Nucleosome

A nucleosome is the basic repeating structural unit of chromatin, the DNA–protein material that forms chromosomes in eukaryotes. Its core consists of approximately 147 base pairs of DNA wrapped around an octamer containing two copies each of the histone proteins H2A, H2B, H3, and H4. Nucleosomes package DNA while regulating its accessibility to the molecular machinery that reads, copies, and repairs it. They are dynamic assemblies rather than fixed protective shells. (nature.com)

Structure and terminology

The nucleosome core particle

The nucleosome core particle comprises the histone octamer and its directly wrapped DNA. The DNA follows approximately 1.65–1.7 left-handed superhelical turns around the histone core. The octamer contains a central H3–H4 tetramer associated with two H2A–H2B dimers. Its architecture depends on the histone fold, a structural motif that mediates interactions between histones and contributes to DNA binding. (nature.com)

The central axis of approximate twofold symmetry is called the dyad axis. Positions along nucleosomal DNA are often described relative to the dyad, allowing researchers to specify where a protein binds or where DNA–histone contacts are disrupted. Histone amino-terminal tails extend from the folded core and can contact DNA, neighboring nucleosomes, and regulatory proteins. (nature.com)

DNA wrapping is stabilized by numerous noncovalent contacts with the histone surface. These contacts predominantly recognize features of the DNA backbone and its geometry rather than a single required nucleotide sequence. Nevertheless, sequences differ in how readily they bend around the octamer, so nucleosomes have sequence preferences without being restricted to one DNA motif. (pubs.acs.org)

Linker DNA and chromatosomes

Adjacent nucleosome cores are connected by linker DNA. Consequently, the nucleosome repeat length includes both the core-associated DNA and the linker segment; it is not identical to the approximately 147-base-pair core length. Repeat lengths vary with linker length. For example, experimentally reconstructed arrays with repeat lengths of 177, 187, 197, and 207 base pairs contain linkers of 30, 40, 50, and 60 base pairs, respectively. (nature.com)

Linker histone H1 can associate with DNA near the nucleosome dyad and entry–exit regions. The resulting assembly is called a chromatosome. H1 is therefore distinct from the eight core histones, not a ninth member of the core octamer. Its binding geometry depends on linker DNA length, trajectory, and the surrounding nucleosome arrangement. (nature.com)

Discovery and structural analysis

The repeating organization of chromatin became established during the 1970s through complementary microscopy and biochemical studies. In January 1974, Ada and Donald Olins published electron-microscopic observations of arrays of spherical chromatin particles, termed nu bodies. In May 1974, Roger Kornberg proposed a repeating chromatin unit containing eight histone molecules and approximately 200 DNA base pairs. These observations helped establish the particulate model of chromatin. (pubmed.ncbi.nlm.nih.gov)

In 1997, Karolin Luger and colleagues reported the nucleosome core particle structure at 2.8-ångström resolution using X-ray crystallography. The structure revealed how the histone octamer organizes DNA and how histone tails extend between DNA turns. That particular particle contained 146 base pairs; the frequently used figure of approximately 147 base pairs describes the canonical core rather than an invariant length for every nucleosomal particle. (nature.com)

DNA accessibility and nucleosome dynamics

Wrapping DNA around histones reduces access for many DNA-binding proteins, but does not make the DNA permanently inaccessible. Nucleosomal DNA undergoes transient partial unwrapping and rewrapping, commonly called nucleosome breathing. Unwrapping generally begins near a DNA entry or exit point and can expose otherwise buried binding sites without requiring complete disassembly of the histone octamer. Single-molecule and kinetic experiments have directly demonstrated this spontaneous behavior. (nature.com)

Cells also alter nucleosomes actively through chromatin remodeling. Remodeling complexes use energy from ATP to change histone–DNA interactions. Depending on the complex and its context, remodeling can reposition nucleosomes, promote histone removal, or exchange histone variants. Experiments with ISW2 and SWI/SNF established that DNA translocation within the nucleosome is integral to their remodeling activity. (pmc.ncbi.nlm.nih.gov)

These processes influence transcription, DNA replication, and DNA repair. DNA must become accessible at appropriate times, but nucleosomes must also be maintained or restored afterward. Thus, chromatin regulation involves controlled exposure and reconstruction, not simply the permanent removal of nucleosomes from active DNA. (pmc.ncbi.nlm.nih.gov)

Positioning and gene regulation

Nucleosome positioning describes where nucleosomes lie along a DNA sequence. Several related measurements must be distinguished:

• Occupancy: how frequently a region is covered by a nucleosome across the sampled molecules or cells.
• Translational positioning: where the nucleosome lies along the DNA.
• Rotational positioning: which face of the DNA helix points toward the histone surface.

