title: 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.
authors.affiliation: INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Andrey
authors.forename: Kiên
authors.initials: K
authors.lastname: Kiêu
authors.forename: Clémence
authors.initials: C
authors.lastname: Kress
authors.forename: Gaëtan
authors.initials: G
authors.lastname: Lehmann
authors.forename: Leïla
authors.initials: L
authors.lastname: Tirichine
authors.forename: Zichuan
authors.initials: Z
authors.lastname: Liu
authors.forename: Eric
authors.initials: E
authors.lastname: Biot
authors.forename: Pierre-Gaël
authors.initials: PG
authors.lastname: Adenot
authors.forename: Cathy
authors.initials: C
authors.lastname: Hue-Beauvais
authors.forename: Nicole
authors.initials: N
authors.lastname: Houba-Hérin
authors.forename: Véronique
authors.initials: V
authors.lastname: Duranthon
authors.forename: Eve
authors.initials: E
authors.lastname: Devinoy
authors.forename: Nathalie
authors.initials: N
authors.lastname: Beaujean
authors.forename: Valérie
authors.initials: V
authors.lastname: Gaudin
authors.forename: Yves
authors.initials: Y
authors.lastname: Maurin
authors.forename: Pascale
authors.initials: P
authors.lastname: Debey
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000166:cytology; D002467:Cell Nucleus / Q000737:chemistry*; D002503:Centromere / Q000737:chemistry*; D004622:Embryo, Mammalian / Q000166:cytology; D005260:Female; D006570:Heterochromatin / Q000737:chemistry*; D021621:Imaging, Three-Dimensional; D008321:Mammary Glands, Animal / Q000166:cytology; D018613:Microscopy, Confocal; D015233:Models, Statistical; D009010:Monte Carlo Method; D009687:Nuclear Proteins / Q000737:chemistry; D011817:Rabbits
chemical_list: D006570:Heterochromatin; D009687:Nuclear Proteins