# Nucleosome Core Particle: Structure, Function, and Dynamics

## Introduction to the Nucleosome Core Particle

The nucleosome core particle (NCP) is the fundamental repeating unit of eukaryotic chromatin, consisting of approximately 147 base pairs of DNA wrapped around a histone octamer. This protein-DNA assembly represents the first level of DNA compaction, reducing the linear length of the genome by roughly six-fold. Without this packaging, the human genome—spanning over two meters of DNA—could not fit within a nucleus that measures only 5–10 micrometers in diameter.

### Historical Context and Discovery

The discovery of the nucleosome emerged from a series of biochemical and biophysical observations in the early 1970s. In 1973, Ada Olins and Donald Olins used electron microscopy to visualize "nu bodies"—regularly spaced bead-like structures along chromatin fibers. Concurrently, Roger Kornberg, building on earlier work by Jean-Pierre Jost and others, proposed that chromatin consists of repeating subunits containing approximately 200 base pairs of DNA associated with an octamer of histone proteins. Kornberg's model, published in 1974, was supported by nuclease digestion experiments showing that chromatin could be cleaved into discrete, repeating fragments. The high-resolution structure of the nucleosome core particle was ultimately solved by Karolin Luger and Timothy Richmond in 1997 using [X-ray crystallography](/knowledge/molecular-biology/x-ray-crystallography) at 2.8 Å resolution, revealing the atomic details of histone-DNA interactions.

### Nucleosome vs. Chromatosome vs. Chromatin

These terms describe different levels of DNA packaging and are frequently confused. The **nucleosome core particle** comprises the histone octamer (two copies each of H2A, H2B, H3, and H4) with 147 base pairs of DNA wrapped in 1.65 left-handed superhelical turns. The **chromatosome** includes the core particle plus linker histone H1 bound to the entry/exit sites of DNA, protecting an additional ~20 base pairs of linker DNA. **Chromatin** is the broader term for the entire complex of DNA and associated proteins (histones and non-histone proteins) within the nucleus. The [Nucleosome Definition](/knowledge/molecular-biology/nucleosome-definition) encompasses the core particle and, in some usages, includes the linker DNA between particles. The [Nucleosome vs Nucleotide](/knowledge/molecular-biology/nucleosome-vs-nucleotide) distinction is critical: a nucleotide is a single monomeric unit of nucleic acid, whereas a nucleosome is a macromolecular complex containing many nucleotides of DNA.

## Structural Components of the Nucleosome Core Particle

### Histone Octamer Composition

The histone octamer is a symmetric protein complex assembled from four histone families: H2A, H2B, H3, and H4. Each histone is present in two copies, yielding an (H3-H4)₂ tetramer flanked by two H2A-H2B dimers. The octamer has a molecular weight of approximately 108 kDa and forms a disk-like structure with a diameter of ~11 nm and a height of ~5.7 nm.

Each core histone protein shares a conserved structural motif known as the **histone fold**, consisting of three alpha-helices (α1, α2, α3) connected by two loops (L1 and L2). The histone fold mediates heterodimerization through a "handshake" interaction: the α2 helix of one histone packs against the α1 and α3 helices of its partner. This arrangement creates a crescent-shaped heterodimer with a central long α2 helix. The H3-H4 dimer pairs form the (H3-H4)₂ tetramer through a four-helix bundle between the α3 helices of the two H3 molecules. Similarly, H2A-H2B dimers associate with the tetramer through interactions between the H2B α3 helix and the H4 α2 helix, as well as between H2A and H3.

The four histone families, while sharing the histone fold, have distinct N-terminal and C-terminal extensions. H2A possesses a C-terminal docking domain that is critical for interactions with the H3-H4 tetramer and a short C-terminal tail that extends beyond the nucleosome surface. H2B has an N-terminal tail that emerges between the two DNA gyres. H3 and H4 have long N-terminal tails that protrude through the DNA superhelix and extend outward from the nucleosome.

### DNA Wrapping and Superhelical Geometry

The 147 base pairs of DNA in the nucleosome core particle follow a left-handed superhelical path around the histone octamer, completing 1.65 turns. The DNA is bent sharply, with an average radius of curvature of ~4.2 nm—a dramatic departure from the ~10 nm persistence length of free DNA. This bending is achieved through periodic distortions of the DNA double helix, with the minor groove facing inward toward the histone surface at 14 distinct sites where the DNA makes primary contacts with the octamer.

