Chromosome Structure and Chromatin Organization: Centromeres, Telomeres, and Nucleosomes

Chromatin Organization

Three Levels of Chromatin Organization

Chromatin is organized into hierarchical structures to efficiently package DNA within the nucleus.

1. 10 nm chain of nucleosomes: "Beads on a string" structure.

2. 30 nm fiber: Helical array of nucleosomes.

3. Further folding: Compaction of 30 nm fibers into higher-order structures.

Nucleosome

The nucleosome is the fundamental unit of chromatin in eukaryotes, absent in bacteria. It consists of DNA wrapped around a histone octamer.

• Molecular Components: ~200 bp DNA and a histone octamer (2x H2A, 2x H2B, 2x H3, 2x H4).

• Structure: Discrete particles connected by linker DNA, visible when chromatin is stretched.

• Testing: Nuclease digestion reveals nucleosome-protected DNA fragments (~145–200 bp).

Features of DNA in a Nucleosome

• Core DNA: 145–147 bp, forms stable nucleosome, bound by core histones.

• Linker DNA: Connects nucleosomes, associated with H1 histone, susceptible to nuclease digestion.

Nucleosomes and Histone Octamers

• Composed of four types of core histones: H2A, H2B, H3, H4.

• Histone H1 acts as a linker, stabilizing higher-order chromatin structure.

• Core histone tails extend from the nucleosome and are sites for post-translational modification.

Histone Conservation and Variants

• Histones are highly conserved across eukaryotes, especially H3 and H4.

• Each histone type has its own gene family, with canonical and variant forms.

• Variants serve specialized functions, such as centromere identity (centromere H3).

Core Histone Structural Homology

• Histone families share a common 3D motif: the histone fold.

• Despite little sequence homology, the structural motif is conserved for DNA binding.

Nucleosome Structure

• Octamer consists of two subcomplexes: 1x H3-H4 tetramer and 2x H2A-H2B dimers.

• DNA interacts mainly with the histone backbone via hydrogen bonds and salt bridges.

Histone H1: Linker Between Nucleosomes

• Not required for nucleosome formation but essential for higher-order chromatin structure.

• Nucleosomes with H1 are called chromatosomes.

Histone Post-Translational Modification

Types of Modifications

• All histone proteins can be covalently modified on N- and C-terminal tails.

• Small modifications: Methylation, Acetylation, Phosphorylation

• Larger modifications: ADP-ribosylation, mono-ubiquitylation, sumoylation

• Modifications can be transient or stably maintained (epigenetic inheritance).

Modification Details

• Methylation: Addition of -CH3 groups to lysine or arginine residues; does not change charge.

• Acetylation: Addition of -COCH3 groups to lysine residues; neutralizes positive charge.

• Phosphorylation: Addition of -PO4 groups to serine or threonine; introduces negative charge.

Table: Histone Post-Translational Modifications

Modification	Added Chemical Group	Amino Acid Modified	Effect on Charges	Other Notes
Methylation	-CH3 (neutral)	Lysine, Arginine	No effect on charge	Mono-, di-, tri-methylation
Acetylation	-COCH3	Lysine	Neutralizes (+) charge	Adds bulky group
Phosphorylation	-PO4 (–) charged	Serine, Threonine	Introduces (–) charge	Regulates chromatin structure

Histone Modifications and Gene Expression

• Modifications can occur on different histones and at different amino acid residues (K, R, S, T).

• Can activate or repress gene expression by altering chromatin accessibility.

The Histone Code

• Multiple modifications at a chromatin region collectively determine transcriptional activity.

• Non-histone proteins "interpret" the histone code, leading to biological outcomes such as chromatin remodeling or DNA repair.

• Some modifications directly affect chromatin structure; most provide binding sites for regulatory proteins.

Nucleosome Assembly and Positioning

Nucleosome Assembly Pathways

• Replication-Coupled Pathway: Requires newly synthesized histones; canonical histones are produced in clusters for efficient supply during DNA replication.

• Replication-Independent Pathway: Occurs during transcription and DNA repair; does not require new histone synthesis.

Replication-Coupled Assembly

• Disassembly of nucleosomes from template DNA during replication.

• Octamers dissociate into tetramers and dimers, which mix with newly synthesized histones.

• Immediate reassembly on daughter DNA duplexes, facilitated by histone chaperones.

Nucleosome Positioning

• Histones reassemble behind RNA polymerase after transcription, but nucleosome positioning can be altered.

• Positioning determines which DNA sequences are in the core versus linker regions, affecting gene regulation.

Summary Table: Key Chromosome and Chromatin Features

Feature	Structure	Function
Centromere	Satellite DNA, CENH3, kinetochore	Chromosome segregation
Telomere	Tandem repeats, T-loop, telomerase	Protects chromosome ends, solves replication problem
Nucleosome	Histone octamer + DNA	DNA packaging, gene regulation

Additional info: Some context and explanations were expanded for clarity and completeness, including the molecular mechanisms of telomere maintenance and histone modification effects on gene expression.