Chromosomes and Chromatin

Abstract

Chromosomes are structures within the nuclei of eukaryotic cells that contain deoxyribonucleic acid (DNA) combined with proteins. Chromatin refers to the material of the chromosomes – DNA plus proteins. Before DNA replication, each chromosome contains a single, very long DNA molecule that basically runs from one end of the chromosome to the other. Core histone proteins package segments of this DNA molecule into nucleosomes, and linker histones further compact the resulting ‘string of beads’ into a 30‐nm chromatin fibre. In mitotic chromosomes, scaffold proteins fold the chromatin fibre into loops along its length. Chromosomes are very dynamic structures and take several forms, but the basic organisation is always related to the structure of mitotic chromosomes. The location of chromosomes in the nucleus, the nature of the loops and modifications to the chromatin fibre are thought to be important in determining which DNA sequences are made available for transcription and other processes.

Key Concepts:

  • In eukaryotic cells, genes are located in chromosomes in the cell nucleus.

  • Before the DNA has been replicated, a chromosome consists of a single very long DNA double helix that is highly coiled and folded by proteins.

  • Five major types of histone proteins, all of them highly basic, neutralise much of the DNA's negative charge and package the DNA into nucleosomes and 30‐nm fibres.

  • The N‐terminal tails of core histones are intrinsically disordered, allowing them to interact with many other proteins and undergo various posttranslational modifications.

  • Transcriptional activation of genes, or readiness for transcriptional activation, is associated with histone acetylation, and inactivation is generally associated with histone methylation.

  • In mitotic chromosomes, the chromatin fibre is folded into loops by attachment to a scaffold of nonhistone proteins.

  • Mitotic chromosome condensation appears to involve two components: compaction of the chromatin at the onset of mitosis, which involves phosphorylation of chromosomal proteins, and establishment of a robust architecture that can withstand spindle forces, which involves condensin.

  • The various chromosome forms that are seen throughout the cell cycle or the life cycle of the organism have closely related structures.

  • A chromosome during interphase retains some aspects of the structure it had during mitosis and is confined to a distinct ‘territory’ within the interphase nucleus.

  • Chromosome banding and chromosome painting are medically important for detecting chromosome abnormalities such as breaks, fusions, translocations and aneuploidy and can be used to track chromosomal rearrangements that have occurred during evolution.

Keywords: centromere; chromosome; chromatin; condensation; condensin; kinetochore; nucleus; structure; transcription; territory

Figure 1.

The nucleosome core and the 30‐nm chromatin fibre. (a) The structure of the nucleosome core has been determined by X‐ray diffraction and consists of 146 base pairs of DNA wrapped 1.6 times around an octamer of core histones (H2A, H2B, H3, H4). Reproduced with permission from Luger et al.. (b)–(e) Histone H1 is required for formation of the 30‐nm chromatin fibre. (b) In very low salt (0.2 mmethylenediaminetetraacetic acid (EDTA)), chromatin fragments (nucleosome oligomers obtained by partial nuclease digestion) unfold to a ‘string of beads’. (c) In high salt (5 mm triethanolamine, 0.2 mmEDTA and 100 mm NaCl), 30‐nm fibres form. (d) With histone H1‐depleted chromatin fragments in very low salt, nucleosomes are unstable and begin to fall apart. (e) In high salt, histone H1‐depleted chromatin cannot form proper 30‐nm fibres. Reproduced from Thoma et al. with permission from The Rockefeller University Press.

Figure 2.

Mitotic chromosomes, scaffolds and loops. (a) Whole mount critical point‐dried human chromosome viewed by transmission electron microscopy. Note the folded 30‐nm fibres that are especially evident at the edges of the chromatids. (b) A critical point‐dried human (HeLa) chromosome viewed by scanning electron microscopy. (c) HeLa chromosome, depleted of histones by treatment with polyanions and spread with cytochrome c for electron microscopy, showing the central scaffold and part of the surrounding DNA ‘halo’. (d) Another histone‐depleted HeLa chromosome showing DNA loops that can be traced emerging from the scaffold and returning to the same point. (e) and (f) Radial loop organisation seen in ultrathin cross‐sections of HeLa mitotic chromosomes swollen in buffers containing 1.0 mm MgCl2 (e) or ethylenediaminetetraacetic acid (f). (g) A portion of a lampbrush chromosome from the newt Notophthalmus viridescens, showing the central axes of the two chromatids from which loops of transcribing chromatin extend laterally. (h) and (i) Central scaffolds of HeLa metaphase chromosomes depleted of histones by treatment with 2 mNaCl. The scaffold has a diffuse, fibrous texture except in (i) where part of one arm appears to have become artefactually condensed during spreading and dehydration. Micrograph in (a) reproduced with permission from DuPraw ; (b), (e) and (f) reproduced from Marsden and Laemmli with permission from Elsevier; (c) and (d) reproduced from Paulson and Laemmli with permission from Elsevier; (g) reproduced from Roth and Gall with permission from The Rockefeller University Press; (h) and (i) reproduced from Paulson with permission from Springer.

