Vannini Group

The Vannini Group aims to understand how deregulation of a protein known as RNA polymerase III can cause cancer. Professor Alessandro Vannini left the ICR in July 2022, his group remains open under Professor Laurence Pearl.

Research, projects and publications in this group

Our research is aimed at mechanistically understanding the role of RNA polymerase III (and associated factors) deregulation in cancer, as well as their interplay with SMC complexes in genome structure and organisation.

The below outlines what the lab is currently focussing on.

Yeast RNA Polymerase III architecture:

We recently obtained the cryo-EM structure of yeast Pol III pre-initiation complex comprising TFIIIB, Pol III and the promoter sequence (Abascal-Palacios et al., Nature, 2018). Using state-of-the-art cryo-electron microscopy (cryo-EM) we obtained reconstructions of Pol III PIC and demonstrated the function of TFIIIB in the rearrangement of Pol III-specific subunits C34 and C37. Our study rationalised the mechanisms leading to DNA strand separation and template-strand loading into the active site and shed light into the general mechanism of gene transcription initiation. Likewise, using structural and biochemical approaches we have analysed the role of the TFIIIC transcription factor in the initial recruitment of TFIIIB to DNA promoters.

The stable association of these transcription factors to the DNA provides a platform for the further recruitment of RNA Pol III. Additionally, these assemblies are relevant for other cellular processes such the correct positioning of nucleosomes close to RNA Pol III-transcribed genes or the specific integration of Ty3 retro-transposons upstream of the transcription start site (TSS). These and other processes depend in the direct interaction of specific factors with components of TFIIIB and TFIIIC machineries.

RNA Polymerase III at type 3 promotors:

We previously demonstrated a redox control of Pol III transcription at the type 3 promoters providing a mechanistic link between Pol III deregulation and cancer (Gouge et al, 2015, Cell). We are now seeking to decipher how the promoter architecture contributes to human Pol III transcription at the type 3 promoters using structural and in vitro techniques.

TFIIIC in genome organisation:

In addition to acting as a transcription factor, TFIIIC has a potential role in genome organisation, with chromatin capture experiments localising extra TFIIIC DNA binding sites at the boundary regions of topological associating DNA domains (TADs). TFIIIC is enriched with and thought to directly interact with known genome structural protein, Condensin II at these sites. To further investigate this interaction, we are characterising human Condensin complexes using integrative approaches.

Eukaryotic transcription relies on three different RNA polymerases: RNA polymerase I (Pol) transcribes ribosomal RNA, RNA Polymerase II synthesizes messenger RNAs and RNA polymerase III produces short and non-translated RNAs, including the entire pool of tRNAs, which are essential for cell growth.

For a long time, it was assumed that only Pol II was regulated whereas Pol I and Pol III, being devoted to house-keeping genes, did not require such control. However, growing evidence show that RNA Polymerase III transcription is tightly regulated. Deregulation of its recruitment has been linked to neurodegenerative diseases and cancer.

RNA Pol III is recruited at only 3 types of promoters. While the type 1 and 2 are conserved from yeast to human, the type 3 promoters are found solely in higher eukaryotes. At the type 1 and 2, TFIIIC binds the promoter sequence to recruit TFIIIB that places the polymerase at the transcriptional start site. In humans, several tumour suppressors proteins and oncogenes interact directly with the transcription factor TFIIIB and, as a consequence, modulate RNA polymerase III occupancy at target genes. During carcinogenesis, this layer of regulation is lost, resulting in an augmented RNA polymerase III transcriptional output. Our research is aimed at mechanistically understanding the role of RNA polymerase III deregulation in cancer.

It is becoming increasingly clear that Pol III (and its associated factors) play a paramount role into genome structure and organisation. These extratranscriptional roles are effected through interactions with transposon machineries, SMC complexes and specific chromatin remodellers; we are aiming to obtain a detailed mechanistic understanding of these fundamental processes.

Professor Laurence Pearl

Head of Division:

Vannini Group, Macromolecular Structural Biology Laurence Pearl (Profile)

Professor Pearl seeks to understand the structural basis for assembly, specificity and regulation of the multi-protein complexes involved in the recognition, repair and signalling of DNA damage, and in the chaperone-mediated stabilisation and activation of cellular signalling pathways. These basic studies provide the means for discovery and development of novel small-molecule inhibitors with application as drugs for the treatment of cancer and other diseases.

