Zach Harvey Professional Photo

I completed my PhD with Dan Jarosz in the Department of Chemical and Systems Biology at Stanford University working on prion epigenetic switches. I then moved to the Vienna BioCenter, where since 2020 I have been working to understand the evolution of complex chromatin regulation, first as an EMBO Postdoctoral Fellow and then an FWF ESPRIT Senior Postdoctoral Fellow in the lab of Frédéric Berger at the GMI.

Where I’ve been

I’m dissecting how the nucleosome has embedded itself in essentially every eukaryotic genomic function at single-residue resolution. Using deep mutational scanning, high-throughput genomics, and artificial intelligence, I’m mapping the nucleosome’s role in processes from gene regulation to genome maintenance to understand how it evolved its diverse array of functions through vanishingly small sequence changes. Understanding these mechanisms at scale will not only allow us to derive the first principles of nucleosome function, but also provide critical insights needed to tackle genomic dysfunction driven by their mutation in disease.

What I’m up to


Nucleosomes as regulatory hubs

Histone proteins are collectively mutated at similar frequencies to major oncogenic drivers, yet only a small fraction of these disease-associated oncohistone mutations occur at canonical sites of post-translational modification. I’m working to chart the largely unknown mechanisms driving these oncohistone mutations. Focusing on transient protein–protein interactions, I recently showed that changes to the nucleosome core domain previously thought to play purely a passive structural role can complete rewire genomic functions like transcription by directing recruitment of elongation complex components (Harvey et al., Cell Reports, 2025). By probing these dynamic, nucleosome-centered interactions rather than treating the histone core as a passive substrate, I am expanding on this discovery to uncover the regulatory logic of the nucleosome: the set of biochemical properties and their context dependence that shape the regulatory network centered on nucleosomes, and how this links to its ultimate function. Using these insights, I aim to design the next generation of therapeutics tackling this important class of oncogenic driver mutation to address this challenge epigenetic context. 

Funding

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Chromatin’s role in adaptation

Chromatin establishes a transcriptional ground state dynamically modified in response to environmental stimuli across all eukaryotes. Although chromatin dynamics have been well-documented and correlated with key biological functions from developmental transitions to environmental stress responses, the mechanisms linking such changes to functional outcomes, and their role in shaping adaptation, remain opaque. By engineering the transcriptional ground state of chromatin (see pre-print and patent), I’m exploring how this critical genomic set point drives adaptive phenotypes, what mechanisms underly it, and how they have been selected for across eukaryotes. Using these insights, I aim not only to establish fundamental principles that have made chromatin essential to eukaryotic life, but also to design the next generation of production hosts for biologics. 

Funding

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Contact

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Dr.-Bohr-Gasse 3, 1030 Vienna, Austria

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