Histone Modifications Lecture Notes

Overview

• Histone modifications are essential for controlling chromatin architecture, nucleosomal positioning, and DNA access.
• Common histones in nucleosomes: H2A, H2B, H3, H4. H1 is a linker histone.
• Histone modifications can lead to gene activation (euchromatin) or silencing (heterochromatin).

Types of Histone Modifications

• Common Modifications: Acetylation, Methylation, Phosphorylation, Ubiquitylation.
• Less Studied: GlcNAcylation, Citrullination, Crotonylation, Sumoylation, Isomerization.

Histone Modifications in Detail

Acetylation

• Neutralizes positive charge on lysine residues, reducing histone-DNA interaction.
• Catalyzed by histone acetyltransferases (HATs) and reversed by deacetylases (HDACs).
• Associated with transcriptional activation.

Methylation

• Can occur on lysine or arginine residues of H3 and H4.
• Arginine methylation generally promotes activation, while lysine methylation can activate or repress depending on the site.
• Stable, but reversible through specific enzymes.

Phosphorylation

• Intermediate in chromosome condensation, transcriptional regulation, and DNA repair.
• Occurs on all core histones, with variable effects.

Ubiquitylation

• Commonly occurs on H2A and H2B.
• Plays a role in DNA damage response.

Enzymatic Regulation

• Methylation: Histone methyltransferases (HMTs) and demethylases (such as KDM1, JmjC).
• Ubiquitylation: Regulated by ubiquitin ligases and deubiquitylating enzymes.

Studying Histone Modifications

• ChIP: Uses antibodies to isolate DNA-bound proteins/modifications, aiding in mapping protein/modification location and abundance.
• Applications: Identifies chromatin structures, gene activity, and regulatory elements.

Histone Modifying Enzymes

• Balance between writers (e.g., HATs) and erasers (e.g., HDACs) controls genetic programs.
• Imbalance can lead to diseases like cancer.
• Potential for drug targeting to correct imbalances.

Characterization and Assays

• HMT Assays: Overcome difficulties like radioactivity, provide easy detection.
• Demethylase Assays: Measure demethylated product, high sensitivity.
• Acetylation & Deacetylase Assays: Measure transfer of acetyl groups, class-specific assays.

Inhibiting Enzymes

• Small molecules can be used to inhibit modifying enzymes for studying roles of modifications.

Histone Modification Readers

• Histone modifications can impact chromatin properties directly or via effector proteins.
• Effector Domains: Recognize specific modifications, translating histone code into cellular actions.

Multivalency and Histone Code Complexity

• Proteins may have multiple binding modules, recognizing complex modification patterns.

References

• Various studies and reviews on histone modifications and their roles in genetic regulation.