DNA provides instructions for how cells should be built and run, yet there are two fundamental
problems: First, the way one cell nucleus can fit the whole DNAs length without entanglement might
seem surprising at first sight. Second, the DNAs features-or genesare complex and often have
contradictory functions. To solve these problems, eukaryotic organisms, from unicellular algae to multi-
tissue plants and animals, wrap their DNA into compact bundles around a group of proteins called
histones, making structures called nucleosomes. The four core histone families H2A, H2B, H3, and H4
act together to regulate DNAs replication and repair during proliferation and cell division, as well as
its transcription into RNA when genes are expressed. Although the structure of nucleosomes and their
histones is universal, eukaryotic genomes contain dozens of copies of each core histone family, which
often differ in their function. For nearly 30 years the function of these so-called variant histones has
been investigated, yet to date, we lack a fundamental understanding of why there are so many of them
and what the evolutionary forces that shaped their emergence were.
Here, I investigate the molecular evolution of one histone variant, H2A.Z, to understand its function
in regulating the genome. Genes encoding H2A.Z have been found in nearly every eukaryote, and in
these cases, H2A.Z is often essential for cell survival. Further, H2A.Z has been investigated in various
organisms, where it was shown to both increase and decrease the expression of genes. This duality is
unusual, and despite decades of work, H2A.Zs function remains difficult to interpret.
A key challenge in studying histone variants and their function has been the sheer complexity of the
cellular systems surrounding nucleosomes. Instead of a single gene encoding a single function, histones
are multifunctional, meaning that perturbing them has pervasive consequences throughout the cell,
complicating interpretations. To bypass this limitation, I have created an experimental system based in
the yeast Schizosaccharomyces pombe where H2A.Z genes from across the tree of life have been
introduced, generating a series of lines that differ vastly in their gene transcription. Leveraging this
variation, I will characterize what defects or altered functions in transcription exist. This will allow me
to conclude (1) what features of H2A.Z are important for its function in transcription, and (2) which
interactors might drive these differences. Thus, this approach moves beyond the fundamentally
correlative methods that have been used to date to study histone variants. In a larger context,
understanding the evolution of H2A.Z and its function will shed light on the fundamental molecular
mechanisms leading to transcriptional diversity and hint at how universal biological systems like
histones and nucleosomes can give rise to the stunning diversity of multicellular life.