Background

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.

Research Programme

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.

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"

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.

Prof Dan Macqueen, University of Edinburgh

Prof Xavier Donadeu, University of Edinburgh

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.

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

• 2021-2023. International Society for Experimental Haematology, Junior PI Committee.
• 2015-2019. Genetics Society Ordinary Committee Member (Representative for Area A - Gene Structure, Function and Regulation).
• Member of the Genetics Society + Local Representative for The Roslin Institute.
• Member of the British Society for Haematology (BSH).
• Member of International Society for Experimental Hematology (ISEH).
• Member of the European Hematology Association (EHA).
• Member of the British Society for Cell Biology (BSBC).
• Associate Member of Brasenose College, University of Oxford (2004-2012).
• Member of the Belgian Society of Biochemistry and Molecular Biology.
• Member of the Belgian Association for Cancer Research (BACR).

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.

• Photographic Distinctions: EPSA, EFIAP, ARPS
• International Photography Awards: >400
• International Filmography Awards: 32
• The Chromatin Laboratory (2015).
• The Genetics Society (2017, Award-Winning Documentary).
• Oxford Through the Lens (2017, Multi-Award Winning Commercial).
• Edinburgh from the Skies (2021, Multi-Award-Winning Film).
• The Easter Bush Campus (2023, Multi-Award-Winning Film).
• Research Experience Placement (2023, Award-Winning Documentary).

Postdocs:

• Dr Uli Sobhiafshar (2023-Present)
• Dr William Ho (2019-2023)
• Dr Darya Deen (2018-2020)
• Dr Louie van de Lagemaat (2016-2017)
• Dr Ali Anvari Azar (2017-2020)

Our long-standing aims are 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.

http://www.ed.ac.uk/roslin/chromatin-biology-epigenetics