Chromatin in the Cell Nucleus: Higher‐order Organisation

Abstract

Chromosome territories (CTs) constitute a major feature of nuclear architecture. Recent progress in three‐dimensional (3D) super‐resolution microscopy further supports the following functional model of chromatin organisation: CTs consist of interconnected assemblies of approximately 1 Mb chromatin domains (CDs). These domains are permeated by a 3D channel system, the so‐called interchromatin compartment (IC), which may serve as a preferential compartment for ribonucleic acid (RNA) transport. Wider parts of the IC are nearly deoxyribonucleic acid (DNA) free, expand between CTs and accommodate splicing speckles and nuclear bodies. The interior of CDs contains transcriptionally silent chromatin, whereas their periphery represents a zone of decondensed, transcriptionally competent chromatin. This perichromatin region borders on the network of IC channels and is the site of RNA transcription and DNA replication. During interphase large‐scale movements of CTs are typically absent, although exceptions may exist. In contrast, chromosome neighbourhood arrangements change profoundly during prometaphase resulting in variable CT neighbourhoods arrangements in cycling cells.

Key Concepts:

  • Each individual chromosome occupies a distinct region (territory) of the nuclear space.

  • Chromosome territories (CTs) do not occupy fixed positions in the nucleus but show a polarised radial orientation: gene‐dense chromatin is typically located towards the nuclear interior and gene‐poor chromatin at the nuclear periphery.

  • During interphase large‐scale movement of chromatin is not typically observed. Nuclear rotational movements are likely essential for chromatin reorganisation during post‐mitotic differentiation.

  • In cycling cells profound repositioning of chromatin occurs during prometaphase, resulting in new CT neighbourhoods in subsequent daughter nuclei.

  • Recently developed 3D super‐resolution light microscopy provides detailed insight into chromatin ultrastructure and increasing evidence for a highly compartmentalised functional organisation of CTs.

  • We postulate that CTs are built up from interconnected approximately 1 Mb chromatin domains (CD). CDs are permeated by a network of channels, which constitute the interchromatin compartment (IC). The IC is connected to nuclear pores. It accommodates splicing speckles and nuclear bodies and provides a compartment for RNA transport. A zone of decondensed chromatin, called the perichromatin region (PR), is located at the periphery of CDs and lines the IC. It constitutes the site of transcription, splicing, DNA‐replication and possibly also DNA‐repair.

Keywords: nuclear architecture; chromosome territories; chromatin domains; interchromatin compartment; perichromatin; chromatin organisation; super‐resolution light microscopy

Figure 1.

