L12 Histone code

Kinetochore Structure

A protein complex assembled on the centromeric DNA of a chromosome. It serves as the attachment site for microtubules of the mitotic spindle during cell division, ensuring proper segregation of chromosomes.

Mitotic Spindle Formation

The mitotic spindle consists of microtubules and associated proteins. During mitosis, centrosomes nucleate microtubules, which grow and attach to the kinetochores. The spindle facilitates alignment of chromosomes at the metaphase plate and their segregation during anaphase.

Chromatin Structure

Chromatin is a dynamic complex of DNA and proteins (mainly histones). It can exist in two states:

• Euchromatin: Loosely packed and transcriptionally active.

• Heterochromatin: Densely packed and transcriptionally silent.

Nucleosomes

The basic unit of chromatin, consisting of ~147 base pairs of DNA wrapped around an octamer of histone proteins (two each of H2A, H2B, H3, and H4). This structure shortens the DNA length significantly.

Histones

These are small, positively charged proteins that facilitate DNA wrapping. H1 (linker histone) further compacts nucleosomes into a 30 nm fiber.

DNA Compaction

DNA is compacted through:

1. Wrapping around histones to form nucleosomes.

2. Folding into higher-order structures (30 nm fibers, loops, and scaffolds).

3. Formation of metaphase chromosomes during cell division.

P5.8. Chromatin Remodeling Complexes

• Function: These protein complexes use ATP to reposition, eject, or restructure nucleosomes. This remodeling changes the accessibility of DNA for transcription factors and other proteins.

• Mechanism:

  1. Chromatin remodelers can slide nucleosomes along DNA.

  2. They can remove or exchange histone subunits.

• Examples:

  • Bromodomains recognize acetylated lysines on histones, promoting an open chromatin state.

  • Chromodomains bind methylated lysines, often associated with repression.

Nucleosome Modifications:

• Acetylation (e.g., by HATs) loosens chromatin, promoting gene expression.

• Deacetylation (e.g., by HDACs) tightens chromatin, repressing transcription.

• Methylation can signal either activation or repression, depending on the context.

Histone Modifying Complexes:

Relation to Gene Expression:

• HATs (Histone Acetyltransferases): Add acetyl groups, reducing histone-DNA interaction and increasing accessibility.

• HDACs (Histone Deacetylases): Remove acetyl groups, stabilizing nucleosomes and repressing genes.

• Methyltransferases: Add methyl groups to histones, which can propagate epigenetic states.

• Relation to Gene Expression: Modifications dictate chromatin's open or closed state, regulating transcriptional access to DNA.

P5.10. Preservation of Histone Modifications During Replication

• Mechanism:

  1. During replication, parental H3-H4 tetramers are randomly distributed to daughter strands, carrying the original modifications.

  2. H2A-H2B dimers dissociate and are replaced by newly synthesized ones.

• Epigenetic Inheritance:

  • The parental modifications serve as a template.

  • Complexes like HATs (for acetylation) and methyltransferases propagate the histone code on newly synthesized histones.

• Open and Closed States:

  • Open State: Maintained by bromodomains, which recruit HATs to acetylate adjacent histones.

  • Closed State: Maintained by HP1, which binds methylated lysines and propagates methylation to adjacent histones, stabilizing heterochromatin.

P5.6. Kinetochore, Mitotic Spindle Formation, and Chromatin Structure

• Chromatin and the Kinetochore:

  • The kinetochore relies on specialized chromatin structures, such as the incorporation of the CENP-A histone variant, which replaces H3 in centromeric nucleosomes.

  • CENP-A facilitates the formation of the kinetochore by creating binding sites for other proteins.

  • Loss of CENP-A disrupts kinetochore assembly, impairing chromosome segregation.

• DNA Damage Response:

  • The H2A.X variant marks DNA damage sites by phosphorylation, facilitating repair processes.

P5.7. Nucleosomes, Histones, and DNA Compaction

• Histone Variants:

  • Different variants such as H3.3, CENP-A, H2A.X, and MacroH2A contribute to specific functions, including transcription regulation, centromere identity, and DNA repair.

• Role of Modifications:

  • Lysine residues on histone tails interact with DNA and neighboring nucleosomes. Modifications like acetylation and phosphorylation influence chromatin compaction and DNA accessibility.

P5.8. Chromatin Remodeling Complexes

• Structural Recognition:

  • Bromodomains in remodelers recognize acetylated lysines, facilitating chromatin opening and transcription activation.

  • Chromodomains bind methylated lysines, stabilizing repressive chromatin states.

• Example of Interdependence:

  • Histone H3 methylation at lysine 9 inhibits phosphorylation at serine 10, which otherwise promotes acetylation of lysine 14, affecting transcription regulation.

Histone Acetylation:

• Neutralizes lysine's positive charge, reducing interaction with DNA and promoting chromatin decondensation.

• Reversible by HDACs, which restore repression.

Methylation and Transcription:

• Lysine methylation can signal transcriptional activation (e.g., H3K4me) or repression (e.g., H3K9me or H3K27me).

Phosphorylation

Aids recruitment of transcription machinery or DNA repair proteins.

Histone Variants and Gene Expression:

• Variants like H3.3 are enriched in actively transcribed regions, while MacroH2A associates with transcriptional silencing.

P5.10. Preservation of Histone Modifications During Replication

• Histone Variants and Parental Histones:

  • Parental H3-H4 tetramers distribute randomly to daughter strands, ensuring partial preservation of modifications.

  • Newly synthesized histones are incorporated alongside parental histones and receive modifications to match the chromatin state.

• Propagation of the Epigenetic State:

  • Modifications are propagated through the recruitment of enzymes (e.g., HATs, methyltransferases) that replicate the parental histone code.

• Histone Variants and Replication:

  • Variants like CENP-A ensure the proper assembly of centromeres, maintaining genome stability through cell divisions.