Dr Douglas Vernimmen (BSc, PhD)

Group Leader

Background

Doug Vernimmen read Biology (BSc) and Molecular Biology (MSc) and gained his PhD in Biochemistry at the University of Liège (Belgium) in 2003. His work was under the supervision of Dr Rosita Winkler (Department of Pathology, Prof Boniver), and was focused on the characterisation of an enhancer element involved in the overexpression of an oncogene in breast cancers. Afterwards, he moved to the University of Oxford to work at the Weatherall Institute of Molecular Medicine as a MRC Postdoctoral fellow, under the supervision of Prof Doug Higgs (Molecular Haematology Unit). Using a-globin regulation as a model, he showed the role of enhancer elements in the recruitment of transcription factors, but also chromosomal looping and epigenetic changes required for gene transcription. During these years, he has developed an international reputation in the chromatin biology field, and more particularly in chromosome looping studies where I developed a quantitative method to measure interaction between different DNA elements (q3C, Chromosome Conformation Capture). Overall, his work has always been dedicated on the understanding of how mammalian genes are switched on and off during differentiation to control cell fate and to specify different lineages, but also how genes are abnormally regulated in genetic diseases such as cancer and thalassaemia.

In 2012, he took a lecturer position at The University of Edinburgh through a Chancellor’s Fellowship, to run his research group at The Roslin Institute. Since then, his work covered the transcription activity in individual cells and the epigenetic regulation in normal and malignant haematopoiesis. His research has also expanded to epigenetic regulation in infectious diseases and more recently comparative genomics.

Qualifications

Photographic qualifications

2022 Associateship of The Royal Photographic Society, ARPS

2016 Excellence of the Photographic Society of America, EPSA

2012 Excellence of the International Federation of Photographic Art, EFIAP

 

Education/Academic qualifications

1996 PhD, University of Liège. Characterisation of a transcription factor involved in HER2 gene overexpression in breast cancers

1994 MSc, University of Liège. Characterisation of cis sequence of the HER2 gene promoter in the BT-474 human mammary adenocarcinoma cell line

1992 BSc, University of Liège

 

Responsibilities & affiliations

Internal Committees

  • 2022- Present. EBR Committee – R(D)SVS.
  • 2022 -Present. GM/Biosafety committee - R(D)SVS.
  • 2013-Present. Genetics Society’s representative for The Roslin Institute.

External Recognition / Esteem

Beside his scientific work, he is also the recipient of ~400 awards and distinctions for his international contribution to Photography and the author of the multi-awards winning Photography Book ‘Oxford Through the Lens’ (ACC Art Books, published in October 2016; Contributors: Sir John Hood, Professor Joe M Crook and Colin Dexter). Book distributed worldwide. Royalties donated to the University of Oxford to support British Education.

Website at http://www.douglasvernimmen.com/

Undergraduate teaching

Tutor of R(D)SVS students

Postgraduate teaching

Since appointment to my current role, I have developed a portfolio of teaching duties covering subjects ranging from basic molecular biology to advanced concepts in my field, spanning both undergraduate (e.g. summer/honours students training), postgraduate taught (Masters) and postgraduate research (PhD) programmes. I also lead the delivery of an innovative approach to teaching and learning by helping PhD students to develop ideas that can impact the future of science through engaging strategic and ethical science discussions.

Open to PhD supervision enquiries?

Yes

Current PhD students supervised

Linjing Lan (2024-2027)

Project: “How CpG islands (CGIs) and Polycomb group (PcG) complexes influence gene expression in fishes of importance to global aquaculture”.

Kamila Malysz (2020-2023)

Project: "Role of Demethylases in Myeloid leukaemia"

Past PhD students supervised

Ailbhe Brazel (2013-2016)

Project: "Long Range Control of Epigenetic Regulation"

Research summary

The understanding on how vertebrate genes are switched on and off during differentiation to control cell fate and to specify different lineages is the molecular basis for any biological phenomenon. My research area is focused on many aspects of chromatin biology with a specific focus on epigenetic regulators. Chromatin Biology is a very strong research area at the University of Edinburgh and the research conducted at the Roslin Institute will take advantage of using many species to develop comparative (epi)genomics approaches to understand the complexity of gene regulation during evolution.

