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  Decoding the epitranscriptome in cancer

   Nuffield Department of Medicine

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  Dr Chunxiao Song  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Cellular RNA is decorated with diverse chemical modifications, which participate in all aspects of RNA biology. The multitude of modifications in RNA adds a new layer to gene regulation, leading to the emerging field of epitranscriptomics. Interest in understanding the functions of RNA modifications, as well as the related molecular mechanisms, has been growing, driving progress in developing chemical and biochemical tools to detect specific modifications within the transcriptomes. New technologies are important for uncovering biological functions, and they can also drive conceptual revolutions. From the perspective of cancer, epigenetic regulation plays pivotal roles in tumour development and maintenance, and aberrant patterns of epigenetic modifications are hallmarks of cancer. Therefore, mapping epigenetic modifications becomes crucial not only to understand the molecular basis of cancer, but also to develop diagnostic and therapeutic opportunities.

Our research aims to decode the chemical modifications of our genome, transcriptome, and proteome in human health and disease – cancer in particular – and translating this information into diagnostic and therapeutic opportunities that ultimately benefit patients. With our unique expertise in chemical biology and genomic technology, we have developed cutting-edge technologies in epigenetics and epitranscriptomics. Previously, we developed the revolutionary TAPS technology for bisulfite-free and base-resolution direct sequencing of DNA methylation (Nat. Biotechnol. 2019, 37, 424) and CAPS+ for improved DNA hydroxymethylation sequencing (J. Am. Chem. Soc. 2023, 145, 7095). Furthermore, we applied our tools to detect the epigenetic information in body fluids for non-invasive early cancer detection (Sci. Adv. 2021, 7, eabh0534). Recently, we developed a novel sequencing method for the RNA modification pseudouridine (ψ) (bioRxiv 2024.2001.2008.574649).

Our future research aims to uncover the transcriptome-wide distribution of ψ and study its role in tumour development. In addition, we will explore the potential clinical application of ψ in the circulating cell-free RNA for cancer diagnostics. We also aim to develop new technologies to sequence other important RNA epitranscriptomic modifications such as N6-methyladenosine (m6A), 5-methylcytidine (m5C), and N7-methylguanosine (m7G).

Students with a Chemistry or Biochemistry or a related science background are welcome to apply. Training opportunities include a wide range of basic and advanced chemical biology, biochemistry, and molecular biology techniques; knowledge in nucleic acid modifications/epigenetics/epitranscriptomics and clinical diagnostics; cutting-edge technologies, such as next-generation sequencing, cell-free RNA sequencing (liquid biopsy), single-cell sequencing, bioinformatics and data analysis skills.

Please quote the project ID Ludwig and indicate the course code RD_CM1 in your application. Please use the project details above for your research proposal.

The Ludwig Institute for Cancer Research studentships are for 4 years and provide an annual tax-free stipend of £21,000 and fees at the home or international rates.

For entry requirements and to apply for this project please visit the University of Oxford DPhil in Clinical Medicine pages

If you plan to apply to more than one Ludwig studentship project, you may list a maximum of two of our projects on your application.

Please note that only applicants who apply for a DPhil in Clinical Medicine via the University of Oxford admissions system will be shortlisted for interview.


Chunxiao Song ([Email Address Removed]) project related enquiries

Alexandra Royer ([Email Address Removed]) - application related enquiries

Do not send your application to these email addresses, only applications submitted visa the University of Oxford admissions system will be considered

Application deadline closes Monday 1st April. Deadline for receipt of references: Friday 5th April.

Biological Sciences (4) Chemistry (6)

Funding Notes

The Ludwig Institute for Cancer Research studentships are for 4 years and provide an annual tax-free stipend of £21,000 and fees at the home or international rates.
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