How does the expression of one gene affect that of its neighbour?

Lead Research Organisation: University of Bath
Department Name: Biology and Biochemistry


A strand of DNA can contain several genes. The expression of one gene may affect the expression of its neighbouring genes. We see this occurring in many circumstances in normal and disease biology. Understanding exactly how this happens is important for appreciating the knock-on effects of genome rearrangements (i.e when DNA is broken and repaired with the result that genes are repositioned) and transgene insertions (as in gene therapy, where a new DNA sequence is inserted into the genome), and hence for understanding disease progression. It will also increase our understanding of how viruses that integrate into the genome and lie dormant can be reactivated through expression changes in nearby genes.

In this proposal we address how such non-autonomous gene expression occurs. As examples we are using the DIRAS3 gene and its neighbour GNG12-AS1. These two genes face each other on the DNA and they are a considerable genomic distance apart, yet the expression of GNG12-AS1 interferes with the expression of DIRAS3, with the result that DIRAS3 expression is lowered. This process is known as "transcription interference". We have recently found that we can epigenetically manipulate GNG12-AS1 expression without mutating or modifying the underlying DNA sequence. This provides us with the means to test two models for transcription interference. The first model considers the two enzymes which enable transcription (polymerases) travelling towards one another and because they cannot pass each other, one or both need to pause to prevent a polymerase collision. The second model considers the expression of one gene simply blocking the accessibility of the other gene to polymerases.

In our experiments we will take into consideration the fact that DNA is folded into looping structures, so that two genes separated by a big genomic distance may in fact be in close proximity, and thus more likely to compete for polymerase when the DNA is folded into loops. We will also track the progress of polymerases between these genes to map pausing positions.

The results of this study will give a deeper understanding of how the genome functions to regulate itself. Emerging technologies for gene editing are providing unprecedented opportunities for gene therapy to treat many diseases. Epigenetic drugs already exist that change gene expression without changing the underlying DNA sequence. The opportunities for epigenetic- and gene therapy make it imperative to better understand the mechanisms of non-autonomous gene expression. The models that we are testing have different implications for epigenetic and gene therapies and will allow us to predict how the genome environment will respond to these therapies.

Technical Summary

Classically it has been presumed that genes are autonomous in their expression. However, there is increasing evidence that in both health and disease, gene expression is not autonomous. In all eukaryotic genomes highly co-expressed genes and housekeeping genes cluster. In cell fate specification, blocks of up or down regulated genes are observed and in cancers we see unusual blocks of genes downregulated. Importantly, the first gene therapy trials had to be stopped as the expression of the introduced gene affected the expression of an oncogenic neighbour. What is less clear is what the underlying mechanisms are for such non-autonomous expression.

Here we take advantage of an emerging model system for the analysis of gene-gene interactions, the DIRAS3/GNG12-AS1 expression in humans. We have discovered that DIRAS3 transcription is modulated through transcriptional interference (TI) from an lncRNA, GNG12-AS1. We have found that we can inhibit GNG12-AS1 either at its transcription level or post-transcriptionally by selective siRNA targeting. We intend to use this system to test two models for TI, one that considers polymerase collision/pausing, and another that transcription of one locus alters promoter accessibility at the other. The techniques that we will use will be allele-specific capture chromatin conformation (C-HiC) and Nuclear run assays (GROseq), R-loop and RNAPII ChIP in combination with gene editing to examine the effects of transcription through specific genomic features on TI.

The results of these studies will lead a better understanding of non-autonomous gene expression, which is key to understanding the potential pitfalls of gene therapy, the effects of genome rearrangements (in cancers or in evolutionary time) as well as guide epigenetic therapies aimed at reversibly modulating gene expression.

Planned Impact

Other than the academic beneficiaries listed above, potential users of this research will ultimately be clinicians and pharma with an interest in gene therapy, epigenetics and diagnosing patients with genomic imprinting disorders. The patients that are likely to finally benefit include those with congenital gene defects and imprinting defects, as well patients with acquired polyfactorial disease (type 2 diabetes, cancer, cardio vascular disease and degenerative neurological diseases) who would be candidates for gene or epigenetic therapies.

