Nucleosomes: Structure and Function


The structure of the nucleosome core particle, the basic repeating unit in eukaryotic chromatin, allows us to view the role of histones in regulating transcription, and in assembling specialized chromatin domains in a structural context. The organization of eukaryotic DNA into chromatin has fundamental implications for our understanding of all cellular processes that use DNA as a substrate.

Keywords: histone; nucleosome; chromatin; DNA; crystal structure; transcription regulation

Figure 1.

Overview of the nucleosome core particle structure, viewed in two different orientations. This schematic representation is derived from the high‐resolution crystal structure, and demonstrates how a 5‐fold compaction of DNA is achieved by wrapping it around the histone octamer core. α Helices of the histone proteins are shown as spirals. H3 is coloured blue, H4 green, H2A yellow and H2B red. The DNA is shown in grey. (a) The nucleosome core particle viewed down the superhelical axis. (b) The same structure is rotated by 90° around the y‐axis to emphasize the disc‐like shape of the particle.

Figure 2.

Architecture of the histone fold and of the nucleosome core particle. (a) Schematic overview of the four histone proteins H3, H4, H2A and H2B. α Helices of the histone fold are shown as solid boxes, α helices and β strands of the histone fold extensions are shown as open boxes and arrows, respectively. Histone tails are shown as dotted lines. The length of α helices, β strands, loops and tails is shown to scale. The components of the histone fold (α1, L1, α2, L2, α3), and the location of the H2A docking domain are indicated. (b) A histone fold dimer (here shown for H3 and H4, shown in blue and green, respectively) is formed by the antiparallel arrangement of two histones. α Helices and loops of the histone fold are indicated (compare with (a)). The orientation is similar to that in (c). (c) The architecture of the histone octamer is revealed by depicting only half of the DNA and associated proteins, in the same view as in Figure a. Unlike (b), this figure shows not only the histone fold regions, but also histone fold extensions and part of the tails. The C‐terminus of each histone protein is labelled C′. Note that most of the tails are disordered and are therefore not included in this picture. Regions of protein–DNA interaction are numbered from the centre of the DNA outwards.

Figure 3.

The nucleosome core particle in a ‘space‐filling’ representation, in which each atom of the histone proteins (coloured as in Figures and ) is shown as a sphere. The DNA is represented by its molecular surface. This side view emphasizes the alignment of the grooves of the DNA across the two gyres of the DNA superhelix, and shows how the histone tails emerge from narrow channels formed by two minor grooves.


Further Reading

Cheung WL, Briggs SD and Allis CD (2000) Acetylation and chromosomal functions. Current Opinion in Cell Biology 12: 326–333.

Division of Intramural Research (NIH). Histone Sequence Database []

Felsenfeld G, Clark D and Studitsky V (2000) Transcription through nucleosomes. Biophysical Chemistry 86: 231–237.

Kornberg RD and Lorch Y (1999) Twenty‐five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285–294.

Krebs JE and Peterson CL (2000) Understanding ‘active’ chromatin: a historical perspective of chromatin remodelling. Critical Reviews in Eukaryote Gene Expression 10: 1–12.

Luger K and Richmond TJ (1998a) DNA binding within the nucleosome core. Current Opinion in Structural Biology 8: 33–40.

Luger K and Richmond TJ (1998b) The histone tails of the nucleosome. Current Opinion in Genetics and Development 8: 140–146.

Research Collaboratory for Structural Bioinformatics. Protein Data Bank []

Strahl BD and Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45.

Thomas JO (1999) Histone H1: location and role. Current Opinion in Cell Biology 11: 312–317.

Widom J (1998) Structure, dynamics, and function of chromatin in vitro. Annual Review of Biophysics 27: 285–387.

Wolffe A (1998) Chromatin: Structure and Function. London: Academic Press.

Wolffe AP and Guschin D (2000) Review: chromatin structural features and targets that regulate transcription. Journal of Structural Biology 129: 102–122.

Workman JL and Kingston RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annual Review of Biochemistry 67: 545–579.

Wu J and Grunstein M (2000) 25 years after the nucleosome model: chromatin modifications. Trends in Biochemical Sciences 25: 619–623.

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Luger, Karolin(Apr 2001) Nucleosomes: Structure and Function. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0001155]