Functional consequences of evolutionary innovation in histone repertoires - histone proteins package DNA into chromatin and regulate all DNA-templated biological processes in eukaryotes

The National Institute of General Medical Sciences awarded University of Massachusetts Boston $249,000 on September 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate the functional consequences of evolutionary innovation in histone H2A repertoires.

The research uses evolutionary innovations in eukaryotic histone proteins to examine how histone repertoires have undergone lineage-specific changes and what selective advantages these changes confer. The project re-engineers ancestral eukaryotic H2A repertoires in yeast and Drosophila to identify functional consequences of evolved histone variants. Specific focus areas include expansion of prior findings that re-engineering an ancestral histone repertoire in S. cerevisiae resulted in impaired DNA damage response (DDR), elucidation of the mechanisms by which the evolved yeast repertoire increases DDR efficiency, and investigation of the Drosophila H2AV fusion histone variant, which the research demonstrates is essential for female fertility and transposon silencing in D. melanogaster.

The work is performed in Seattle, Washington, with a period of performance running from September 1, 2026, through August 31, 2029. The award is structured as a Project Grant, the standard assistance type for investigator-initiated basic research awards under NIGMS.

While core histones primarily function in genome packaging, histone variants can replace core histones at unique genomic locations for specialized roles such as DNA damage response (DDR) or gene expression. Despite their essential functions, histone repertoires have undergone distinct lineage-specific changes. Such evolutionary novelty via gene fusions, duplications, or sequence divergence is unexpected in conserved protein families and suggestive of an adaptive advantage. This proposal will use evolutionary innovations in eukaryotic histone H2A repertoires to investigate the causes and consequences of evolutionary turnover of histone proteins. The most common eukaryotic H2A repertoire is made up of core histone H2A, and histone variants H2A.X and H2A.Z that are involved in DDR and gene regulation, respectively. However, two evolutionary shifts, both likely selectively advantageous, have occurred in yeast and drosophila H2A repertoires. In yeast, H2A.X entirely replaced core H2A, which we demonstrate improves DDR. In drosophila, H2A.X fused with H2A.Z, giving rise to a unique H2AV variant. We hypothesize that this fusion enriches DDR at heterochromatin, which potentially restricts DDR-based transposition events to gene-poor regions. We find that the fusion histone H2AV is essential for female fertility and transposon silencing in D. Melanogaster. This proposal will identify functional consequences of these evolutionary innovations by RE-engineering the ancestral eukaryotic H2A repertoire in yeast and flies. In aim 1, we expand on our finding that RE-engineering an ancestral repertoire in S. Cerevisiae resulted in impaired DDR. This confirmed our hypothesis that the evolved yeast repertoire provides an advantage by increasing DDR efficiency. We will elucidate the mechanism and coevolutionary strategies that accompany this innovation. In aim 2, we will recreate the ancestral dipteran repertoire by separating H2AV into H2A.X and H2A.Z, uncoupling DDR and gene regulation functions. We will interrogate the rescue of relevant biological functions, including DNA repair, fertility, and transposition and changes to organismal chromatin packaging. Finally, in aim 3, we will utilize the tools from aims 1 and 2 to study the divergence of eukaryotic core H2A. Histones have tail sequences that are heavily post-translationally modified and play crucial roles in higher-order chromatin packaging and protein interactions. The high sequence divergence across eukaryotic histone tails suggests that tails could facilitate unique lineage-specific functions. By engineering different tail sequences in yeast and flies, aim 3 will reveal changes to chromatin packaging and changes to processes such as mating and quiescence in yeast, and fertility and development in flies. Together, these three aims will seed future projects in my lab to interrogate the unexpected but advantageous CO-evolving chromatin landscape across eukaryotes.