We will reach these clinical stakeholders by targeting specific professional organisation bodies (British Society for Gene and Cell Therapy BSGCT, European Network for Congenital Imprinting Disorders; Wellbeing of Women charity) and contribute to their meetings to publicise our project.

We will also include specific Biotech companies that interact with these professional organisations in the conferences we organise (Via CR@B and the Biochemical Society) and arrange for them to participate in our student placement schemes.

Our research topics (genome evolution, genomic imprinting, the clashing of polymerases) are very accessible to members of the public with an interest in science and its application to disease. An ideal venue for public engagement locally is the Bath Royal Literary and Science Institute (BRLSI). The Department has strong links with the BRLSI and have participated in several of their public events. In addition we participate in Science Cafe and a MOOC on "Inside Cancer"
Description EPSRC Studentship: Mathematical and bioinformatics based tools to explore the impact of gene editing on the geometric principles governing the 3D structure of the genome
Amount £90,000 (GBP)
Organisation University of Bath 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 07/2022
Description Leverhulme Trust
Amount £410,983 (GBP)
Organisation University of Bath 
Sector Academic/University
Country United Kingdom
Start 04/2021 
End 03/2024
Description Gene expression regulated by 5hmC in colon cancer 
Organisation University of Bristol
Department School of Biochemistry Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution Our research has highlighted that 5hmC affects gene expression and alternative splicing and we contacted a group in the Biomedical Sciences at the University of Bristol to examine whether splicing can be tested in colon cancer. We have expertise in DNA methylation, chromatin biology and gene expression analysis.
Collaborator Contribution The group has a unique resource of colon cancer cell lines that can be grown as organoids.
Impact We have a strong body of preliminary data to support a new project grant to the MRC. This grant was submitted in 2019 and has been successful. Work on this has started in Jan 2020
Start Year 2017
Description Higher order chromatin structure and mathematical modelling 
Organisation University of Bath
Department Department of Mathematical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution The data that we are generating is of interest to a group in the Dept of Mathematical Biology. The post-doc on this MRC grant has generated a number of C-HiC profiles that will be utilised to generate mathematical predictions of genome organisation. This is likely to result in high impact papers and we have already added a PhD student funded by the EPSRC to this project. The student is based in my lab, but has access to expertise in the Milner Centre for evolution and is co-supervised by member in the Dept of Maths
Collaborator Contribution The collaborator has helped to design a PhD project utilising our data and has set up a seminar series to promote mathematical biology at the University. She has mentored post doctoral and PhD students in the group.
Impact This is a multi-disciplinary academic collaboration involving mathematical modelling using string and knot theory and biochemistry data such as chromatin conformation and gene expression. It also relies on bioinformatic analysis to address epigenetic factors such as DNA methylation into the model. The outcome so far has been to successfully apply for an EPSRC studentship and the student has started in Oct 2018.
Start Year 2017
Description Cancer Research @ Bath 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Cancer Research @ Bath (CR@B) is a local network of clinicians, academics and members of the public who meet informally twice a year to exchange information about the local research occurring in Bath and how this can potentially be applied to the clinic for the benefit of patients. Members of the public, and charitable donors with an interest in cancer treatment and research also regularly attend these meetings so talks and activities are pitched in lay terms. Understanding how genes are regulated and switched on and off is relevant to cancer therapies.
Outcomes of this activity:
1. The University of Bath broadened the cancer research network to link up with the universities of Bristol, Cardiff and Exeter to form a collaborative cancer research community (GW4CANCER), in which the 4 universities can identify research strengths and whereby individual researchers can find collaborators. Within this community we can share equipment and research facilities and apply for DTP studentships.
2. e-cancer has invited members of the network to write reviews and has filmed speakers at several events.
3. New collaborations between my group and Prof Ann Wiliams in Bristol has ensued and we are currently applying for further funding
Year(s) Of Engagement Activity 2018,2019,2020,2021