The DNA double helix is underwound relative to canonical B-form DNA, with an average of 10.2 base pairs per helical turn rather than the 10.5 observed in solution. This underwinding facilitates the tight bending required for wrapping. The superhelix can be described using a coordinate system where positions are designated as superhelix locations (SHLs) numbered from 0 at the dyad axis (the central base pair, which sits on the twofold symmetry axis of the particle) to ±7 at the entry/exit points. The dyad is the point of pseudo-twofold symmetry in the nucleosome, and the DNA sequence is not necessarily palindromic but the protein arrangement is symmetric.

### Histone Tails and Post-Translational Modifications

The N-terminal tails of histones—approximately 15–30 amino acids long—extend through the minor grooves of the wrapped DNA and protrude from the nucleosome surface. These tails are intrinsically disordered in solution but become structured upon binding to specific partners. The tails are the primary sites for post-translational modifications (PTMs), including acetylation of lysine residues, methylation of lysine and arginine residues, phosphorylation of serine and threonine residues, and ubiquitination of lysine residues.

The modification landscape is complex and functionally significant. For example, acetylation of H3K27 (lysine 27 of histone H3) and H4K16 neutralizes the positive charge of the lysine side chain, weakening histone-DNA interactions and promoting a more open chromatin conformation. Methylation of H3K4, H3K36, and H3K79 is generally associated with actively transcribed genes, whereas methylation of H3K9 and H3K27 correlates with transcriptional repression. These modifications are written by specific enzymes (e.g., histone acetyltransferases such as p300/CBP, histone methyltransferases such as SUV39H1 for H3K9) and removed by erasers (e.g., histone deacetylases such as HDAC1, demethylases such as LSD1). The functional consequences of these modifications are mediated largely through reader proteins that recognize specific marks—for instance, the bromodomain recognizes acetyl-lysine, and the chromodomain recognizes methyl-lysine. The [Histone Nucleosome](/knowledge/molecular-biology/histone-nucleosome) relationship is central to understanding how these modifications influence chromatin function.

## High-Resolution Structure Determination

### X-ray Crystallography of Nucleosome Core Particles

The determination of the nucleosome core particle structure at atomic resolution required overcoming significant technical challenges. The first high-resolution structure, solved by Luger and colleagues in 1997, used nucleosome core particles reconstituted from recombinant Xenopus laevis histones and a 146-base-pair palindromic DNA sequence derived from human alpha-satellite DNA. Crystals were grown by vapor diffusion in hanging drops containing 40–50 mM potassium cacodylate (pH 6.0), 50–80 mM KCl, and 5–10 mM manganese chloride, with PEG 2000 as precipitant. The structure was phased using multiple isomorphous replacement with heavy atom derivatives (e.g., tantalum cluster compounds) and refined to 2.8 Å resolution with an R-factor of 23.5%.

Subsequent structures improved resolution and provided insights into sequence-dependent variations. A 2.5 Å structure using a different DNA sequence revealed that DNA bending is accommodated by localized kinks at specific base-pair steps, particularly at pyrimidine-purine dinucleotides. Later structures of nucleosomes containing histone variants (e.g., CENP-A, H2A.Z) and modified histones have been solved, revealing how these changes alter the structural dynamics of the particle.

### Cryo-Electron Microscopy Advances

Cryo-electron microscopy (cryo-EM) has emerged as a powerful complementary approach for studying nucleosome structure, particularly for large complexes and dynamic states. Unlike X-ray crystallography, cryo-EM does not require ordered crystals and can capture multiple conformational states from a single sample. Single-particle cryo-EM analysis of nucleosome core particles has achieved resolutions of 3–4 Å, sufficient to resolve the DNA backbone and histone side chains.

The advent of direct electron detectors and improved image-processing algorithms (e.g., RELION, cryoSPARC) has enabled near-atomic resolution structures of nucleosome complexes with [chromatin remodelers](/knowledge/molecular-biology/chromatin-remodelers), histone chaperones, and [transcription factors](/knowledge/molecular-biology/transcription-factor). Cryo-EM has been particularly valuable for visualizing the nucleosome in complex with large macromolecular assemblies, such as the SWI/SNF [chromatin remodeling](/knowledge/molecular-biology/chromatin-remodeling) complex, where the conformational flexibility of the complex precludes crystallization. The [Nucleosome Structure](/knowledge/molecular-biology/nucleosome-structure) determined by these methods provides the structural framework for understanding all nucleosome functions.

