Alex Miller

PhD thesis

Transient immune activation and the emergence of persistent transcriptional and  chromatin states in plants#

Plant immune responses are highly dynamic, with brief responses in small numbers of cells potentially having lasting effects on surrounding tissue. My research investigates whether these short-lived immune events can cause persistent changes in gene expression and chromatin. My Master’s work in the Harris lab demonstrated that CRISPR-based activation at endogenous immune loci is possible, although its consequences remain unclear. Recent studies have identified rare “primary responder” (PRIMER) cells that respond early to pathogen exposure and show distinct gene expression and chromatin profiles, but it remains unclear what happens to these cells after the initial response. By combining CRISPR-based activation with Cre/lox systems that permanently record which cells have responded, alongside single-cell profiling, my research aims to track these cells over time and determine how pathogen exposure shapes longer-term cellular states in plants.

Who or what inspired you to pursue your research interests?

My research emerged following a period in which I completed my Bachelor’s and Master’s degrees whilst undertaking a number of experiences in the plant genetics world. I was especially taken by the efforts of various university departments, research institutes and agritech companies to tackle the worldwide issues facing our planet and food systems, and therefore was inspired to contribute directly by pursuing a PhD. My Master’s project in the Harris lab was both an enjoyable and challenging opportunity, and one which was particularly important in my desire to return to the department and work at the frontline of plant epigenetics.