Projects

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. We are using skeletal muscle formation (myogenesis) in Salmonids as a very valued teleost species in aquaculture but also as a paradigm to study evolutionary biology.

Projects

Dr 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 ATACseq and sc-RNAseq at single cell resolution to study the dynamics of transcriptional changes during myogenic lineage commitment in Atlantic salmon.

Linjing Lan, PhD Student (2024-2027)

1^st Supervisor: Dr Doug Vernimmen

2^nd Supervisor: Prof. Dan Macqueen

Project: “Myogenic regulatory evolution after the salmonid whole genome duplication”.

By using phylogenetics, transcriptomics and epigenomics, Linjing has analysed the myogenic regulatory factors (MRFs) gene family, including MyoD, Myf5, MRF4 (Myf6) and Myog (Myogenin) to provide insights in how MRF paralogues have been retained during evolution. By integrating data from different tissues and life stages she has fully mapped the regulatory elements of each MRF paralogue which has revealed both conservation and divergence of syntenic regions. Her data have addressed how these may be differentially regulated in time and space, an essential feature of subfunctionalisation for this gene family.

Kamila Malysz, PhD Student (2020-2024).

Project: “Deciphering the role of epigenetic regulators across many cell types”. 

Kamila used CRIPSR/Cas9 generated KOs followed by multidisciplinary technologies, such as high-throughput sequencing (RNAseq & ChIPseq), biochemistry (western blots) and structural cell biology (electron microscope).

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"