Evolutionary Insights into H2A.Z Function in Gene Regulation

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.