The precise location of chromatin domains within the cell nucleus has seen growing recognition in the past decade as an additional mechanism of controlling gene expression in both plants and animals (Dekker et al., 2017). Consequently, international efforts are devoted to understanding the organising principle of this organelle in plants, and notably the nature and the role of functional compartments on gene expression (Graumann et al., 2013;Sotelo-Silveira et al., 2018). The European cooperation 'Impact of Nuclear Domains on Gene Expression and Plant Traits' (INDEPTH) brings together molecular cell biologists, plant physiologists, bioinformaticians, image analysts and computer scientists. They aim to address the question of how nuclear architecture, chromatin organisation and gene expression are connected in plants, particularly in relation to traits of interest such as biomass, reproduction and resistance to pathogens (https:// www.brookes.ac.uk/indepth/). The kick-off meeting of the INDEPTH consortium took place in Clermont-Ferrand, France, on 12-14th March 2018, where more than 80 researchers set the agenda for the coming four years of research and collaboration.The kick-off meeting of the INDEPTH consortium revolved around an exciting overall theme of an increased appreciation about how gene expression can be affected by the sequestering of loci within different nuclear compartments. The meeting showed promising technological advances that will overcome challenges particular to plant tissues both in the detection of single-locus positions and in dedicated image analysis. Another emerging theme is the development of new approaches that will combine information gained from microscopic images that provide single-cell resolution with the information that is gained from conformation-capture techniques that represent an average view of multiple cells in a tissue. Together with the characterisation of nuclear structures that are specific to plants, these techniques will allow this community to gain insight into the plant-specific mechanisms of gene expression control and to compare and contrast these with the mechanisms identified in yeast and mammalian model organisms.
Organisation of the INDEPTH consortiumA key component of the INDEPTH COST Action (Box 1) is its organisation into five complementary workgroups (Fig. 1), whose activities were introduced at the kick-off meeting. Three of the workgroups focus on evaluating plant chromatin domains at different scales, from imaging nuclear domains (workgroup 1) through analysis of the function of chromatin domains in controlling gene expression (workgroup 2) to assessing their effect on plant phenotypes and their dynamics during stresses (workgroup 3). Workgroup 4 is involved in tackling the challenge of storage and sharing of 'omics'-based and image data, something that has relevance to a much wider community of researchers beyond the INDEPTH consortium, and workgroup 5 organises training and dissemination of INDEPTH outputs from each of the other four workgr...