Current research interests

The projects below are our long-standing aim to understand 1) the role of transcriptional & epigenetic regulators during differentiation and cell identity together with the complexity of their isoforms; 2) how these genes are differentially regulated between species and 3) the role of regulatory element controlling epigenetic regulation across species. Kamila Malysz, PhD Student (2020-2024). Project: “Deciphering the role of epigenetic regulators across many cell types”. We use CRIPSR/Cas9 generated KOs followed by multidisciplinary technologies, such as high-throughput sequencing (RNAseq & ChIPseq), biochemistry (western blots) and structural cell biology (electron microscope). Uli Sobhiafshar, Postdoc (2023-present) Project: “Optimisation of an in vitro model to investigate the complex genomic basis for cellular myogenesis in Atlantic salmon”. We use both ATACsea and sc-RNAseq at single cell resolution to study the dynamics of transcriptional changes during myogenic lineage commitment. Linjing Lan, PhD Student (2024-2027) Project: “How CpG islands (CGIs) and Polycomb group (PcG) complexes influence gene expression in fishes of importance to global aquaculture”. We use affinity purification approach (Bio-CAP) followed by high-throughput sequencing to identify CGIs in species sharing a common ancestor 270 million years ago and thus represent broad evolutionary diversity within the fish clade. Research students PhD Students: Linjing Lan (2024-2027) Project: “How CpG islands (CGIs) and Polycomb group (PcG) complexes influence gene expression in fishes of importance to global aquaculture”. Kamila Malysz (2020-2023) Project: "Role of Demethylases in Myeloid leukaemia" Ailbhe Brazel (2013-2016) Project: "Long Range Control of Epigenetic Regulation" Honours & Summer Students: • Summer 2024: John-Vincent Beauvais (University of Strasbourg, France). Project: " Bioinformatics analysis of single cell RNAseq data, Atlantic salmon muscle cells”. • Summer 2023: Georgia Goddard (University of Edinburgh). Project: "Characterisation of UTX KO in HEK cells” • Hons Project 2023: Julia Rodriguez Suarez (University of Edinburgh, First Class Degree). Project: "Investigating the role of UTX isoforms” • Summer 2021: Hannah Mallon (The Royal Veterinary College of London). • BSc Project 2018: Elise Georges (University of Paris-Sud, First Class Degree). Project: "Chromosomal Alterations in Acute Myeloid Leukaemia" • Hons Project 2017: Miren Urrutia Iturritza (University of Edinburgh, First Class Degree). Completed a MSc student at the Karolinska Institute, Stockholm • Summer 2015: Justin Auerbach (University of Edinburgh). Project: "CRISPR/Cas9 mediated enhancer deletion in mouse ES cells" • Hons Project 2015: Irene Kallimasioti (University of Edinburgh). Completed a PhD student at University of Edinburgh. • Summer 2014: Sarah Mounedji (University of Edinburgh). Project: "Generation of knock-in cells with a fluorescent reporter gene" • Summer 2014: Ami Patrick (Universityv of Edinburgh). Project: "Analysis of epigenetic regulators expression in normal haematopoietic and leukaemic cells"

Past research interests

Background 1. The Chromatin Lab, the Developmental Biology Division and The Roslin Institute. The new Roslin Institute (launched in 2011) has developed a broad panel of interests, and has a wide portfolio spanning genetics and developmental biology. The Developmental Biology Division aims to enhance fundamental knowledge of the control of cellular growth and differentiation, to underpin the development of better disease intervention strategies. We advance our understanding of function in these essential biological processes through mechanistic studies at the cell, tissue and whole organism level with particular focus on stem cells, tissue and organ development, tissue damage and repair and regulatory networks in development. The regulation of gene expression is at the basis all these biological processes and the mission of the Chromatin Lab is to bring new angles to the institute with our expertise in chromatin and epigenetics. The overall aim of the Chromatin Laboratory is to understand how mammalian genes are switched on and off during differentiation to control cell fate and to specify different lineages, but also how genes are abnormally regulated in genetic diseases such as cancer. More specifically, we aim to understand the role of enhancers in this process, using haematopoiesis as a model system. 2. Epigenetics and Transcription Regulation. Epigenetics is the study of the changes in gene expression due to modifications to the genome that do not involve a change in the nucleotide sequence. It is now clear that one form of epigenetic regulation involves the establishment/removal of histone post-translational modifications. These changes are catalysed by a panel of different enzymes (called chromatin-modifying enzymes or epigenetic regulators), which target specific genes for activation or inactivation. The last decade has led to the identification of many of these enzymes, which are required for transcription regulation, cell cycle and differentiation. Today, the field is just beginning to understand the regulation of these enzymes and the biological significance of histone modifications. These enzymes have also generated a clinical interest since drugs can be designed to modulate their activity, which has launched the development of epigenetic therapy. Remote regulatory sequences (enhancers) have been defined as DNA elements responsible for increasing the transcription level of a target gene, located sometimes very far away. What do these sequences really do and how do they work at very large distances? These have been questions of major interest over the last two decades. Today it is well accepted that remote enhancers function as docking sites for the recruitment of the general transcription machinery, which would be subsequently transferred to a target promoter by a looping mechanism. Over the last decade, the Encyclopedia of DNA Elements (ENCODE) project aimed to map all functional elements (e.g. enhancers, promoters, coding regions, methylated DNA sequences) in the human genome. The recent “completion” of the ENCODE project (2012) has revealed that there are many more enhancers than expected. Also, genome-wide associated studies (GWAS) showed that many single nucleotide polymorphisms (SNPs), associated with susceptibility/resistance to a disease, have been found outside gene coding sequences emphasizing the importance of enhancers. Research Programme Our current research programme is focused on two main aspects of enhancers: 1. Enhancer Activity. Summary: There is a body of evidence that variation of expression at a single cell basis occurs (subpopulations). This highlights the need for techniques to approach chromatin architecture in single cells, as this would directly capture cell-to-cell variation. We use genetic engineering techniques in order to make models in which we can visualise transcription activity in individual cells. Funding: Early Stage Investigator Start-up Fellowship, British Society for Haematology (BSH). 2. Enhancer Functions. Summary: During development and cell differentiation, epigenetic regulators are required to dramatically alter epigenetic programmes and therefore gene expression states to create new cell-specific profiles. Our aim is to understand how transcription enhancers control the epigenetic programme using an approach integrating molecular biology, bioinformatics and genetics. We will also test existing compounds and produce new inhibitors for epigenetic regulators in leukaemia. These have strong potential for the development of epigenetic therapy in the future. Funding: Kay Kendall Leukaemia Fund. Research students PhD Students:- Ailbhe Brazel (2013-2016) Project: "Long Range Control of Epigenetic Regulation" Honours Students: -Miren Urrutia Iturritza (2017) -Eirini Kallimasioti Pazi (2015) Summer Students: -Justin Auerbach (2015) Project: "CRISPR/Cas9 mediated enhancer deletion in mouse ES cells" -Ami Patrick (2014) Project: "Analysis of epigenetic regulators expression in normal haematopoietic and leukaemic cells" -Sarah Mounedji (2014) Project: "Generation of knock-in cells with a fluorescent reporter gene" Collaborative Activity Prof Juri Rappsilber, University of Edinburgh Dr Peter Hohenstein, University of Edinburgh Dr Andrew Smith, University of Edinburgh Prof Doug Higgs, University of Oxford Prof Willem Ouwehand, University of Cambridge Dr Yufeng Tong, University of Toronto Prof Peter Andrews, University of Sheffield Prof David Hume, University of Edinburgh Prof Kamil Kranc, University of Edinburgh Prof Chris Ponting, University of Edinburgh