## Nucleosome Core Particle Dynamics and Stability

### Histone-DNA Contacts and Salt Bridges

The stability of the nucleosome core particle arises from an extensive network of non-covalent interactions between the histone octamer and DNA. Each histone dimer contributes to DNA binding through several structural elements: the L1 and L2 loops, the α1 helix, and the N-terminal ends of the α2 and α3 helices. These elements form a positively charged surface that interacts with the negatively charged phosphate backbone of DNA.

The primary contacts occur at 14 sites where the minor groove of DNA faces inward toward the histone surface. At each site, an arginine side chain (typically from H3 or H4) inserts into the minor groove, making hydrogen bonds with the phosphate groups on both DNA strands. For example, H3 arginine 45 (H3R45) inserts into the minor groove near the dyad, while H4 arginine 45 (H4R45) contacts DNA at superhelix location 1.5. These arginine side chains are critical for nucleosome stability; mutation of these residues to alanine reduces nucleosome stability by several kilocalories per mole.

Electrostatic interactions between the positively charged histone surface and the negatively charged DNA phosphate backbone contribute significantly to binding. The overall binding free energy of DNA to the histone octamer is approximately −20 to −30 kcal/mol under physiological conditions (150 mM KCl, pH 7.5, 25°C). This substantial free energy reflects the large buried surface area (~3,200 Ų of DNA buried per nucleosome) and the numerous hydrogen bonds and salt bridges formed.

### Nucleosome Breathing and Unwrapping

Despite the overall stability of the nucleosome, the particle is not static. **Nucleosome breathing** refers to the spontaneous, transient unwrapping of DNA from the histone octamer, particularly at the entry/exit sites. This unwrapping occurs on timescales of milliseconds to seconds and involves the breaking of histone-DNA contacts at the periphery of the particle while the central region (near the dyad) remains stably bound.

Site-specific FRET (Förster resonance energy transfer) experiments have measured the kinetics of DNA unwrapping. The outer 10–20 base pairs at each end unwrap with a rate constant of approximately 1–10 s⁻¹, whereas unwrapping of the central 60 base pairs is much slower (rate constants < 0.01 s⁻¹). This gradient of stability reflects the increasing number of histone-DNA contacts toward the dyad. The equilibrium constant for full unwrapping is extremely unfavorable (K_eq ≈ 10⁻⁶ to 10⁻⁸), meaning that at any given moment, only a tiny fraction of nucleosomes are fully unwrapped.

The unwrapping dynamics are modulated by ionic conditions. Increasing salt concentration (e.g., from 50 mM to 300 mM NaCl) weakens electrostatic interactions and increases the rate of unwrapping. Divalent cations such as Mg²⁺ at concentrations of 1–5 mM can stabilize the wrapped state by screening the negative charges of DNA. Temperature also affects dynamics, with higher temperatures increasing the amplitude of breathing fluctuations.

### Role of Histone Variants

Histone variants—non-allelic isoforms of the canonical histones—introduce structural and functional diversity into nucleosomes. The major variants include H2A.Z, H2A.X, CENP-A (a centromere-specific H3 variant), and H3.3. These variants differ from canonical histones in their primary sequence and can alter nucleosome stability and dynamics.

H2A.Z, which shares ~60% sequence identity with canonical H2A, is enriched at promoters and regulatory elements. Nucleosomes containing H2A.Z exhibit altered stability: the H2A.Z-H2B dimer interface is less stable than that of canonical H2A-H2B, facilitating dimer exchange and nucleosome remodeling. Structural studies show that H2A.Z creates an extended acidic patch on the nucleosome surface and alters the interaction between the H2A.Z C-terminal region and the H3-H4 tetramer.

CENP-A, the centromere-specific H3 variant, differs substantially from H3 in its N-terminal tail and loop 1 region. CENP-A-containing nucleosomes are structurally distinct, with a more compact conformation and altered DNA wrapping. These differences are essential for kinetochore assembly and centromere function.

H3.3, which differs from canonical H3 by only four amino acids, is incorporated into nucleosomes at transcriptionally active loci and regulatory regions. The amino acid changes (particularly alanine 31 and serine 31 in the N-terminal tail) affect post-translational modification patterns and interactions with histone chaperones, influencing nucleosome dynamics and turnover.

