Histone Modifications and Epigenetics Notes

Course Information: Histone Modifications and Epigenetics BS2091 - From Genes to Proteins 2025-26 SEM2 with Prof. Thomas Schalch.
Key Concept: Positive feedback loop driving constitutive heterochromatin spreading and maintenance, identified by the involvement of Su(var)3-9 and HP1 proteins.

Ability to define epigenetics and describe its biological role.
Understand the reader-writer-eraser concept in epigenetics.
Comparison of lysine methylation and acetylation regarding their chemical nature and biological function.
Associate specific histone marks with genomic features.
Describe and apply the technique of chromatin immunoprecipitation (ChIP).
Elucidate the molecular mechanisms of constitutive heterochromatin formation.

An epigenetic trait is defined as a stably heritable phenotype resulting from changes in a chromosome without alteration in the DNA sequence.
Example: One of two X-chromosomes can be epigenetically silenced, affecting phenotype visibility.
Illustrative Cases:
- Diverse blood cells with identical genotypes exhibit variation (e.g., metastatic cells with elevated histone H3K18 acetylation).
- The Arabidopsis phenotype, where a genetically identical organism displays differences due to epigenetic mutations.
- Individuals with the same genetic composition have different coat colors, determined by epigenetic silencing.
References for further reading:
- Berger SL et al. (2009).
- C.D. Allis et al. (2015).

Characteristics of an epigenetic system:
- Gene-specific.
- Inducible.
- Stable.
- Reversible.
Requirements for Phenotypic Change:
- Readout of downstream pathways leading to a change in phenotype.
Chromatin Features:
- Presence of histone variants.
- Complex post-translational modifications on DNA (5-methylcytosine).
- The role of DNA methyltransferases.

Core histones H3 and H2A possess important variant forms that are crucial for specific functions.
Post-translational modifications can be identified on histones, with specific markers indicated for various modifications.

Key post-translational modifications on nucleosomes include:
- Methylation: Indicated by red flags.
- Acetylation: Shown by green lollipop symbols.
- Phosphorylation: Depicted as yellow stars.
- Ubiquitylation: Marked with purple balloons.

The hypothesis posits that distinct histone modifications act sequentially or in combination to form a 'histone code'. This code is interpreted by proteins leading to various cellular outcomes.
Implications: Specific patterns of histone modifications serve as cis-regulatory elements that dictate gene expression.
References: Strahl BD & Allis CD (2000).

Activities facilitating the installation, removal, and interpretation of histone modifications are termed readers, writers, and erasers.

Establishment Phase:
1. A sequence-specific initiator recruits epigenetic writers and erasers.
2. Writers and erasers establish specific chromatin modification patterns.
3. Modification patterns attract readers.
4. Readers recruit machinery for gene silencing or activation, leading to a phenotype change.
Maintenance Phase:
1. Readers drive positive feedback loops to enforce their marks.
2. The system operates independently of the initial stimulus.
3. Progeny inherit the epigenetic state independently of the initiator.

Various levels of DNA folding: 2 nm (DNA fiber) → 11 nm (first-level of chromatin fiber) → 20-30 nm (higher-order structures) → 700 nm (chromatine loops) → 1400 nm (mitotic chromosome).
Topological Features: Includes topologically associated domains (TADs) and compartments of hetero- and euchromatin.

Euchromatin:
- Decondensed and transcriptionally active regions.
- Early replicating with hyperacetylated histones.
- Gene marks include H3K4, H3K36, and H3K79 methylation.
Heterochromatin:
- Highly compacted, transcriptionally silenced regions.
- Late replicating and characterized by hypoacetylation and DNA methylation.
Types of Heterochromatin:
- Constitutive Heterochromatin: Irreversibly silenced regions (pericentric, containing α-satellite repeats).
- Facultative Heterochromatin: Can become transcriptionally active (example: inactive X chromosome in mammals).

Lysine Methylation: Involves histone methyltransferases adding methyl groups (states: mono-, di-, tri-methylation).
Lysine Acetylation: Removes the positive charge of lysine, facilitated by histone acetyltransferases and removed by histone deacetylases.

ChIP is utilized to:
- Identify where specific histone modifications are located.
- Reveal binding sites of gene regulatory factors.
- Techniques include qPCR for targeted data and ChIP-seq for whole-genome distribution analysis.

Overview: Enzymes that specialize in lysine methylation using S-adenosylmethionine (SAM) as a cofactor and methyl donor.
Subfamilies involved in disease, particularly cancer.
Notable marks: H3K27, H3K9, H3K4, H4K20, H3K36.

RNAi machinery and chromatin regulators involve various proteins (e.g., Chp2, Swi6) and are essential for gene silencing.
Role: Suppresses gene expression, controls mating-type switching, and ensures chromosome segregation.

Clr4 deposits H3K9 methylation, linking to gene silencing through chromodomain proteins that recruit silencing factors.

HP1 proteins bind to H3K9me2/3, facilitating the interaction with client proteins through specific motifs.
Notably features a 'chromodomain-linker-chromoshadow domain' structure, establishing their role in heterochromatin function.

Chromodomains serve as readers for methylated lysine residues, employing an aromatic cage mechanism to recognize target modifications

The histone code hypothesis posits that histone modifications can regulate genome functions and phenotypes.
Distinct histone modifications are associated with writers, readers, and erasers, contributing to chromatin signaling and gene expression regulation.
Understanding the dynamics of these marks is challenging; however, H3K9 di- and trimethylation exemplify the significance of feedback loops in maintaining repressive chromatin structures.