Mechanism of transcriptional gene silencing induced by convergent transcription in human cells and its application in breast cancer.

Lead Research Organisation: University of Oxford
Department Name: Sir William Dunn Sch of Pathology

Abstract

All organisms consist of cells that multiply through cell division. The genetic code, which defines each cell type, is stored within DNA molecules. DNA contains coding regions called genes. Genes are transcribed into messenger RNA (mRNA) molecules, which are in turn translated into proteins, a process called gene expression. It is important that each cell makes the right levels of proteins, which is achieved by controlled gene expression. Uncontrolled gene expression can lead to cancer or cell death. One of the most important mechanisms for the regulation of gene expression is gene silencing. Gene silencing in human cells requires the presence of small RNA molecules (siRNA), which activate the RNAi pathway. This leads to recognition and distruction of target mRNA in the cytoplasm. Another type of gene silencing is the establishment of specific modifications on DNA, which leads to inhibition of gene transcription, also called transcriptional gene silencing (TGS). Little is understood about the mechanism of TGS in humans. The work proposed in this fellowship application will use available knowledge about TGS from other organisms to investigate and explore the details of how TGS can be induced in humans and by what mechanism. This work has important implications given that it can lead to development of new research tools with a great potential for therapeutic application.

Technical Summary

All organisms consist of cells that multiply through cell division. The genetic code, which defines each cell type, is stored within DNA molecules. DNA contains coding regions called genes. Genes are transcribed into messenger RNA (mRNA) molecules, which are in turn translated into proteins, a process called gene expression. It is important that each cell makes the right levels of proteins, which is achieved by controlled gene expression. Uncontrolled gene expression can lead to cancer or cell death. One of the most important mechanisms for the regulation of gene expression is gene silencing. Gene silencing in human cells requires the presence of small RNA molecules (siRNA), which activate the RNAi pathway. This leads to recognition and distruction of target mRNA in the cytoplasm. Another type of gene silencing is the establishment of specific modifications on DNA, which leads to inhibition of gene transcription, also called transcriptional gene silencing (TGS). Little is understood about the mechanism of TGS in humans. The work proposed in this fellowship application will use available knowledge about TGS from other organisms to investigate and explore the details of how TGS can be induced in humans and by what mechanism. This work has important implications given that it can lead to development of new research tools with a great potential for therapeutic application.

Planned Impact

There is widespread interest in the transcriptional gene silencing (TGS) in human cells. However, very little is understood about the exact mechanism. The understanding of the properties of TGS in human cells is quickly outstripping the very limited amount that is known about induced gene expression regulation on transcriptional level. This project would therefore have an impact not only in biological fields, but also potentially in fields such as nanotechnology and biotechnology.
The project would open up fundamentally novel questions about TGS mechanism, and will therefore not only determine the role of TGS in gene regulation, but will also be relevant to development of a new research tool. This research proposal may be particularly interesting for scientific community, not only because of providing a new knowledge, but also for potential use of CT as a new tool for knocking down genes on transcriptional level in mammalian cells. There are no efficient commercially available tools for switching off the genes on transcriptional level at the moment.
The idea of CT induced TGS in human cells has been filed as patent by Isis Innovations at Oxford University and was received with great interest from various biotech companies. This project will help to develop a range of useful tools for scientific community as well as new therapeutic agents, which will be of great benefic for general public.
 
Description Elucidating the mechanism of RNA dependent DNA damage response and its role in cancer
Amount £1,947,610 (GBP)
Funding ID 24866 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2023
 
Description Rosetrees Trust Seed award
Amount £10,000 (GBP)
Organisation Rosetrees Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2017 
End 12/2017
 
Description Classification of endogenously produced small RNA 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution My lab covers experimental part of this project, supervision of the experiments as well as relevant consumables.
Collaborator Contribution Prof Enright provides bioinformatical expertise and supervision of Dr Davis.
Impact we generated data that are useful for other projects in my lab
Start Year 2014
 
Description Dicer in alternative polyadenylation in humans 
Organisation Manchester University NHS Foundation Trust
Department Biochemistry
Country United Kingdom 
Sector Hospitals 
PI Contribution Dr Kaspar Burger, PostDoc in my lab performed several experiments, which led us to create a model for Dicer function in alternative polyadenylation. We were meeting with our collaborators regularly to discuss obtained data and further development of the project.
Collaborator Contribution Dr Andre Furger's lab provided initial data set in this project, which included sequencing data of RNA isolated from nuclear and cytoplasmic fractions from wt and Dicer knockdown cells.
Impact Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, Gullerova M, Furger A. Genome Res. 2016 Jan;26(1):24-35. doi: 10.1101/gr.193995.115. Epub 2015 Nov 6.
Start Year 2014
 
Description public lecture, TV and magazine interviews 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I have wide-ranging experience in disseminating information to a popular audience. As The Best Young Scientist of Slovak Republic (2008) and a winner of L'Oreal/UNESCO Women in Science Award UK and Ireland (2011) I have received significant media attention. I have extensive experience with radio and newspaper interviews in both countries, Slovakia and UK. Also, I gave a public lecture in Slovakia, which was broadcasted nation-wide.

I received many emails from students and public, expressing motivation and interest in science in general and also my research.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013