Knowledge exchange

I developed track record in KE activities associated with my research expertise that have made a significant impact on the activities of both researchers within and outside UoE. I recently built a portfolio of collaboration and engagement with non-academic partners which provides evidence for the societal impact and knowledge exchange opportunities created by my research programme. Beyond KE delivering impact on the research community, I also have been very active at developing public engagement activities

Project activity

Our projects are based on our long-standing aim to understand 1) the role of transcriptional & epigenetic regulators during differentiation and cell identity together with the complexity of their isoforms; 2) how these genes are differentially regulated between species and 3) the role of regulatory element controlling epigenetic regulation across species.

Past project grants

2022-2023 ISP Early Career Grant
2020-2023: Melville Trust for the Care and Cure of Cancer
2018: The Genetics Society Summer Studentship
2017: Academic Networking Fund –
Chromatin, Epigenetics and Transcriptional Regulation –2018.
2017-2020: Kay Kendall Leukaemia Fund – Research Grant.
2016: Training Grant from the Genetics Society
2016: One-off Meeting Sponsorship - The Genetics Society
2015: Academic Networking Fund –
The Edinburgh Haematopoiesis Network.
2013-2016: Early-Stage Investigator Start-up Fellowship
"British Society for Haematology" (U.K.)
2013-2015: Lady Tata Memorial Trust (U.K.)
2013 : Grant from The Roslin Foundation
2012-2017: Chancellor’s Fellowship from the University of Edinburgh (U.K.)
2011 : Travel Fellowship from the "Elimination of Leukaemia Fund" (U.K.)
2009 : Travel Fellowship from the "Epigenome Network of Excellence" (Austria)
2008 : Travel Fellowship from the "British Society for Haematology" (U.K.)
2004-2005 : Travel Fellowship from the "Leon Fredericq Foundation" (Liège
2001-2002 : Fellowship from the "National Funds for Scientific Research" (F.N.R.S.)
1999-2001 : Fellowship from the "National Funds for Scientific Research" (F.N.R.S.)
1997-1999 : Fellowship from the "National Funds for Scientific Research" (F.N.R.S.)
1999-2000 : Grant from the regional "Fondation pour promouvoir la Recherche à l'Université de Liège"
1999 : Grant from the national "Ministère de la Communauté Française de Belgique"
1998 : Grant from the regional "Centre Anticancéreux près l'Université de Liège", Belgium
1997 : Grant from the regional "Centre Anticancéreux près l'Université de Liège", Belgium

View all 39 publications on Research Explorer

More video

In the press

Welcome to the Chromatin Laboratory (2013), run by Dr Douglas Vernimmen and part of the Developmental Biology Division at The Roslin Institute. Dr Vernimmen introduces his laboratory and gives insight into his team's work, before each of his team members gives a brief overview of their position and role.

The Easter Bush Campus (2023) is a short documentary of breath-taking aerial views of one of the top Veterinary Schools in the world. The Royal (Dick) School of Veterinary Studies was established by William Dick in 1823. As part of the University of Edinburgh, the old campus was originally based in the centre of the Capital City of Scotland, and moved south of the city in 2011, to the new Easter Bush Campus. This film is a whirlwind tour through all that Easter Bush has to offer.

Research Experience Placement (2023) is a short documentary directed by student Georgia who describes the skills she developed during her very first experience in the research laboratory of Doug Vernimmen.