## Role in DNA Packaging and Chromatin Structure

### The 10-nm Fiber and Beads-on-a-String

The nucleosome core particle is the building block of the 10-nm chromatin fiber, often described as "beads on a string." In this configuration, nucleosome core particles are connected by linker DNA of variable length (typically 20–80 base pairs), giving a repeating unit of 160–220 base pairs per nucleosome. The 10-nm fiber represents the first level of DNA compaction, achieving a packing ratio of approximately 6–7 base pairs per nanometer of fiber length.

The 10-nm fiber is the default state of chromatin under low ionic strength conditions in vitro (e.g., 10 mM Tris-HCl, pH 7.5, without added salt). Under physiological ionic conditions, the fiber undergoes further compaction, but the 10-nm fiber remains an important functional state, particularly for actively transcribed genes where higher-order compaction is reduced.

### Higher-Order Folding and the 30-nm Fiber

Under conditions of moderate ionic strength (e.g., 100–200 mM KCl or 1–2 mM MgCl₂), the 10-nm fiber folds into a more compact structure historically termed the 30-nm fiber. The existence and structure of the 30-nm fiber in vivo has been debated, but in vitro studies have defined two principal models: the one-start solenoid and the two-start zigzag.

In the **solenoid model**, consecutive nucleosomes follow a helical path with approximately 6 nucleosomes per turn, and the linker DNA bends smoothly between adjacent nucleosomes. In the **zigzag model**, nucleosomes alternate between two stacks, with linker DNA crossing between them, creating a more open structure. Cryo-EM and electron tomography studies of reconstituted chromatin fibers have provided evidence for the zigzag arrangement, where nucleosomes i and i+2 interact through their faces, and linker DNA adopts a straight conformation.

The formation of higher-order chromatin structures requires the linker histone H1. H1 binds to the entry/exit sites of DNA on the nucleosome, stabilizing the chromatosome and promoting fiber compaction. H1 has a central globular domain that binds to the nucleosome dyad and a long C-terminal tail that interacts with linker DNA. The presence of H1 increases the compaction of chromatin fibers by approximately 2-fold compared to H1-depleted chromatin.

The [Nucleosome Chromatin](/knowledge/molecular-biology/nucleosome-chromatin) relationship is hierarchical: nucleosomes assemble into the 10-nm fiber, which folds into higher-order structures that are further organized into chromosome territories within the nucleus. The [Nucleosome Model](/knowledge/molecular-biology/nucleosome-model) of chromatin structure has evolved from a static, regular repeating array to a dynamic, heterogeneous polymer where nucleosome positions and modifications vary across the genome.

## Nucleosome Core Particle in Gene Regulation

### Nucleosome Positioning and Transcription Factor Binding

The position of nucleosomes along DNA profoundly influences gene regulation. Nucleosomes occlude the DNA sequence from sequence-specific DNA-binding proteins, including transcription factors and RNA polymerase. A nucleosome positioned over a promoter can prevent [transcription initiation](/knowledge/molecular-biology/transcription-initiation) by blocking the assembly of the preinitiation complex.

Nucleosome positioning is determined by multiple factors: intrinsic DNA sequence preferences, ATP-dependent [chromatin remodelers](/knowledge/molecular-biology/chromatin-remodelers), histone chaperones, and transcription factor competition. DNA sequence influences positioning through base-pair-step preferences that affect DNA bendability. For example, poly(dA:dT) tracts are rigid and resist wrapping around the histone octamer, creating nucleosome-free regions. Conversely, sequences with alternating A/T and G/C dinucleotides at ~10-base-pair intervals (AA/TT/AT dinucleotides at positions where the minor groove faces inward) favor nucleosome formation.

Genome-wide nucleosome mapping has revealed a stereotypical organization at gene promoters: a nucleosome-free region (NFR) of approximately 150 base pairs flanked by well-positioned nucleosomes (the −1 and +1 nucleosomes). The +1 nucleosome is typically positioned ~50 base pairs downstream of the transcription start site (TSS) and represents a barrier to RNA polymerase II. During transcription elongation, RNA polymerase must traverse nucleosomes, a process facilitated by histone chaperones (e.g., FACT, facilitates chromatin transcription) that promote nucleosome disassembly and reassembly.

### ATP-Dependent Chromatin Remodeling Complexes

ATP-dependent chromatin remodeling complexes use the energy of ATP hydrolysis to alter nucleosome structure and position. These complexes belong to four families: SWI/SNF, ISWI, CHD, and INO80/SWR1. All share a conserved ATPase domain of the SF2 helicase superfamily but differ in their accessory subunits and mechanisms.

