Bourbousse Clara, Benhamed Moussa, Barneche Fredy
Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France.
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.
Methods Mol Biol. 2018;1675:3-30. doi: 10.1007/978-1-4939-7318-7_1.
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.
染色质景观的动态重塑是许多（即便不是所有）植物发育转变和适应性反应中精心编排的一个反复出现的主题。调控基因和结构基因组元件上染色质特性的时空变化触发了不同转录环境的建立，在某些情况下，这种变化可以表观遗传的方式遗传下去。长期以来，在复杂或难以获取的细胞群体中生成特定染色质图谱面临技术挑战，这阻碍了对干细胞分化（包括配子发生）过程中植物细胞可塑性的研究，以及对各种器官中营养细胞特化的研究，还有对等位基因特异性基因调控的研究。在提高基于基因组技术的灵敏度以及分离特定细胞类型方面的最新进展，使得克服这些限制成为可能。这些进展暗示了从核小体可及性和组成到高阶染色质组织和基因组拓扑结构等多层次的调控事件。因此，毫不奇怪，揭示染色质动态和表观遗传过程对基因表达的影响程度，正在彻底改变当前对植物分子遗传学和（表观）基因组学的看法，以及它们在生态进化生物学中的前景。在这里，我们介绍目前用于探测全基因组染色质变异的方法，本章将详细介绍这些方法的实验方案，重点是植物模式物种拟南芥。
