Investigating RNA quality control using omics

Posted on: 23 April 2024 by Stuart Fulton in April 2024 Posts

A photo of Chania harbour by night
Chania harbour by night

Stuart Fulton is a final year PhD Student in the Department of Molecular and Clinical Cancer Medicine. He recently attended The Focused Meeting on Integrative Omics of Nuclear Functions in Chania, Crete, and told us about his trip and current research.

My research

I joined the Papamichos-Chronakis Lab in October 2019 as a PhD student on the BBSRC Newcastle Liverpool Durham DTP. Since joining, I have been studying the mechanisms of nuclear RNA quality control in Saccharomyces cerevisiae.

Quality control of mRNA production is a crucial step in controlling how our genes work within our cells. Problems with this process are associated with a variety of human diseases, including cancer. Evidence suggests that RNA quality control is linked to the process of transcription – the process by which DNA is read and copied to produce RNA. Sometimes different copies or versions of the same gene are produced, either intentionally, or by mistake. The cell therefore requires mechanisms to understand the difference between an intended RNA version and a mistaken one. RNA copies produced by mistake must be quickly destroyed to prevent the production of faulty proteins.

The mechanisms which prevent the production of these mistaken RNAs remain poorly understood. A better understanding of these mechanisms will allow us to better understand how they go wrong in diseases, offering the potential for the development of future treatments.

Integrative Omics of Nuclear Functions

I attended The Focused Meeting on Integrative Omics of Nuclear Function held in Chania, Crete and organised by The International Union of Biochemistry and Molecular Biology (IUBMB). The scope of the meeting was to provide a wider perspective of how advanced genomic, proteomic, and imaging approaches can be combined to investigate nuclear structure and function.

The meeting was broken up into the following sessions:

  • Chromatin modifications
  • Nuclear architecture
  • Structural proteomics
  • Multi-omics data integration
  • Quantitative approaches to transcription
  • Chromatin in health and disease
  • Chromatin and metabolism
  • Single cell genomics and proteomics
  • DNA replication and repair
  • Spatial and interaction proteomics

Presenting my research

I was delighted to be selected to deliver an oral presentation on my research, in addition to a poster presentation. In my presentation I showcased advances of my recent project on developing a novel genome-wide Next Generation Sequencing assay, "3’-5’ RACE-Seq." This innovative technique is designed to quantitatively detect and map alternative transcription initiation and termination events, crucial for studying mRNA production quality control. My presentation sparked considerable interest, with several research groups expressing interest in collaboration and applying our technique to their research questions. I appreciated the opportunity to receive feedback and suggestions for further experiments or controls, which we have since taken on board and addressed. I was also able to utilise a “Lunch with a speaker” session to discuss with an international speaker the potential for integration of machine learning into my research.

During the conference there were also various social events, including a welcome drinks reception and an excursion to Chania old town and dinner in Chania old harbour. The opportunities to network, and to share ideas were particularly valuable.

Overall, the opportunity to present my work at an international conference, and to collect feedback, suggestions and ideas was particularly valuable to me and was hugely beneficial in planning the final months of my PhD studies. I would like to thank the Institute for the travel grant that enabled my visit.