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Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming

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Plant Chromatin Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1675))

Abstract

Dynamic reshuffling of the chromatin landscape is a recurrent theme orchestrated in many, if not all, plant developmental transitions and adaptive responses. Spatiotemporal variations of the chromatin properties on regulatory genes and on structural genomic elements trigger the establishment of distinct transcriptional contexts, which in some instances can epigenetically be inherited. Studies on plant cell plasticity during the differentiation of stem cells, including gametogenesis, or the specialization of vegetative cells in various organs, as well as the investigation of allele-specific gene regulation have long been impaired by technical challenges in generating specific chromatin profiles in complex or hardly accessible cell populations. Recent advances in increasing the sensitivity of genome-enabled technologies and in the isolation of specific cell types have allowed for overcoming such limitations. These developments hint at multilevel regulatory events ranging from nucleosome accessibility and composition to higher order chromatin organization and genome topology. Uncovering the large extent to which chromatin dynamics and epigenetic processes influence gene expression is therefore not surprisingly revolutionizing current views on plant molecular genetics and (epi)genomics as well as their perspectives in eco-evolutionary biology. Here, we introduce current methodologies to probe genome-wide chromatin variations for which protocols are detailed in this book chapter, with an emphasis on the plant model species Arabidopsis.

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Acknowledgments

The authors thank Chris Bowler for constant support, Vincent Colot (IBENS, Paris France) and François Roudier (ENS, Lyon France) for helpful discussions and sharing unpublished data. They are also grateful to Damarys Loew (Curie Institute, Paris France) and Julie Law (Salk Institute for Biological Studies, San Diego USA) for helpful discussions. Work by the authors is supported by the CNRS, ANR-11-JSV2-003-01, Investissements d’Avenir Labex MEMOLIFE ANR-10-LABX-54 to FB, by PSL Research University to FB and CB, and by Université Paris-Saclay to MB.

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  1. Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d’Ulm, F-75005, Paris, France

    Clara Bourbousse & Fredy Barneche

  2. Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France

    Moussa Benhamed

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  1. Clara Bourbousse
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Correspondence to Fredy Barneche .

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  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

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Bourbousse, C., Benhamed, M., Barneche, F. (2018). Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming. 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_1

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