Nuclei of chicken neurons in tissues and three-dimensional cell cultures are organized into distinct radial zones

Abstract

We used chicken retinospheroids (RS) to study the nuclear architecture of vertebrate cells in a three-dimensional (3D) cell culture system. The results showed that the different neuronal cell types of RS displayed an extreme form of radial nuclear organization. Chromatin was arranged into distinct radial zones which became already visible after DAPI staining. The distinct zones were enriched in different chromatin modifications and in different types of chromosomes. Active isoforms of RNA polymerase II were depleted in the outermost zone. Also chromocenters and nucleoli were radially aligned in the nuclear interior. The splicing factor SC35 was enriched at the central zone and did not show the typical speckled pattern of distribution. Evaluation of neuronal and non-neuronal chicken tissues showed that the highly ordered form of radial nuclear organization was also present in neuronal chicken tissues. Furthermore, the data revealed that the neuron-specific nuclear organization was remodeled when cells spread on a flat substrate. Monolayer cultures of a chicken cell line did not show this extreme form of radial organization. Rather, such monolayer cultures displayed features of nuclear organization which have been described before for many different types of monolayer cells. The finding that an extreme form radial nuclear organization, which has not been described before, is present in RS and tissues, but not in cells spread on a flat substrate, suggests that it would be important to complement studies on nuclear architecture performed with monolayer cells by studies on 3D cell culture systems and tissues.

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

“…Interestingly, this organisation seems to be conserved in most vertebrates (Berchtold et al 2011;Küpper et al 2007;Koehler et al 2009;Neusser et al 2007). For mammals and Arabidopsis thaliana, the relative positioning of chromosomes was found to be partially transmitted through mitosis and maintained at least transiently in a mirror-symmetrical pattern in sister nuclei Essers et al 2005;Gerlich et al 2003; Thomson et al 2004;Walter et al 2003).…”

Three-dimensional architecture of tandem repeats in chicken interphase nucleus

“…Whole-mount FISH on chicken tissue fragments was carried out as described in Berchtold et al (2011) with some modifications. Briefly, permeabilized tissues were soaked in 40 % formamide on 2×SSC for 2 days, then placed in a hybridization buffer for oligonucleotide probes, heat-denatured simultaneously with probes at 85°С for 10 min, and hybridized at 28°С for 2-3 days.…”

“…Secondly, chicken was among the first organism, together with human and other primates, for which preferred localization of gene-poor chromosomes towards the nuclear periphery during interphase was shown (Habermann et al 2001;Skinner et al 2009). Moreover, highly ordered distribution of heterochromatin was recently demonstrated for certain chicken cell types (Berchtold et al 2011). Finally, chicken genome contains relatively low amount of repetitive DNA (Hughes and Piontkivska 2005;Wicker et al 2005), and some of the classes of tandem repeats are segregated among macro-and microchromosomes (Matzke et al 1990;Shang et al 2010;Ishishita et al 2014).…”

Chromosome Territory Organization within the Nucleus

“…Nonrandom, radial nuclear chromatin arrangements appear to be conserved across a wide evolutionary spectrum, ranging from primates and other mammalians [31,[68][69][70][71] to birds, [72,73], hydra [74], plants [75], and ciliates [76]. A considerable amount of heterochromatin is situated at the nuclear periphery, while other heterochromatin surrounds the nucleoli.…”