Figure 3.

Condensin regulates the structure of the vertebrate mitotic chromosome. (a) The condensin complex is composed of five subunits; two subunits (SMC2 and SMC4) are adenosine triphosphatases (ATPases) and are part of both the condensin I and condensin II complexes. Three non‐SMC subunits are specific for each condensin complex: CAPH, CAPD and CAPG are only present in condensin I, whereas CAPH2, CAPD3 and CAPH2 are only part of condensin II. (b) Chicken mitotic chromosomes stained with an antibody recognising the SMC2 subunit of condensin: Left panel, DNA, stained with DAPI (4′, 6‐diamidino‐2‐phenylindole); right panel, condensin. The condensin complex is present in the axial region of each chromatid. (c) Mitotic chromosomes lacking both condensin complexes are not well organised and acquire a fuzzy appearance in low ionic strength solutions. (d) Condensin loading on mitotic chromosomes functions both to stabilise chromosome structure and also to direct localisation of several nonhistone chromosome proteins. (e)–(g) Role of condensin at centromeres. When the chromosomes are aligned on the metaphase plate and the kinetochores (red) of sister chromatids are attached to spindle microtubules (green) emanating from opposite poles (the configuration known as bi‐orientation), the DNA between the two sister kinetochores (represented in (g) as a spring) becomes stretched. Condensin acts on this region to constrain the stretch, possibly by catenating the centromeric DNA. In the absence of condensin (f), the centromeric chromatin can be abnormally pulled by the attached microtubules (arrows) causing defects in executing mitosis.

Figure 4.

Condensin and RCA co‐operate in the assembly of the vertebrate mitotic chromosome. (a) During anaphase, chromatids segregate to opposite poles and normally maintain a compact structure. (Chromosomes, white; microtubules, green.) (b) Without condensin, chromosomes collapse during anaphase separation, indicating an important role for the condensin complex in maintaining anaphase chromosome structure. (c) The requirement for condensin in anaphase can be overridden by keeping the recently discovered mitotic condensation factor RCA (for ‘regulator of chromosome architecture’) active during anaphase. (d) Diagram illustrating the role of condensin and RCA in mitotic chromosome structure. Condensin loads onto the chromosomes early in mitosis and is essential for maintaining their structure and organisation, but it is not essential for global chromatin compaction. RCA regulates mitotic chromatin compaction and its activity is mediated by protein phosphorylation. (e) In anaphase, RCA becomes inactive due to the activation of the protein phosphatase 1 (PP1).

Figure 5.

Specialised chromosome structures and chromosome organisation in interphase. (a) Schematic representation of a mitotic chromosome. The two sister chromatids (white) are held together at the centromere and this defines the region where the kinetochore is assembled. The inner kinetochore (red) lies underneath the outer kinetochore (green), which mediates the interaction with the spindle microtubules (blue). Each sister chromatid contains a single linear DNA molecule and the terminal ends are called telomeres (pink). (b) and (c) Immunofluorescence localisation of the inner kinetochore protein CENP‐A (b and c, red), the outer kinetochore component Hec1 (c, green), and kinetochore microtubules (c, blue); (d) fluorescence in situ hybridisation (FISH) with telomeric‐specific DNA (d, pink). Courtesy of J Dorrens, University of Edinburgh. (e) and (f) Each chromosome maintains a defined territory within the interphase nucleus. In a hybrid chicken cell containing one CHO (Chinese hamster ovary) chromosome, hybridisation with CHO genomic DNA reveals that the single CHO chromosome present in the cell (f) is not dispersed within the interphase nucleus (e) but maintains a compact organisation and a distinct territory. (g) Multicolour FISH (or ‘chromosome painting’) allows the identification of specific chromosomes and chromosome regions. In this case, a human nucleus and chromosomes were probed with DNA ‘paints’ prepared from gibbon chromosomes to identify chromosomal rearrangements that have occurred since these two species diverged from a common ancestor. Reproduced with permission from Ferguson‐Smith and Trifonov .

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Further Reading

De Wulf P and Earnshaw WC (eds) (2009) The Kinetochore: From Molecular Discoveries to Cancer Therapy. New York: Springer.

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Scherer S (2008) A Short Guide to the Human Genome. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Turner BM (2001) Chromatin and Gene Regulation: Molecular Mechanisms in Epigenetics. Oxford, UK: Blackwell Science.

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Paulson, James R, and Vagnarelli, Paola(Mar 2011) Chromosomes and Chromatin. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005766.pub2]