Epigenome engineering: priming chromatin for pathogen resistance

Brief

Plants can become more resilient to pathogen challenge after priming treatments, which is associated with changes to chromatin. This project uses epigenome engineering to re-sculpt chromatin to improve performance under pathogen pressure.

Importance of Research

Epigenome engineering aims to harness the plants natural defense and memory systems to improve resilience.

Project Summary

Plants defend themselves against pathogens by activating a suite of antimicrobial defense genes. Interestingly, plants exposed to certain pathogens can become more resistant to subsequent pathogen challenge, indicating that a type of immunity has been formed. In this ‘primed’ state, key antimicrobial defense genes are turned on more rapidly as compared to non-primed ‘naïve’ plants, which contributes to their heightened resistance. However, it is currently unknown how this elevated transcriptional response is achieved. Recent research suggests that epigenetic changes in chromatin may help form the basis for this immunological memory. For instance, particular chromatin marks can be laid down that help recruit transcriptional machinery. However, precisely which chromatin features drive priming, and how they achieve their function, remains mysterious. This project aims first to understand the pathogen primed state.

What will the successful application do?

The project will consist of three stages. In the first stage, genome-wide chromatin profiling by ChIP-seq/CUT&Tag and ATAC-seq will be used to identify the chromatin features of primed vs non-primed plants. In the second stage, epigenome engineering tools based on the recently described CRISPR system, will be used to deposit chromatin marks at precise genomic locations. The final stage will investigate whether these epigenome-engineered plants are more resistant to pathogens.

Training Provided

The student will gain expertise in a range standard molecular biology techniques (cloning, genotyping, qRT-PCR, western blots). Additionally, the student will help to develop cutting-edge CRISPR based epigenome engineering tools, and will learn genomics (wet lab and computational approaches), and plant pathology techniques.

Funding Notes:

Enhanced four-year postgraduate studentships, starting in October 2025, will again be awarded by the Gatsby Charitable Foundation. The maintenance stipend in the first year will be £24,235 (to increase by 4% annually). In addition to this, there is an annual payment of £5,500 for department laboratory fees, and £700 for books, conferences and travel. Tuition fees are also paid by the Foundation.

The final award of the grant is conditional on the student obtaining a first or upper second class degree before the start of the Sainsbury PhD Studentship.

It would be expected that the studentship holder spend six months during their 3^rd or 4^th year at another university/institute to gain additional experience. The student can cim up to an additional £3,000 to assist in covering the extra expenses.

How to apply:

Prospective candidates are invited to contact Dr Jake Harris ([Email Address Removed]) with their curriculum vitae and a short description of why they are interested to work on this research area (500 words max).

Enquiries:

[Email Address Removed]