during plant growth and development, the distribution of histone modifications can be analyzed at a genome-wide scale through chromatin immunoprecipitation assays followed by sequencing of the isolated genomic DNA. Here, we present a protocol for systematic analysis of the distribution and dynamic changes of selected histone modifications, during flower development in the model plant Arabidopsis thaliana. This protocol utilizes a previously established floral induction system to synchronize flower development, which allows the collection of sufficient plant material for analysis by genomic technologies. In this chapter, we describe how to use this system to study, from the same set of samples, chromatin and transcriptome dynamics during early stages of flower formation.
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Acknowledgments
The authors would like to thank Sacha Preuss, Craig Pikkard, Kerstin Kaufmann, David Pose Padilla, and Markus Schmid whose ChIP protocols inspired the one described in this chapter. We further thank Laurent Journot and the team of the mgx sequencing platform in Montpellier for discussion on multiplexing procedures and for performing flexible library preparations and sequencing runs. We thank Laura Gregoire for input on visualization possibilities of multiple data sets. The work leading to this protocol was funded by the French National Agency Young Researcher grant for the ChromFlow project (ANR JCJC, project SVSE2-1206 01 to CCC), the Centre National de la Recherche Scientifique for a CNRS-Higher Education Chair (position 0428–64 to CCC), the Université Grenoble Alpes for an UGA-UJF Initiative Chair (to CCC), and a Marie Curie Intra-European Fellowship within the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° 327377 (to JE).
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Engelhorn, J., Wellmer, F., Carles, C.C. (2018). Profiling Histone Modifications in Synchronized Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_16
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DOI: https://doi.org/10.1007/978-1-4939-7318-7_16
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