The **SWI/SNF family** (e.g., yeast SWI/SNF, human BAF) slides and evicts nucleosomes, creating nucleosome-free regions at promoters and enhancers. The **ISWI family** (e.g., yeast ISW2, human ACF) slides nucleosomes to regular spacing, promoting chromatin assembly and repression. The **CHD family** (e.g., yeast Chd1, human Mi-2) slides nucleosomes and is involved in transcription elongation. The **INO80/SWR1 family** exchanges histone variants, such as replacing H2A with H2A.Z at promoters.

The mechanism of nucleosome sliding involves the ATPase domain binding to the nucleosome at a specific location (the SHL2 site, approximately 20 base pairs from the dyad) and using ATP hydrolysis to translocate DNA around the octamer. The ATPase pulls DNA toward itself, creating a loop that propagates around the nucleosome, effectively moving the histone octamer relative to the DNA sequence. This process occurs in steps of 1–3 base pairs per ATP hydrolysis event, with rates of 1–10 base pairs per second under optimal conditions (1 mM ATP, 5 mM MgCl₂, 25°C).

The [Nucleosome Sliding](/knowledge/molecular-biology/nucleosome-sliding) process is essential for establishing and maintaining nucleosome positioning patterns that regulate gene expression. Disruption of chromatin remodeling complexes is associated with human diseases, including cancers (e.g., mutations in SMARCB1/SNF5, a SWI/SNF subunit, occur in malignant rhabdoid tumors) and developmental disorders.

## Methods to Study Nucleosome Core Particles

### Micrococcal Nuclease Digestion and Sequencing

Micrococcal nuclease (MNase) is an endo-exonuclease that preferentially cleaves linker DNA between nucleosomes, leaving the nucleosome-protected DNA intact. This property forms the basis for determining nucleosome positions genome-wide.

The standard protocol involves: (1) crosslinking cells with 1% formaldehyde for 10 minutes at room temperature to preserve chromatin structure; (2) isolating nuclei and digesting with MNase (typically 0.1–1 U per microgram of DNA) at 37°C for 5–15 minutes in buffer containing 50 mM Tris-HCl (pH 7.5), 5 mM CaCl₂, and 0.1% NP-40; (3) stopping the reaction with 10 mM EGTA; (4) purifying the protected DNA fragments (~147 base pairs for mononucleosomes); and (5) sequencing the fragments (MNase-seq). The resulting reads are aligned to the reference genome, and nucleosome occupancy is calculated as the density of fragment midpoints.

MNase-seq has revealed that nucleosome positions are not random but are influenced by DNA sequence, chromatin remodelers, and transcription. However, MNase has sequence bias—it cleaves A/T-rich regions more readily—and overdigestion can lead to nucleosome repositioning artifacts. Careful calibration of digestion conditions is essential for reliable results.

### Single-Molecule FRET

Single-molecule Förster resonance energy transfer (smFRET) provides real-time measurements of nucleosome dynamics. In a typical experiment, a donor fluorophore (e.g., Cy3) is attached to one position on the histone octamer or DNA, and an acceptor fluorophore (e.g., Cy5) is attached to another position. Changes in FRET efficiency report on distance changes between the two fluorophores.

For studying DNA unwrapping, a common design places the donor on the histone octamer (e.g., at H2A residue 114) and the acceptor on DNA at various distances from the dyad. When the DNA is wrapped, the fluorophores are close (high FRET); when the DNA unwraps, the distance increases (low FRET). These experiments have revealed that DNA unwrapping occurs in discrete steps, with partial unwrapping of 10–20 base pairs occurring rapidly (milliseconds) and complete unwrapping occurring rarely (seconds to minutes).

smFRET has also been used to study nucleosome sliding by remodelers, histone exchange, and the effects of histone modifications on nucleosome stability. The technique requires careful labeling stoichiometry and surface immobilization (e.g., via biotin-streptavidin linkage to a PEG-passivated quartz surface) to avoid artifacts.

### Electrophoretic Mobility Shift Assays

The electrophoretic mobility shift assay (EMSA) is a simple, quantitative method to study nucleosome formation and stability. Nucleosome core particles migrate more slowly than free DNA in native polyacrylamide gels due to their larger size and reduced negative charge density. A typical EMSA uses a 5% polyacrylamide gel (29:1 acrylamide:bis-acrylamide) in 0.5× TBE buffer, run at 4°C and 10 V/cm.

