Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism.

Area of Science:

• Molecular Biology
• Epigenetics
• Chromatin Biology

Background:

• Eukaryotic chromosomes feature functional compartments marked by specific histone modifications.
• The precise mechanisms linking histone marks to chromosome compartmentalization remain unclear.
• Constitutive heterochromatin, a transcriptionally silent compartment, is notably marked by H3K9me2 and 3.

Purpose of the Study:

• To elucidate the molecular mechanisms underlying histone modification-driven chromosome compartmentalization.
• To investigate the role of heterochromatin protein 1 (HP1) and associated proteins in forming functional chromatin compartments.

Main Methods:

• Investigated interactions between HP1, SUV39H1, and TRIM28.
• Analyzed the phase separation of H3K9me2 and 3-modified nucleosomal arrays and protein complexes.
• Characterized the biophysical properties of the resulting liquid droplets, including density and DNase resistance.

Main Results:

• HP1, SUV39H1, and TRIM28 form complexes that engage multivalently with H3K9me2 and 3-modified chromatin.
• These complexes and marked chromatin undergo liquid-phase separation, forming dense, macromolecule-enriched droplets.
• The formed droplets exhibit heterochromatin-like characteristics, resisting DNase and excluding transcription factors like TFIIB.

Conclusions:

• Histone modifications, particularly H3K9me2 and 3, can drive chromosome compartmentalization through promoting phase separation.
• The HP1-SUV39H1-TRIM28 complex plays a key role in establishing these heterochromatin-like structures.
• Phase separation offers a general biophysical mechanism for how histone marks regulate higher-order chromatin organization.