4-Year Funded PhD — Application Deadline: 17 September 2026

How much does epigenetic variation contribute to rapid adaptation? This PhD project uses CRISPR/Cas9 and SunTag-based epigenomic editing in apomictic dandelions to test whether epialleles drive heritable trait variation across generations.

Project:

Pioneering transient epigenome editing in a wild, non-model plant species to establish causal links between DNA methylation, gene expression, and inherited traits.

Details:

Start date: To be determined
Duration: 18 months initially, extended to 4 years upon positive assessment
Location: Hugo R. Kruyt building, Utrecht University
Department: Department of Biology, Faculty of Science
Hours: 36–40 hours per week
Salary: scale P, CAO NU

What you will do:

• Develop and use CRISPR/Cas9-based technologies to target DNA methylation maintenance machinery, inducing genome-wide hypomethylation to identify genes regulated by methylation
• Deploy an advanced, inducible SunTag-TET1cd epigenomic editing system to target specific candidate epialleles, proving causal links between DNA methylation and gene expression
• Investigate the transgenerational stability of epigenetic marks over multiple generations

What we are looking for:

• MSc in molecular biology, genetics, biotechnology, plant sciences, or a related field
• Experience in molecular biology techniques
• Ability to communicate and organise work effectively
• Good command of both written and spoken English

Experience with CRISPR/Cas9, Agrobacterium-mediated transformation, bioinformatics, DNA methylation analysis, or plant tissue culture is welcome but not required.

We Offer:

• A position for 18 months, extended to 4 years upon positive assessment
• 8% holiday pay and 8.3% year-end bonus
• Pension scheme, partially paid parental leave, and flexible terms of employment
• Professional development opportunities, sports and cultural activities

About the project:

This is a collaborative project between Utrecht University and the Netherlands Institute of Ecology (NIOO-KNAW) in Wageningen, coordinated by Prof. Koen Verhoeven. You will work within the Translational Plant Biology group under the supervision of Dr. Jason Gardiner. See the full project page for more details.

Project:

Engineering epigenetic memory systems in plants

Details:

Start date: Flexible
Location: Hugo R. Kruyt building, Utrecht University

Project Description:

We are seeking a motivated MSc student to join our research team investigating how epigenetic mechanisms like DNA methylation can be engineered to create synthetic memory systems in plants. The project will involve:

• Designing and testing synthetic DNA methylation-sensitive promoters
• Characterizing epigenetic memory circuits in Arabidopsis
• Developing new tools for targeted epigenome editing
• Applying these systems to control agriculturally relevant traits

Core competencies:

• Background in molecular biology, plant biology, genetics, or related field
• Interest in epigenetics and synthetic biology
• Basic laboratory skills (PCR, cloning, plant transformation is a plus)
• Ability to work independently and as part of a team
• Good communication skills in English

We Offer:

• Hands-on training in cutting-edge epigenetics and synthetic biology techniques
• Access to state-of-the-art facilities and equipment
• Collaborative and supportive research environment

Project:

Investigating transposon dynamics under biotic stress using visual flower readouts

Details:

Start date: Flexible
Location: Hugo R. Kruyt building, Utrecht University

Project Description:

What if you could watch the genome reshaping itself in real time—just by looking at flowers? In Petunia hybrida W138, transposons leave visible red spots when they move, turning flowers into living readouts of genome dynamics. This project will use this system to explore how abiotic stress, simulated through heat and salt treatments, influences transposon activity.

The W138 cultivar carries the dTph1 transposon in the ANTHOCYANIN1 (AN1) gene, disrupting anthocyanin production, resulting in white flower petals. When dTph1 is excised, AN1 can be restored in that cell lineage, resulting in the generation of red-pigmented spots. This provides both a genetic and visual model to follow excision events under stress.

The project will involve:

• Using image-based methods to automate counting of pigment spots on petals
• Applying qPCR assays to quantify the proportion of genomic DNA with dTph1 insertion
• Refining image analysis to account for spot size and flower size
• Distinguishing between early and late excision events
• Applying SA and JA treatments to study stress-induced transposon dynamics

Core competencies:

• Background in molecular biology, plant biology, genetics, or related field
• Interest in transposon biology and plant stress responses
• Basic laboratory skills (qPCR, plant cultivation, treatment applications)
• Interest in image analysis and quantitative methods
• Ability to work independently and as part of a team
• Good communication skills in English

We Offer:

• Training in cutting-edge transposon biology and plant stress research
• Experience with both molecular and computational approaches
• Access to the unique Petunia W138 visual transposon system
• Collaborative research environment with international connections

Potential Research Areas:

• Epigenetic regulation of plant development
• Synthetic epigenetic circuits
• Targeted DNA methylation/demethylation tools
• Epigenetic memory in crop plants