To measure nucleosome stability, a competitive EMSA can be performed: pre-formed nucleosomes are incubated with increasing concentrations of competitor DNA (e.g., a 147-base-pair fragment without sequence preference), and the fraction of nucleosomes that remain intact is quantified. The salt stability of nucleosomes can be assessed by incubating nucleosomes with increasing NaCl concentrations (0.6–1.2 M) and analyzing the dissociation products by native gel electrophoresis. These assays provide thermodynamic information about nucleosome stability under defined conditions.

## Common Pitfalls and Misconceptions

### Nucleosome vs. Chromatosome

A frequent error is using "nucleosome" and "chromatosome" interchangeably. The nucleosome core particle contains 147 base pairs of DNA and the histone octamer. The chromatosome includes the linker histone H1 and approximately 166 base pairs of DNA (the core 147 plus ~10 base pairs on each side protected by H1). H1 is not part of the nucleosome core particle, and its absence does not prevent nucleosome formation. In experimental contexts, "nucleosome" often refers to the core particle, but in chromatin biology, the term can include the linker DNA and H1. Be precise about which entity you mean.

### Histone Modifications vs. Histone Variants

Students often conflate post-translational modifications of histones with histone variants. Histone modifications are covalent chemical changes to amino acid side chains (e.g., acetylation of lysine, methylation of arginine) added and removed by enzymes. Histone variants are alternative protein isoforms encoded by different genes (e.g., H2A.Z, H3.3) that are incorporated into nucleosomes during replication-independent assembly. Modifications are dynamic and reversible; variants are stable components of the nucleosome. Both affect chromatin function but through different mechanisms.

### Static vs. Dynamic View

A common misconception is that the nucleosome is a rigid, static structure. In reality, nucleosomes are highly dynamic: DNA breathes and unwraps, histone octamers slide along DNA, histone dimers exchange, and entire nucleosomes are assembled and disassembled. These dynamics are essential for DNA accessibility and are regulated by ATP-dependent remodelers, histone chaperones, and post-translational modifications. The high-resolution crystal structures represent an average, stable conformation, not the full conformational landscape.

Another misconception is that nucleosome positioning is solely determined by DNA sequence. While sequence plays a role, ATP-dependent remodelers, transcription factors, and histone chaperones actively reposition nucleosomes. The steady-state [nucleosome organization](/knowledge/molecular-biology/nucleosome-organization) reflects the balance of these competing activities.

## Summary and Key Takeaways

The nucleosome core particle is a remarkable molecular machine that packages DNA while remaining dynamically responsive to cellular needs. Its structure—147 base pairs of DNA wrapped around a histone octamer—is conserved across eukaryotes, reflecting its fundamental importance. The histone fold, the arginine-mediated minor groove contacts, and the modifiable histone tails all contribute to a particle that is simultaneously stable and dynamic.

The [Nucleosome Concept](/knowledge/molecular-biology/nucleosome-concept) has evolved from a static packaging unit to a central regulatory element in all DNA-templated processes. Understanding nucleosome structure and dynamics is essential for comprehending transcription, replication, repair, and chromosome segregation.

## Frequently Asked Questions

### What is the nucleosome core particle?

The nucleosome core particle is the fundamental repeating unit of eukaryotic chromatin, composed of 147 base pairs of DNA wrapped in 1.65 left-handed superhelical turns around a histone octamer containing two copies each of histones H2A, H2B, H3, and H4. It is the first level of DNA compaction and provides the structural basis for higher-order chromatin organization.

### How many histone proteins are in a nucleosome core particle?

The histone octamer contains eight histone proteins: two copies each of H2A, H2B, H3, and H4. These are organized as an (H3-H4)₂ tetramer flanked by two H2A-H2B dimers. The linker histone H1, when present, binds to the entry/exit sites of DNA but is not part of the core particle.

### What is the difference between a nucleosome and a chromatosome?

The nucleosome core particle consists of the histone octamer plus 147 base pairs of DNA. The chromatosome includes the core particle plus linker histone H1 bound to the DNA entry/exit sites, protecting an additional ~20 base pairs of linker DNA (total ~166 base pairs). H1 stabilizes the wrapped state and promotes higher-order chromatin folding.

