Computational Modelling Group

Epigenetics

Epigenetics referes to the study of biological processes that regulate gene transcription within the cell that are heritable mitoticaly and/or meioticaly but that do not involve changes in the DNA sequence. This include regulation of DNA packaging within the nucleus through chromatin remodelling involving histone modifications and chemical changes to the DNA itself such as cytosine methylation.

Within the Faculty of Medicine there are several groups generating large data sets assessing DNA methylation genome-wide utilising both array based platforms and direct sequencing of bisulphite converted DNA. Analysis of DNA methylation variation between individuals in relation to disease state adds an order of magnitude in complexity to genome wide association analysis of DNA sequence variation as methylation values are quantitative rather than binary and vary over time, between tissues and with environmental exposure.

For queries about this topic, contact John Holloway.

View the calendar of events relating to this topic.

Projects

Centre for Doctoral Training in Next Generation Computational Modelling

Hans Fangohr, Ian Hawke, Peter Horak (Investigators), Susanne Ufermann Fangohr, Ryan Pepper, Hossam Ragheb, Emanuele Zappia, Ashley Setter, David Lusher, Alvaro Perez-Diaz, Kieran Selvon, Thorsten Wittemeier, Mihails Milehins, Stephen Gow, Ioannis Begleris, Jonathon Waters, James Harrison, Joshua Greenhalgh, Rory Brown, Robert Entwistle, Paul Chambers, Jan Kamenik, Craig Rafter

The £10million Centre for Doctoral Training was launched in November 2013 and is jointly funded by EPSRC, the University of Southampton, and its partners.

The NGCM brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK.

Identifying factors required for DNA methylation using the imprinting control protein ZFP57

Deborah Mackay (Investigator)

Mutation of ZFP57 in humans is associated with widespread loss of DNA methylation at imprinted genes, and clinical features including congenital anomalies and developmental delay (Mackay et al, 08). This indicates that ZFP57 is required for DNA methylation of imprinted genes necessary for normal development.
We propose to identify the DNA sequences targeted by ZFP57, and its protein cofactors. This work will give insight into the biology of imprinting, indicate mechanisms of disease, and identify novel imprinted genes.

Imprinting Disorders Finding Out Why

Karen Temple (Investigator)

We are conducting a research project to determine the cause and clinical impact of widespread imprinting aberrations in human development. We are recruiting patients with possible or definite imprinting disorders (due to methylation loss or gain at an imprinted loci)

including Silver Russell syndrome, Transient Neonatal diabetes, Beckwith Wiedemann syndrome, Angelman syndrome Prader Willi syndrome, UPD 14 syndromes and Pseudohypoparathyroidism.

Transgenerational inheritance of allergy in a multi generational cohort

John Holloway (Investigator)

The aim of this project is to determine the vertical transmission of DNA methylation by identification of CpG sites by microarray analysis of 450,000 CpG sites in 252 women of the IoW cohort that are associated with allergic sensitization and testing whether the identified methylation patterns are vertically transmitted to their offspring and whether modifiable environmental conditions during gestation affect DNA methylation.

People

Hans Fangohr
Professor, Engineering Sciences (FEE)
John Holloway
Professor, Medicine (FM)
Karen Temple
Professor, Medicine (FM)
Peter Horak
Reader, Optoelectronics Research Centre
Deborah Mackay
Reader, Medicine (FM)
Christopher Bell
Lecturer, Biological Sciences (FNES)
Ian Hawke
Lecturer, Mathematics (FSHS)
Gaia Andreoletti
Postgraduate Research Student, Medicine (FM)
Alice Ball
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Ioannis Begleris
Postgraduate Research Student, Engineering Sciences (FEE)
Rory Brown
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
Paul Chambers
Postgraduate Research Student, Engineering Sciences (FEE)
Caroline Duignan
Postgraduate Research Student, Biological Sciences (FNES)
Robert Entwistle
Postgraduate Research Student, Engineering Sciences (FEE)
Stephen Gow
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Greenhalgh
Postgraduate Research Student, Engineering Sciences (FEE)
James Harrison
Postgraduate Research Student, Engineering Sciences (FEE)
William Hurndall
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Jan Kamenik
Postgraduate Research Student, Engineering Sciences (FEE)
Konstantinos Kouvaris
Postgraduate Research Student, Electronics and Computer Science (FPAS)
David Lusher
Postgraduate Research Student, Engineering Sciences (FEE)
Gregory Parkes
Postgraduate Research Student, Engineering Sciences (FEE)
Alvaro Perez-Diaz
Postgraduate Research Student, Engineering Sciences (FEE)
Daniel Power
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Craig Rafter
Postgraduate Research Student, Engineering Sciences (FEE)
Hossam Ragheb
Postgraduate Research Student, Engineering Sciences (FEE)
Sonya Ridden
Postgraduate Research Student, Mathematics (FSHS)
Kieran Selvon
Postgraduate Research Student, Engineering Sciences (FEE)
Ashley Setter
Postgraduate Research Student, Engineering Sciences (FEE)
Jonathon Waters
Postgraduate Research Student, Engineering Sciences (FEE)
Thorsten Wittemeier
Postgraduate Research Student, Engineering Sciences (FEE)
Emanuele Zappia
Postgraduate Research Student, Engineering Sciences (FEE)
Matthew Higgins
Undergraduate Research Student, Biological Sciences (FNES)
Shaun Maguire
Undergraduate Research Student, Biological Sciences (FNES)
Susanne Ufermann Fangohr
Administrative Staff, Civil Engineering & the Environment (FEE)
Mihails Milehins
Alumnus, University of Southampton
Brian Bonney
None, None
Roshan Sood
None, None