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Researchers in this group

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Email: [email protected]

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Location: Chelsea

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Professor Laurence Pearl's group have written 215 publications

Most recent new publication 8/2024

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News and discoveries from Vannini Group

17/12/20

Computer generated model of RNA polymerase III transcribing DNA into RNA

Image: RNA Polymerase III. Credit: Alessandro Vannini/Jeroen Claus, Phospho Biomedical Animation

Scientists have created a three-dimensional map of a complex of molecules that plays a fundamental role in life – and which when it goes wrong is linked to increased sensitivity to viral infections and neurodegenerative diseases, and potentially also to cancer.

Their research has revealed the structure of the protein complex in human cells in stunning detail and shown precisely how this is affected by different mutations. It is set to act like a treasure map for guiding future research, and could lead to new targeted drugs for a range of diseases. In addition to neurodegenerative conditions and viral infection, the researchers also believe that there is a link between altered regulation of the protein complex and cancer.

The protein complex, known as RNA polymerase III or Pol III, reads DNA to decode ‘housekeeping’ genes and helps create the proteins that form the basic building blocks of cells. Cancer cells often hijack this process to fuel their rapid growth and division.

Capturing the detailed big picture of the protein complex

Three years ago, scientists at The Institute of Cancer Research, London, unveiled the structure of Pol III in yeast – describing it as akin to a Van Gogh painting due to capturing the detailed big picture of the protein complex.

Now the same team of scientists, working with colleagues in Germany, has revealed the three-dimensional structure of the human version of the protein complex – as well as mapping the precise structural effects of a wide range of disease mutations relating to neurodegeneration and increased sensitivity to infection by viruses. This could guide the way towards efforts to target the protein complex with new drugs.

The study, funded by Wellcome and Cancer Research UK, is published in Nature Communications today.

The team at The Institute of Cancer Research (ICR) made use of two Nobel Prize-winning scientific techniques – Cryo-EM, which won the Nobel Prize in Chemistry in 2017, and gene editing with ‘CRISPR’ – which won the Nobel Prize in Chemistry in October this year.

Precise, high resolution structure

Applying these two techniques to human cells in the lab, the researchers created many detailed images of the protein complex in its healthy form, and when affected by various mutations. They then grouped these together to obtain a precise, high-resolution structure of the protein machinery in action or when malfunctioning.

Researchers believe cancer cells take advantage of Pol III to keep them fuelled with the protein building blocks they need for rapid growth and division, while mutations in Pol III can also lead to neurodegenerative disease in humans. Researchers can now explore in the lab whether this is a promising therapeutic target in cancer.

By being able to visualise the 3D structure of human Pol III in detail, the researchers managed to map more than 85 per cent of known genetic mutations associated with Pol III very precisely. This allowed researchers to narrowly define the areas where these mutations occur and helped them interpret the mutations’ effects at a molecular level.

They found that mutations affecting the development of the central nervous system, for example, tend to cluster in specific hotspots, often between the same subunits of the protein complex.

Could be used to help design new drugs

The findings offer information on the potential effect that mutations could have on the binding of potential drugs. Drugs work by binding to protein targets, so the new structural information could eventually be used as a 3D map to help design new drugs.

The study confirms the overall similarity between the human version of Pol III and its yeast counterpart, but also highlights specific structural differences that weren’t known before and are of functional significance.

Study leader Professor Alessandro Vannini, Team Leader and Professor of Integrative Structural Biology at The Institute of Cancer Research, London, said:

“The Pol III protein complex is fundamental to life – decoding our DNA and ensuring our cells can build the proteins they need to grow and divide. And we believe it could have a role in the development of cancer.

“Our findings provide a vivid, extremely detailed three-dimensional map of Pol III, showing the structure of its various active sites, and how these are affected by various mutations linked to neurodegenerative diseases and viral infections. We hope our work can act as a 3D treasure map for the future discovery of new treatments targeting the Pol III complex.”

First author Dr Ewan Ramsay, Post Doctoral Training Fellow at The Institute of Cancer Research, London, said:

“We used very exciting techniques in this study – a revolutionary type of microscopy called Cryo-EM and a technology to edit genes known as CRISPR. This allowed us to create and visualise the human structure of the extremely important protein complex Pol III, which hadn’t been done before.

“Both of these techniques have won Nobel Prizes in the last three years and continue to revolutionise the field of structural and cell biology.”

Professor Paul Workman, Chief Executive of The Institute of Cancer Research, London, said:

“This exciting study reveals how a vital component of life functions in human cells – and crucially how it malfunctions too.

“This is a fantastic example of the importance of fundamental or ‘basic’ science. Understanding the inner workings of cells is an essential foundation for determining what goes wrong in cancer, neurodegeneration and other diseases, paving the way for potential new treatments.”

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