Long-read DNA sequencing analysis of the retrotransposon epigenome

Mammalian genomes are typically composed of ~50% mobile DNA-derived sequences, including retrotransposons. As new retrotransposon insertions can be mutagenic, host defence pathways have evolved to limit retrotransposon mobility. Many of these pathways involve DNA base modifications, such as 5-methylcytosine (5mC), that reduce retrotransposon transcription.

This project will use state-of-the-art long-read DNA sequencing technologies to analyse epigenomic modifications applied to retrotransposons, to understand how they are repressed and how they can evade that repression.

In particular, it will apply Oxford Nanopore Technologies (ONT) sequencing, to survey the 5mC landscape of various cell and tissue types from multiple mammalian species, and then use CRISPR-Cas9 base editing to understand how 5mC regulates retrotransposon loci and families. 

You'll be part of a diverse team with a shared interest in transposable elements. You will have opportunities to work with CRISPR-Cas9 systems for genetic manipulation, Oxford Nanopore Technologies (ONT) long-read sequencing technologies, and mammalian cell culture models.

You'll gain a working knowledge in Unix command-line and basic bioinformatics. You will also be supported in career development, building a publication record, and applying for awards. You will work independently and collaboratively, with opportunities to grow your professional network.

Mater Research is located in the Translational Research Institute (TRI) building, which incorporates four floors of laboratories, facilities for research support, administration and teaching, and a range of state-of-the-art core facilities.

This project is supported by the Research project scholarship.

Learn more about the Research project scholarship.

Your application will be assessed on a competitive basis.

We take into account your:

• previous academic record
• publication record
• honours and awards
• employment history.

A working knowledge of retrotransposon biology would be of benefit to someone working on this project.

You will demonstrate academic achievement in the field of genetics and the potential for scholastic success.

A background or knowledge of mammalian cell culture and molecular biology is highly desirable.

You must submit an expression of interest (EOI) by 22 July, 2026 22 July, 2026.

Before you apply

1. Check your eligibility for the Doctor of Philosophy (PhD).
2. Prepare your documentation.
3. If you have any questions about whether the project is suitable for your research interests, contact Professor Geoffrey Faulkner (geoffrey.faulkner@mater.uq.edu.au).

When you apply

To apply, submit an expression of interest (EOI) for the program. You don't need to apply separately for the project or scholarship. How to submit an EOI

In your EOI, complete the ‘Scholarship/Sponsorship’ section with the following details:

1. Are you applying for an advertised project: 'Yes'
2. Project: 'Research project scholarship'
3. Scholarship Code Listed in the Advertisement: RETROTRANSPOSON-FAULKNER
4. Link to Scholarship Advertisement: https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/long-read-dna-sequencing-analysis-retrotransposon-epigenome

Submit an EOI