Chromosome territories and subchromosomal domains. (a) Left: Painting of the two X chromosomes in a female human fibroblast nucleus (green) shows the variable shape of CTs and the different conformation of the inactive X chromosome (arrow), which can be identified by colocalisation with the intensely DAPI‐stained Barr body (right). (b) Top: two human X chromosomes in a human fibroblast metaphase plate are shown after multicolour FISH with four differentially labelled segments each covering one half of the long (q)‐arm (green, blue) and the short (p)‐arm (yellow, red). Bottom: Z‐projections of light optical sections through the Xa‐ and Xi‐territory of a human fibroblast nucleus following 3D FISH with the same probe sets demonstrate four separate domains of these segments within the Xa‐ and Xi‐territory. Owing to the more extended shape of Xa‐compared to Xi‐territories, these segments are better discernible in Xa‐territories. Reproduced with permission from Teller et al.. (c) Multicolour 3D FISH to a human fibroblast reveals the two CTs of the human chromosome 11 (blue) together with the particular gene‐dense region 11p15.5 (green, yellow and red). For the delineation of this region of approximately 2.6 Mb differentially labelled DNA probes were used as shown in the inset. Z‐projections of light optical serial sections illustrate different shapes of this region and in the lower CT an impressive, frequently observed extension of this segment from the CT surface. Reproduced from Albiez et al. and Küpper et al. () with permission from Springer. (d) Simultaneous delineation of all chromosome territories in a human fibroblast nucleus (left) and of mitotic chromosomes in a prometaphase rosette (right) by multicolour FISH. Light optical midsections with false colour representation of all CTs and prometaphase chromosomes, respectively, are shown. Examples of individual CTs and mitotic chromosomes are denoted with their respective karyotypic number (for details see Bolzer et al., ). (e) Gene‐density‐correlated chromatin arrangement in the nucleus. Left: idiogram of a human chromosome 12. The bars indicate the sequential arrangement of gene‐dense and gene‐poor segments along the chromosome. Middle: delineation of gene‐dense and gene‐poor segments on metaphase chromosomes 12 after FISH with two differently labelled probe sets as indicated on the idiogram. Right: partial 3D reconstruction of a human lymphocyte nucleus after 3D‐FISH of two differently labelled sets of large insert clones from human chromosome 12 carrying sequences from several gene‐dense (green) and several gene‐poor chromosome segments (red), respectively. This nucleus illustrates two neighbouring chromosome 12 territories with distinct gene‐density‐correlated radial nuclear arrangement. Reproduced from Küpper et al. with permission from Springer. (f–g) ‘Inverted’ nuclear architecture in mouse rod cell nuclei. (f) A light optical confocal section through the middle part of the nucleus after 3D‐FISH delineating the radial arrangement of pericentromeric major mouse satellite (blue) in the nuclear centre, surrounded by the L1‐rich gene‐poor chromatin (red) and the peripheral layer of gene‐dense euchromatin enriched in B1 sequences (green). (g) Reorganisation of nuclear architecture in rod nuclei during post‐natal development (P0–P28) and in a 9‐month‐old mouse (9m) delineated with the same probe sets as described in (f). Exit of the cell cycle occurs around day 6 after birth but the inverted architecture is reached only after day 28. Reproduced from Solovei et al. with permission from Elsevier.

Figure 2.

Chromatin dynamics. Live cell observations of RPE1 cells stably transfected with photo‐activable GFP (paGFP) tagged to histone H4. H4‐paGFP is used as switchable highlighter of chromatin (green). H2B‐mRFP is used for an in vivo chromatin counterstain (red). paGFP fluorescence was activated in selected areas of interphase nuclei and paGFP fluorescent chromatin was traced (a) through interphase and (b) through mitosis. (a) Little large‐scale dynamics of chromatin is observed during an observation period of up to 30:00 h covering interphase. (b) In contrast the chromatin pattern in the emerging daughter nuclei after mitosis differs from the mother nucleus as demonstrated by the compact zone of paGFP fluorescent chromatin in the prophase nucleus and the scattered distribution of the same chromatin in daughter nuclei. Reproduced from Strickfaden et al. with permission from Landes Bioscience.

Figure 3.

Nuclear topography of nascent RNA and Ser2P‐RNA Polymerase II by high‐resolution microscopy and the chromosome territory–interchromatin compartment (CT–IC) model. (a) Current view of the functional nuclear architecture described by the chromosome territory–interchromatin compartment model. Reproduced from Cremer and Cremer with permission from Cold Spring Harbor Laboratory Press. (b) Nuclear topography of nascent RNA and Ser2P‐RNA Pol II. a: Lateral (x, y), optical section recorded with structured illumination microscopy (compare Schermelleh et al., ) from a DAPI‐stained (grey) mouse cell nucleus (C127 cell line), shows nascent RNA (green) and Ser2P‐RNA Polymerase II (red). Bar, 10 μm. b: ×3 Magnification of region marked in a. Bar, 2 μm. c–f: ×3 Magnification of four regions marked in (b) Bar, 500 nm. g: Axial, midsection (x, z) of the same nucleus. Bar, 2 μm. h: ×3 Magnification of region marked in g. Bar, 500 nm. Note the enrichment of nascent RNA and Ser2P‐RNA Pol II signals at the periphery or on fibrillar protrusions of CDs. Reproduced from Markaki et al. with permission from Cold Spring Harbor Laboratory Press.

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Cremer, Marion, Markaki, Yolanda, Zunhammer, Andreas, Cremer, Christoph, and Cremer, Thomas(Apr 2012) Chromatin in the Cell Nucleus: Higher‐order Organisation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005768.pub2]