Divergence and selectivity of expression-coupled histone modifications in budding yeasts

Area of Science:

• Epigenetics and Gene Regulation
• Molecular Biology
• Yeast Genetics

Background:

• Histone modifications are crucial regulators of gene expression.
• The specific roles of different histone marks, like H3K9ac and H3K4me3, at individual genes are not fully understood.
• Understanding these roles is key to deciphering gene expression control.

Purpose of the Study:

• To investigate and compare genome-wide patterns of H3K9ac and H3K4me3 in budding yeast.
• To determine the functional selectivity of these histone modifications at individual genes.
• To explore the association of H3K4me3 and H3K9ac with gene expression stability and divergence between species.

Main Methods:

• Genome-wide profiling of H3K9ac and H3K4me3 marks in budding yeast.
• Analysis of modification patterns in relation to gene expression levels and characteristics (DPN and OPN genes).
• Comparative analysis of histone modification patterns and expression divergence between S. cerevisiae and S. paradoxus orthologous genes.

Main Results:

• Widespread differences observed between genome-wide H3K9ac and H3K4me3 patterns.
• H3K4me3 is associated with essential, periodically expressed 'DPN' genes, suggesting expression stability.
• H3K9ac is linked to non-essential, responsive 'OPN' genes, indicating expression variability.
• Inter-species expression divergence correlates with H3K4me3 changes, but not H3K9ac changes.

Conclusions:

• H3K4me3 and H3K9ac exhibit distinct genome-wide distributions and functional associations.
• H3K4me3 may play a role in stabilizing average gene expression and driving evolutionary expression divergence.
• H3K9ac appears to be involved in regulating gene responsiveness and expression variability.
• These findings suggest different evolutionary roles for distinct histone modifications in gene regulation.