Targeting transposable elements in cancer

Transposable elements (TEs), also known as “jumping genes” are repetitive genomic elements that represent almost half of the human genome. TEs harbour regulatory elements and transcription factor binding sites, and cancer cells often reactivate TEs, which promotes oncogenic gene expression. Recent studies have shown that transcription factors can hijack TEs to alter 3D genome structure, thereby triggering transcriptional response. A deeper understanding of the regulatory role of TEs in gene expression is crucial for developing novel TE-based cancer therapies.

This project is focused on understanding the context-dependent oncogenic roles of TEs in cancer, particularly their impact on alterations in 3D genome architecture. To do this, you will use Hi-C coupled with Nanopore long-read sequencing to study selected TEs and establish their role in gene regulation and cancer treatment response. 

Ideally, we are seeking a candidate with prior research experience, proficiency in cellular and molecular biology, and/or knowledge of at least one computational language (e.g., Python, R) would be an advantage. Techniques and datasets you will have access to include Hi-C, CUT&RUN, ATAC-seq, RNA-seq, Nanopore, and single-cell data. We have access to HPC to streamline any large data processing and machine learning applications.

Interested candidates, please email a cover letter explaining your interest in the position and relevant experience along with a CV and transcripts to joanna.achinger@adelaide.edu.au.