### How does DNA wrap around the histone octamer?

DNA wraps around the histone octamer in a left-handed superhelix, completing 1.65 turns. The DNA minor groove faces inward at 14 sites where arginine side chains insert into the groove and make contacts with the phosphate backbone. The DNA is underwound relative to B-form DNA, with ~10.2 base pairs per turn, facilitating the tight bending required for wrapping.

### What techniques are used to determine nucleosome structure?

The primary techniques are X-ray crystallography and cryo-electron microscopy. X-ray crystallography provided the first atomic-resolution structures (2.5–2.8 Å) using reconstituted nucleosome core particles. Cryo-EM has enabled structures of nucleosome complexes with remodelers, chaperones, and transcription factors at near-atomic resolution, capturing multiple conformational states.

### Why are histone tails important?

Histone tails are intrinsically disordered N-terminal extensions that protrude from the nucleosome surface. They are the primary sites for post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination) that regulate chromatin structure and function. Tails also mediate inter-nucleosome interactions and binding of regulatory proteins.

### What is nucleosome sliding?

Nucleosome sliding is the ATP-dependent movement of the histone octamer along DNA without dissociation. ATP-dependent chromatin remodeling complexes (SWI/SNF, ISWI, CHD, INO80/SWR1) translocate DNA around the octamer, repositioning nucleosomes to expose or occlude regulatory sequences. Sliding occurs in steps of 1–3 base pairs per ATP hydrolysis event.

### How does nucleosome positioning affect gene expression?

Nucleosomes occlude DNA from transcription factors and RNA polymerase. A nucleosome positioned over a promoter prevents [transcription initiation](/knowledge/molecular-biology/transcription-initiation), while a nucleosome-free region at the promoter allows factor binding. The +1 nucleosome downstream of the transcription start site acts as a barrier that must be overcome during transcription elongation. Nucleosome positioning is thus a key determinant of gene activity.

## Key Takeaways

- The nucleosome core particle consists of 147 base pairs of DNA wrapped 1.65 times around a histone octamer (two each of H2A, H2B, H3, H4), representing the first level of DNA compaction.
- Histone proteins share a conserved histone fold that mediates dimerization, while their N-terminal tails protrude from the particle and are the primary sites for regulatory post-translational modifications.
- Nucleosome stability arises from extensive histone-DNA contacts, including arginine side chains inserted into the DNA minor groove at 14 sites, with a binding free energy of approximately −20 to −30 kcal/mol.
- Nucleosomes are dynamic: DNA breathes and unwraps at the entry/exit sites on millisecond timescales, and ATP-dependent remodelers slide or evict nucleosomes to regulate DNA accessibility.
- Histone variants (H2A.Z, H3.3, CENP-A) and post-translational modifications modulate nucleosome stability and function, creating regulatory diversity.
- Nucleosome positioning along the genome is non-random and influences transcription, replication, and repair by controlling access to DNA sequences.
- Key experimental methods include MNase-seq for genome-wide positioning, smFRET for real-time dynamics, EMSA for stability measurements, and X-ray crystallography/cryo-EM for high-resolution structure determination.

## Further Reading

- Uberbacher EC, Bunick GJ. *Structure of the nucleosome core particle at 8 A resolution*. Journal of biomolecular structure & dynamics. 1989. [PubMed 2684220](https://doi.org/10.1080/07391102.1989.10507747)
- Luger K et al. *Crystal structure of the nucleosome core particle at 2.8 A resolution*. Nature. 1997. [PubMed 9305837](https://doi.org/10.1038/38444)
- Hammonds EF, Morrison EA. *Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA*. Methods in molecular biology (Clifton, N.J.). 2023. [PubMed 36427150](https://doi.org/10.1007/978-1-0716-2847-8_13)
- Kim TH et al. *Correlating histone acetylation with nucleosome core particle dynamics and function*. Proceedings of the National Academy of Sciences of the United States of America. 2023. [PubMed 37011222](https://doi.org/10.1073/pnas.2301063120)
- Bilokapic S, Strauss M, Halic M. *Cryo-EM of nucleosome core particle interactions in trans*. Scientific reports. 2018. [PubMed 29728587](https://doi.org/10.1038/s41598-018-25429-1)
- Furukawa A et al. *Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome*. iScience. 2022. [PubMed 35265811](https://doi.org/10.1016/j.isci.2022.103937)

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* [Nucleotide Formation: Biosynthesis and Assembly of DNA/RNA Building Blocks](/knowledge/molecular-biology/nucleotide-formation)