4D Chromatin dynamics in cycling cells

Abstract

This live cell study of chromatin dynamics in four dimensions (space and time) in cycling human cells provides direct evidence for three hypotheses first proposed by Theodor Boveri in seminal studies of fixed blastomeres from Parascaris equorum embryos: (I) Chromosome territory (CT) arrangements are stably maintained during interphase. (II) Chromosome proximity patterns change profoundly during prometaphase. (III) Similar CT proximity patterns in pairs of daughter nuclei reflect symmetrical chromosomal movements during anaphase and telophase, but differ substantially from the arrangement in mother cell nucleus. Hypothesis I could be confirmed for the majority of interphase cells. A minority, however, showed complex, rotational movements of CT assemblies with large-scale changes of CT proximity patterns, while radial nuclear arrangements were maintained. A new model of chromatin dynamics is proposed. It suggests that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements.

Radial Organization in the Mammalian Nucleus

“…The linear genomic sequence is organized into structural domains that form the building blocks of the higher-order three-dimensional (3D) architecture of the genome. Chromosomes typically condense into distinct masses known as chromosome territories (CTs), whose existence was proposed already more than a century ago by the Austrian anatomist Carl Rabl and the German biologist Theodor Boveri (Strickfaden et al, 2010), and later confirmed in multiple cell types and species Cremer et al, 2006). At the sub-chromosomal level, structural domains comprise megabase (Mb)-sized cytobands visible in metaphase chromosomes, and A/B compartments identified by Hi-C (Lieberman-Aiden et al, 2009), as well as smaller domains spanning from several kilobases (kb) up to a few Mb, including topologically associating domains (TADs) (Dixon et al, 2012) and long-range chromatin loops (Rao et al, 2014).…”

The fractal globule as a model of chromatin architecture in the cell

“…How are meters of DNA packed inside the 5-μm-diameter nucleus of a cell? Recent developments in imaging (Strickfaden et al 2010 ; Müller et al 2004 ; Berger et al 2008 ; Cremer and Cremer 2010 ; Yokota et al 1995 ) and chromosome capture techniques (Ohlsson and Göndör 2007 ; Miele and Dekker 2009 ; Van Berkum and Dekker 2009 ; Duan et al 2010 ) provided new insights into this problem. Before looking at specific observations, however, it is worth asking a question: what kind of DNA structures do we expect to find in this packing?…”

“…They should persist at least for the duration of single cell cycle, as chromosomal architecture is re-established upon mitosis. Recent photo-activation experiments beautifully demonstrated that chromosomal architecture is maintained for 10–15 h and is completely reset upon mitosis (Strickfaden et al 2010 ). Mechanisms that suppress stand passing and otherwise stabilize the fractal globule as well as the rest of chromatin architecture during the interphase are yet to be established.…”

Reflections on the organization and the physical state of chromatin in eukaryotic cells

“…Despite the necessity to replicate the genome during S-phase, the nuclear positioning of chromosome territories (CTs) and CDs are relatively stable throughout interphase, though not strictly fixed (Figs. 2A and 2B) (Strickfaden et al 2010). In early microscopy studies, the definition of $1 Mb CDs was based on replication domains (RDs) (Takebayashi et al 2017).…”

“…(B) RPE1 cell expressing pa-GFP-H4 and PCNA-RFP showing S-phase stability. Throughout the different sub-phases of S-phase the global appearance and relative geometry of the photoactivated pattern remains unchanged despite a modest broadening in widths of the photoactivated lines(Strickfaden et al 2010). (C) U2OS cell that was replication-labeled with fluorophore-tagged nucleotides in S-phase and then cultured for several cell generations until it was fixed.…”