University of Dundee

Gene Expression

Characterisation of enhancer DNA methylation and its impact in gene expression and disease

The School of Life Sciences at the University of Dundee is a world-class academic institution with a reputation for the excellence of its research, its high quality teaching and student experience, and the strong impact of its activities outside academia. With 900 staff from over 60 countries worldwide the School provides a dynamic, multi-national, collegiate and diverse environment with state-of-the-art laboratory, technology and teaching facilities.

BBSRC Eastbio PhD Programme: Developing and applying a high - throughput platform in barley to screen for resistance and enhanced susceptibility to aphids

Aphids are economically important pests globally, and can cause significant yield loss of crops, including barley. Currently there are no commercial barley cultivars that are resistant against aphids, and only limited sources of partial resistance have been reported to date. As a consequence, control of aphids mainly relies on the use of insecticides.  In this project we aim to address the lack of available resistance in cereals to aphids pests by identifying new resistance sources in barley.

MRC DTP 4 Year PhD Programme: Dealing with proteotoxic stress: How do cells tidy up when trash piles up?

Degrading proteins in a timely manner to dispose of misfolded and damaged proteins is essential for a healthy cell. In ageing cells and organisms, there is a deterioration in the ability of cells to clear proteins resulting in the accumulation of misfolded proteins. Deposition of misfolded protein aggregates is a hallmark of many neurodegenerative diseases. It is not understood why quality control systems and the degradation capacity of a cell decline with age.

MRC DTP 4 Year PhD Programme: Revealing dynamic and elusive early-mitotic events using state-of-the-art live-cell light sheet imaging

To maintain their genetic integrity, eukaryotic cells must segregate their chromosomes properly to opposite spindle poles during mitosis. This process has important medical relevance because chromosome mis-segregation plays causative roles in human diseases such as cancers and congenital diseases. To prepare for proper chromosome segregation, kinetochores – the spindle attachment sites on chromosomes – must correctly interact with spindle microtubules (MTs) during early mitosis.

MRC DTP 4 Year PhD Programme: mRNA cap regulation in embryonic stem cell function

Embryonic stem cells are pluripotent cells derived from early embryos that retain the ability to differentiate into all somatic cells.  Pluripotency is dependent on the expression of key pluripotency regulators.  On receiving signals to differentiate, gene expression profiles are reshaped to repress pluripotency factors and to express the proteins required of the new cell lineage.  We investigate how cellular signalling pathways influence the gene expression machinery during differentiation and pluripotency to determine which proteins are expressed.  Our focus is on understanding how cellul

MRC DTP 4 Year PhD Programme: mRNA cap regulation in T cell function

We are interesting in how cells respond to extra cellular signals by co-ordinating the expression of hundreds or thousands of genes.  In particular we are interested in gene expression changes when a T cell encounters an antigen, and when an embryonic stem cell receives a developmental signal.  Our focus is on the role of the mRNA cap, which recruits the factors that mediate RNA processing and translation.  The enzymes which form the cap also influence transcription.

MRC DTP 4 Year PhD Programme: Dissecting the epigenetic regulation of enhancer function in hematopoiesis

The epigenetic mark of DNA methylation is established by DNMT (DNA methyltransferase) enzymes and has been shown to correlate with transcriptional states and influence cell identity and tumorigenesis in mammalian cells. The recent discovery that TET (Ten-Eleven-Translocation) enzymes produce 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxycytosine (5caC) and mediate active DNA demethylation in the genome has opened a new avenue to understand how DNA methylation dynamics affect transcriptional programs1.

BBSRC EASTBIO PhD Programme: The link between protein O-GlcNAcylation and intellectual disability

Understanding and controlling the balance between pluripotent self-renewal and differentiation is the major aim of the field of stem cell biology and it is the limiting factor for successful, safe, widespread use of embryonic stem cells (ESCs) in a clinical setting. In recent years it has become clear that these ESC functions are regulated by environmental cues (growth factors, nutrient supply, other cells) via signalling pathways operating on several proteins.

BBSRC EASTBIO PhD Programme: Understanding gene networks influencing straw digestibility for industrial biotechnology

Huge potential exists for using waste plant biomass (straw, grain husks etc) as a renewable and sustainable feedstock for making fuels and chemicals or as animal feed. Using plant biomass for industrial biotechnology in a bio-based economy will displace the use of oil and fossil fuels, thereby reducing carbon dioxide emissions and mitigating climate change. Plant biomass is largely composed of plant cell walls which are naturally recalcitrant to being broken down into components that can be fermented into useful products or used in industrial processes.

BBSRC EASTBIO PhD Programme: Prediction of protein-protein interaction sites from genetic variation data

Our research has focused for more than 20 years on developing effective computational methods to predict the function, structure and specificity of proteins from the amino acid sequence.  This has included work to characterise and predict protein-protein interactions from 3D structural information (e.g. [1]) as well as from sequences and related data (e.g. [2, 3]).