Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming

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.

Light and temperature shape nuclear architecture and gene expression

“…Is there a tissue and cell specific nuclear organization signature and how/when is it acquired? The discovery and application of cutting-edge technologies in super-resolution imaging, genome editing and chromatin conformation capture, coupled to high-sensitivity next generation sequencing and mass spectrometry, are leading the field of plant nuclear architecture to a period of “enlightenment” [ 16 , 18 , 19 , 26 , 61 , 62 , 63 ].…”

“…In particular, Chromatin Conformation Capture (3C), padlock Fluorescence In Situ Hybridization (FISH) and live three-dimensional (3D) imaging have opened new avenues to the field [ 15 , 16 ]. These techniques have already contributed to major scientific discoveries such as the existence of topologically associating chromatin domains (TADs) in large plant genomes and clustering of co-regulated genes [ 17 , 18 , 19 ].…”