Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei

Abstract

In eukaryotes, the interphase nucleus is organized in morphologically and/or functionally distinct nuclear “compartments”. Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation. This raises the question of whether nuclear organization principles exist and, if so, whether they are identical in the animal and plant kingdoms. We addressed this issue through the investigation of the three-dimensional distribution of the centromeres and chromocenters. We investigated five very diverse populations of interphase nuclei at different differentiation stages in their physiological environment, belonging to rabbit embryos at the 8-cell and blastocyst stages, differentiated rabbit mammary epithelial cells during lactation, and differentiated cells of Arabidopsis thaliana plantlets. We developed new tools based on the processing of confocal images and a new statistical approach based on G- and F- distance functions used in spatial statistics. Our original computational scheme takes into account both size and shape variability by comparing, for each nucleus, the observed distribution against a reference distribution estimated by Monte-Carlo sampling over the same nucleus. This implicit normalization allowed similar data processing and extraction of rules in the five differentiated nuclei populations of the three studied biological systems, despite differences in chromosome number, genome organization and heterochromatin content. We showed that centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation, suggesting that repulsive constraints or spatial inhomogeneities underlay the spatial organization of heterochromatic compartments. The proposed technique should be useful for identifying further spatial features in a wide range of cell types.

Non-random chromosome arrangement in triploid endosperm nuclei

“…In control nuclei from seed coat and root tissues, we observed a frequency distribution of the number of CCs centering around 8 to 9 (Fig. 1d), with an average of seven to eight CCs (Table 2), respectively, as previously reported for somatic Arabidopsis cell types (Andrey et al 2010;Fransz et al 2006). As expected, a higher number of CCs were formed in endosperm nuclei (12.4 in average, Table 2); the increase, however, was not proportional to the ploidy level (Fig.…”

“…Although euchromatin loops emanating from CCs likely explain the regular dispersion of centromeres (de Nooijer et al 2009;Fransz et al 2002), they do not intuitively explain a planar alignment in flattened nuclei where one would predict a random distribution. In the light of our observation and former models (de Nooijer et al 2009;Andrey et al 2010), it is tempting to propose a hypothetical connective scaffold between centromeres that would favor a regular dispersion in native 3D arrangements while constraining it to a planar alignment in flow-sorted nuclei upon flattening (Online Resource 1).…”

“…This observation was unexpected because in Arabidopsis somatic nuclei, CCs (containing centromeres) show an apparent preferential localization at the nuclear periphery (Armstrong et al 2001;Fransz et al 2002). In 3D nuclei, CCs follow a distribution with a regular spacing, which can be modeled by introducing a repulsive constraint between CCs (Andrey et al 2010). Although euchromatin loops emanating from CCs likely explain the regular dispersion of centromeres (de Nooijer et al 2009;Fransz et al 2002), they do not intuitively explain a planar alignment in flattened nuclei where one would predict a random distribution.…”

The many faces of plant chromatin: Meeting summary of the 4th European workshop onplantchromatin 2015, Uppsala, Sweden

“…Previous results demonstrated a non-random, regular spatial distribution of chromocenters in Arabidopsis leaf cell nuclei with an apparent repulsion. 34 New spatial statistical models (sets of mathematical and/or computational rules that generate spatial patterns) incorporating novel constraints between compartments and nuclear envelope were presented, demonstrating a preferential peripheral localization of chromocenters.…”

“…Development of biosensors for different chromatin marks combined with live-cell imaging techniques will be a great asset to chromatin dynamics research. Novel tools for studying the organization of chromatin within the nuclear space were presented, 30,34 which can help to address the molecular mechanisms governing the 3-dimensional nuclear organization, its dynamics and role in plant development.…”