10-1. Organization of Eukaryotic Chromosomes into Chromatin

10-1. Organization of Eukaryotic Chromosomes into Chromatin

Introduction to Chromatin Structure

Chromatin is the complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. Its organization is essential for chromosome function, gene regulation, and the compaction necessary to fit large eukaryotic genomes into the nucleus.

• Chromatin organization is crucial for proper chromosome segregation during cell division.

• It plays a significant role in the regulation of gene expression in eukaryotic cells.

• Without compaction, eukaryotic chromosomes could not fit into the nucleus.

Histone Proteins and Nucleosomes

Composition of Chromosomes

• Each chromosome consists of approximately half DNA and half protein.

• About half of the chromosomal proteins are histone proteins, which are small, basic proteins that tightly bind DNA.

• The remaining proteins are nonhistone proteins, which are diverse and perform various nuclear functions (e.g., scaffolding, regulation, enzymatic activity).

Histone Types and Nucleosome Core Particles

• There are five main types of histone proteins: H1, H2A, H2B, H3, and H4. These are highly conserved among eukaryotes.

• Nucleosome core particles are the fundamental units of histone organization, each consisting of two molecules each of H2A, H2B, H3, and H4 (forming an octamer).

• Approximately 146 base pairs of DNA (core DNA) wrap around each histone octamer to form a nucleosome.

Table: Histone Protein Characteristics

Histone	Ratio of Basic/Acidic Amino Acids	Molecular Weight (Da)	Number of Amino Acids	Location
H1	5.4	23,000	224	Linker DNA
H2A	1.3	13,960	129	Nucleosome
H2B	1.7	13,774	125	Nucleosome
H3	2.8	15,273	135	Nucleosome
H4	2.5	11,236	102	Nucleosome

Nucleosome Assembly and Chromatin Structure

Nucleosome Assembly

• Histones H2A and H2B assemble into dimers; H3 and H4 also form dimers.

• Two H3-H4 dimers form a tetramer, which then associates with two H2A-H2B dimers to form the histone octamer.

• DNA wraps around the octamer, compacting the DNA about sevenfold—this is the first level of DNA condensation.

Chromatin Structure: The 10-nm Fiber

• In its least condensed state, chromatin appears as a 10-nm fiber ("beads-on-a-string" morphology) under electron microscopy.

• The "beads" are nucleosomes; the "string" is linker DNA connecting nucleosomes.

• The nucleosome-based model of chromatin was proposed by Kornberg in 1974.

Higher-Order Chromatin Structure

Solenoid Structure and the 30-nm Fiber

• The 10-nm fiber is not typically observed under normal cellular conditions.

• Under physiological (in vitro) conditions, nucleosomes coil into a 30-nm fiber (solenoid structure), with six to eight nucleosomes per turn.

• Histone H1 stabilizes the solenoid structure.

Chromosome Scaffold and the 300-nm Fiber

• During interphase, chromatin exists as a 30-nm fiber or more condensed forms.

• Chromatin forms loops (20–100 kb) attached to a nonhistone protein chromosome scaffold, creating the 300-nm fiber.

• The scaffold provides structural support and determines chromosome shape.

Further Compaction: Metaphase Chromosomes

• During mitosis, chromatin becomes maximally condensed (up to 1400 nm in diameter).

• Loops are anchored to the scaffold at MARS (matrix attachment regions).

• Metaphase chromatin is compacted approximately 250-fold compared to the 300-nm fiber.

Functional Roles of Chromatin Condensation

Importance of Higher-Order Structure

• Chromosome compaction is essential for efficient separation of chromosomes during anaphase of mitosis.

• Chromatin loops play a regulatory role in gene expression.

• Active transcription occurs in loop segments distant from MARS; larger loops tend to have more active transcription.

Nucleosome Dynamics During DNA Replication

Disassembly and Reassembly of Nucleosomes

• During DNA replication, nucleosomes must be temporarily disassembled to allow replication fork passage.

• Experimental evidence shows that old histones are retained as single molecules, dimers, or tetramers.

• After replication, nucleosomes are reassembled from a mix of old and new histone proteins.

Mechanism of Nucleosome Inheritance

• As the replication fork progresses, nucleosomes break down into H3-H4 tetramers and H2A-H2B dimers.

• H3-H4 tetramers reassociate randomly with one of the sister chromatids.

• H2A-H2B dimers are reassembled from both old and new histones.

Example: Nucleosome Inheritance

• After DNA replication, each daughter DNA molecule receives a mixture of old and new histone proteins, ensuring the propagation of chromatin structure and epigenetic information.

Summary Table: Levels of Chromatin Organization

Level	Structure	Diameter	Description
1	DNA double helix	2 nm	Linear DNA molecule
2	Nucleosome ("beads-on-a-string")	10 nm	DNA wrapped around histone octamers
3	Solenoid (30-nm fiber)	30 nm	Coiled nucleosomes stabilized by H1
4	Looped domains (300-nm fiber)	300 nm	Loops attached to scaffold proteins
5	Condensed chromosome (metaphase)	700–1400 nm	Maximally compacted for cell division

Additional info:

• Epigenetic modifications (e.g., methylation, acetylation) of histone tails can influence chromatin structure and gene expression.

• Nonhistone proteins include structural maintenance proteins, transcription factors, and chromatin remodeling complexes.