New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Abstract

The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair. Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components. This is the result of the incorporation of variant histones and post-translational modifications of histone amino acid side chains. The resulting changes in nucleosome structure, stability and dynamics affect the compaction of nucleosomal arrays into higher-order structures. It is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed. This implies that chromatin structure must also be viewed in the context of specific biological functions.

Figure 1. Primary, secondary and tertiary structure of chromatin

The primary structure is shown as nucleosomal arrays consisting of nucleosomes with canonical histones (shown in light blue and yellow) and combinations of different histone variants (shown in green, purple and light blue). Nucleosomes with canonical or histone variants may vary in the degree of post-translational modifications (PTMs; such as acetylation, methylation, phosphorylation, ubiquitylation and sumoylation), generating the possibility for nucleosomes with a large number of different ‘colours’. Histone variants and PTMs may affect nucleosome structure and dynamics. The spacing between nucleosomes may vary on the basis of the underlying sequence, action of chromatin-remodelling enzymes and DNA binding by other factors (for example, transcription activators). Short-range nucleosome–nucleosome interactions result in folded chromatin fibres (secondary chromatin structure, lower left panel). Fibre–fibre interactions, which are defined by long-range interactions between individual nucleosomes, are also affected by the primary structure of chromatin fibres, including PTMs, histone variants and spacing of nucleosomes. Secondary and tertiary structures are stabilized by architectural proteins, such as linker histone H1, methyl-CpG-binding protein 2 (MeCP2), heterochromatin protein 1 (HP1), high mobility group (HMG) proteins, poly(ADP-ribose) polymerase 1 (PARP1), myeloid and erythroid nuclear termination stage-specific protein (MENT), Polycomb group proteins and many others. Transitions between the different structural states are indicated by double arrows; these may be regulated by changes in patterns of PTMs, binding or displacement of architectural proteins, exchange of histone variants and chromatin-remodelling factors.

Figure 2. Nucleosome structure and the acidic patch: a common interaction interface for many nucleosome-interacting proteins

The structure of the nucleosome (Protein Data Bank code 1AOI) is viewed down the superhelical axis of the DNA. Histones H3, H4, H2A and H2B are shown in light blue, green, yellow and red, respectively. The figure indicates the amino-terminal α-helix of H3 (H3αN), which organizes the penultimate 10 bp of the DNA, and the carboxy-terminal end of the H2A docking domain. Acidic residues on H2A and H2B (the ‘acidic patch’) that are involved in the interaction with the H4 tail and with nucleosome-interacting proteins (such as the latency-associated nuclear antigen (LANA) peptide, interleukin-33 (IL-33), regulator of chromosome condensation 1 (RCC1), silent information regulator 3 (Sir3) and high mobility group nucleosome-binding domain-containing protein 2 (HMGN2)) are indicated in bright red; additional residues that are implicated in the interaction interfaces with the proteins listed above are shown in dark blue. Note that the number of total histone residues implicated in all of these protein–protein interfaces is relatively small, and that all cluster in a contained region on the surface of the histone octamer. In the absence of these factors, the interaction of the H4 tail from a neighbouring particle with the acidic patch mediates nucleosome–nucleosome interactions, thereby promoting chromatin folding. By using similar interactions with acidic patch on the nucleosome, the proteins listed above may compete with the H4 tail and modulate chromatin structure.

Figure 3. The many structural states of the nucleosome

a | Structural states of the nucleosome that are likely to be interchangeable. These include the tetrasome, which is formed by the wrapping of ~80 bp DNA around an (H3–H4)₂ tetramer. Hexasomes (nucleosomes lacking one H2A–H2B heterodimer) are intermediate states during nucleosome assembly or disassembly, as well as during transcription of nucleosome templates by RNA polymerase II. Both hexasomes and fully formed nucleosomes may undergo spontaneous structural transitions that are characterized either by the transient release of the DNA ends (DNA breathing) or by a transient opening of the interface between histone subcomplexes (open state). Some of the specific states may be favoured by DNA sequence, histone variant incorporation or post-translational modifications (PTMs). Histone variants are likely to be incorporated by similar pathways. b | Nucleosomes may also exist in alternative states that vary in the direction of the handedness of the DNA superhelix (left-handed versus right-handed) or in the stoichiometry (hemisome) and structural states (lexosome) of histones. These alternative structures, if they do indeed exist in vivo, would affect DNA accessibility and the interaction of nuclear factors with chromatin.

Figure 4. Two models for chromatin secondary structure

The solenoid model is characterized by interactions between consecutive nucleosomes (n, n + 1; a,b), whereas the zigzag model implies interactions between alternate nucleosomes (n, n + 2; c,d). The alternative nucleosomes are numbered from N1 to N8. In the solenoid model proposed by Rhodes and colleagues, the 30 nm chromatin fibre is an interdigitated one-start helix in which a nucleosome in the fibre interacts with its fifth and sixth neighbour nucleosomes. Alternative helical gyres are coloured blue and magenta (b). In the zigzag model, the chromatin fibre is a two-start helix in which nucleosomes are arranged in a zigzag manner such that a nucleosome in the fibre binds to the second neighbour nucleosome. Alternative nucleosome pairs are coloured blue and orange (d). The two models also differ in the trajectory and degree of bending of the DNA that connects two nucleosomes (linker DNA). Figure is reproduced, with permission, from REF. © (2011) Elsevier.

Figure 5. Nucleosome–nucleosome interactions mediated by histone tails and the nucleosomal surface

a | Nucleosome–nucleosome interactions in the crystal structures of unconnected 147 bp nucleosomes (Protein Data Bank (PDB) code 1AOI).b | Nucleosome– nucleosome interactions, as seen in the low-resolution tetranucleosome structure of four connected nucleosomes (PDB code 1ZBB; only two nucleosomes are shown). The resolution of this structure does not reveal the location of the H4 tail. A cartoon at the bottom of each panel shows the relative arrangement of the two nucleosomes with respect to each other. Residues constituting the acidic patch are shown in red, and the H4 tail (in a) is shown in green; it is not resolved in the structures shown in b.

Figure 6. A model for chromatin tertiary structure by interdigitation of nucleosomal arrays

The dynamic motion of arrays, possibly aided by nucleosome remodelling factors and histone-modifying enzymes, enables partial decompaction by the ‘unpeeling’ of an unfolded array (light blue) from the large-scale interdigitated tertiary chromatin fibre. As a result, this ‘string of pearls’ (shown on the left) slides out of the compact array and becomes more accessible as it is removed from the interdigitated stacks (shown on the right). This unpeeling process from the surface of the fibre facilitates transcription factor access. The fractal nature of the interdigitated chromatin fibre enables access to even DNA that is buried deep within the fibre.