A region can therefore have substantial nucleosome occupancy without containing one precisely positioned nucleosome in every cell. (nature.com)

Positioning reflects DNA sequence preferences, remodeling activity, competition with DNA-binding proteins, and constraints imposed by neighboring particles. Nucleosomes can conceal binding sites for transcription factors or help define accessible regulatory regions. Their distribution near promoters is consequently an important component of gene expression regulation. (nature.com)

The relative contribution of DNA sequence has been debated. Genome-wide reconstitution experiments demonstrated substantial sequence-dependent organization, whereas other experiments found that intrinsic histone–DNA interactions did not explain most precise nucleosome positions in living cells. The distinction between broad occupancy preferences and exact positioning is important: sequence preferences contribute to organization, but cellular factors also establish and reshape it. (nature.com)

Histone modifications and variants

Nucleosomes differ in both their histone composition and their chemical modification state. Histone modifications include acetylation, methylation, phosphorylation, and ubiquitination. Such changes can alter nucleosome dynamics directly or influence the binding and activity of other chromatin-associated proteins. Their effects depend on the modified residue and molecular context; a modification should not automatically be interpreted as a universal switch for transcription. (pmc.ncbi.nlm.nih.gov)

One experimentally established example is acetylation of lysine 16 on histone H4. In reconstructed nucleosome arrays, this modification inhibits compact fiber formation and interactions between fibers. It also changes the activity of a chromatin-remodeling enzyme, illustrating that one modification can affect both physical packing and protein–chromatin interactions. (pubmed.ncbi.nlm.nih.gov)

Histone variants substitute for particular canonical histones and provide specialized nucleosomal properties. A prominent example is CENP-A, an H3 variant associated with centromeres, where chromosome segregation machinery assembles. Structural studies showed that human CENP-A nucleosomes contain an octameric histone core while differing from canonical H3 nucleosomes in features important for centromeric identity. (nature.com)

Assembly, recycling, and chromatin inheritance

Histone chaperones are proteins that bind histones and regulate their assembly, handling, or exchange. They help preserve nucleosome density and composition during processes that disturb chromatin, including transcription and replication. Their functions overlap but are not interchangeable. (nature.com)

During DNA replication, nucleosomes ahead of the replication machinery are disrupted. Parental histones are recycled onto newly synthesized DNA, while newly produced histones supply additional material needed to rebuild chromatin. Experiments have shown that the chaperone ASF1 contributes to local recycling of parental H3 variants. (nature.com)

Histone recycling contributes to the maintenance of chromatin-associated information studied in epigenetics. However, this does not mean that complete nucleosomes are copied intact in the same manner as DNA sequences. Parental histones are redistributed, new histones are incorporated, and modification patterns are maintained through additional molecular processes. (nature.com)

Higher-order organization

Nucleosome arrays are often depicted as “beads on a string.” This describes an extended arrangement, but not every configuration inside a cell nucleus. Linker histones, linker DNA geometry, and interactions among nucleosomes can produce more compact arrangements. (pubmed.ncbi.nlm.nih.gov)

A regular 30-nanometer fiber historically served as a major model for the next level of chromatin organization. Such compact fibers can form under particular experimental conditions, but they are not a universal description of chromatin inside cells. ChromEM tomography of human interphase and mitotic cells revealed irregular, flexible chromatin chains with varying packing densities rather than a uniform hierarchy of regular fibers. These observations distinguish the well-established nucleosome core structure from more variable higher-order organization. (pubmed.ncbi.nlm.nih.gov)

Experimental methods and limitations

Nucleosomes are investigated through complementary approaches:

• Structural methods: X-ray crystallography and cryo-electron microscopy resolve histone–DNA contacts and interactions with associated proteins. (nature.com)
• Genome-wide mapping: MNase-seq combines micrococcal nuclease digestion with sequencing of protected DNA fragments to infer nucleosome distributions. (nature.com)
• Accessibility profiling: ATAC-seq measures transposase access to chromatin and provides information about accessible regions and nucleosome organization. (nature.com)
• Single-molecule measurements: fluorescence-based experiments monitor transient DNA unwrapping and protein access to nucleosomal sites. (nature.com)

Each method measures a different aspect of chromatin. In particular, a protected DNA fragment is not an unambiguous record of an identical particle in every cell. Micrococcal nuclease has sequence-dependent cleavage preferences, and digestion can preferentially eliminate some nucleosomal DNA. Comparisons with chemical mapping have demonstrated biases in MNase-derived maps. Structural reconstructions, accessibility assays, and nucleosome mapping therefore require interpretation in light of their experimental conditions and the properties they directly measure. (rcastoragev2.blob.core.windows.net)

References

1. Crystal structure of the nucleosome core particle at 2.8 Å resolutionnature.com
2. Nucleosome Dynamics as Modular Systems that Integrate DNA Damage and Repairpmc.ncbi.nlm.nih.gov
3. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectorynature.com
4. Linker histone defines structure and self-association behaviour of the 177 bp human chromatosomenature.com
5. Spheroid chromatin units (v bodies)pubmed.ncbi.nlm.nih.gov
6. Chromatin structure: a repeating unit of histones and DNApubmed.ncbi.nlm.nih.gov
7. Chromatin Structure: A Repeating Unit of Histones and DNAcir.nii.ac.jp
8. Rapid spontaneous accessibility of nucleosomal DNAnature.com
9. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosomenature.com
10. The histone chaperone SPT2 regulates chromatin structure and function in Metazoanature.com
11. The DNA-encoded nucleosome organization of a eukaryotic genomenature.com