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Staff Profile

Dr Mark Hirst

Senior Lecturer in Biology



I completed my PhD in the laboratory of David Porteous at the MRC Human Genetics Unit in Edinburgh in 1988 and from there moved to Oxford to work in the laboratory of Kay Davies within the institute of Molecular Medicine at the John Radcliffe Hospital. During this period I spent time working in as a visiting PI in the laboratoryof Charles Laird (FHCRC, Seattle, USA) and as a visiting researcher in the laboratory of Alan Wolffe (NIH, Bethesda, USA). I moved to the Open University in 1999.

Current University Role

Senior Lecturer in Human Genetics

Head of Cell and Molecular Biology (Dept Life, Health and Chemical Sciences)

Member of University GM Safety Committee

Member of Life and Biomolecular Sciences Committee (academic review of Affiliated Research Centres).


Genetical Society of Great Britain, American Society of Human Genetics, the British Society of Human Genetics, The Clinical Molecular Genetics Society and the American Association for the Advancement of Science.

Other Activities (present and past)

I currently act as a Scientific Advisor to the UK Fragile X Society, a family support group serving the needs of fragile X families within the UK. This involves writing synopses of research papers in lay-terms, advising the Society on recent research progress and on advances leading to clinical trials, both pharamacological and in the area of gene therapy. 

-Scientific Editor for Molecular Biology and Genetics for Nature Encyclopedia of Life Sciences (2002-2005)

-National Institutes of Health (USA) RFA grant review committee member (1999)

-National Institutes of Health (USA) Fragile X Mental Retardation Centres review panel member (2003)

-MRC Advisory Board Member (2003-2006)

-Specialist Adviser for the European Medicine Evaluation Association for orphan drugs for Fragile X treatment (2003)

-Member of MENCAP panel on the implications of molecular diagnosis for fragile X: submission to the Nuffield Council on Bio-ethics report on genetic testing. (1992)


    BSc (Hons) 2.1 Biochemistry and Molecular Biology. UMIST  1985

    PhD University of Edinburgh (MRC Human Genetics Unit) 1988.

Teaching Interests


-SK195 Human Genetics and Health Issues (Level 1, 10 points)

-SXR376 Molecular Basis of Human Disease: How genetic variation affects susceptibility to HIV infection (Level 3, 15 points, Laboratory based Course)

-S377 Molecular and Cell Biology (Level 3 30 points) 

- SXL288 Practical Science (Biology and Health) (level 2, 30 points)

Research Interests

My post-doctoral research has focused primarily on triplet repeat instability, working on both human Fragile X syndrome and its genetics and Huntington’s disease. In recent years, I have developed a major collaborative study at the Open University examining the expansion of the CAG triplet array that underlies Huntington’s disease. This project is based upon a novel variant of the R6-1 mouse model for HD created by Dr Gill Bates. During routine colony screening, a novel CAG truncation event occurred allowing the isolation of a new line of animals carrying a significantly shorter CAG length and a noticeably later onset of ‘disease’ features, allowing an extended window into some of the early events associated with CAG expansion that can be examined in this model.

Localised CAG expansion in specific regions of the brain and in specific cell populations can now be studied within the context of their neurophysiological status. My laboratory has developed methods to profile expansions in both genomic DNA and mRNA populations, allowing us to identify neuronal populations where the presence of a transgeneic protein with increased number of glutamine residues might drive dysfunction. In particular, we have focussed on the cells in the cortico-striatal axis, where collaborative work with Dr Kerry Murphy's laboratory has identified very early dysfunction in dopaminergic cells that can be reveresed pharmacologically.



Working with Prof Kay Davies (Oxford, 1988-1993) we used novel human DNA markers isolated from a chromosome microdissection library, in combination with YAC and physical mapping, to create the first long range map across the Xq27-28 region; mapping that was at the forefront of the developing technologies of human genome analysis in the late 1980’s and early 1990’s, integrating the use of chromosome microdissection, cell hybrid analysis, YAC screening, PFGE and FISH to first identify DNA markers flanking the Fragile X region and then to clone and identify the mutated region and detect abnormal methylation.

These studies led to the first identification of methylation mutations in fragile X individuals. I undertook an extensive screening of fragile X cohorts and published the first cases of molecular prenatal diagnosis for fragile X syndrome, published in Lancet in 1991. The Oxford FMR1 DNA probes are still used for carrier diagnosis world-wide. Unusual cases requiring detailed molecular investigation arose from collaborative screening programmes and from these I characterised six FMR1 deletions further contributing to our understanding of the disease mechanism. Population studies on a large fragile X cohort with genetic markers established a clear founder effect within European families for fragile X syndrome. We described the first accurate localisation of FRAXE and FRAXF and subsequently cloned the expanded triplets underlying these fragile sites. DNA probes for FRAXE and FRAXF are routinely used in diagnostics. I developed a PCR/sequencing technique which allowed me to analyse in detail the structure of over 100 normal human FMR1 arrays. Population profiling showed that precursor arrays with long stretches of uninterrupted repeats are associated with high risk founder haplotypes. Application of this sequencing technology has also been used in population studies, where we discovered an Asian specific FMR1 allele.

With this knowledge of FMR1 array structure, I developed a cloning system in which I have isolated a range of normal, precursor, premutation and expanded arrays, funded as a personal award from the Wellcome Trust (1993-1999). These form the basis for experiments studying array instability in several model systems including yeast and mouse. Transgenic studies in yeast are one focus of laboratory work and genetic screens have identified one pathway involving the key DNA replication components FEN1 and EXO1 as influencing CGG expansion. The homologous human genes have now been cloned and are being examined by deletion, over-expression and mutagenesis in both yeast and human cells, where we have developed two FEN1 directed ribozymes for gene ablation. Cloned arrays mimicking fragile X expansions are being used in several models systems to study instability and gene silencing, including work using Xenopus oocyte extracts that show the assembly of chromatin around the CGG arrays is influenced by the length of array and it’s methylation status. Work with CGG arrays has proven technically difficult, with analysis of repeat instability limited by the properties of the repeat itself, being refractory to the PCR studies that are really required to answer key questions of how expansion arises and how the cellular and physiological environment in defined groups of cells influences this process.

Current Research


Understanding the relationship between somatic expansion of CAG repeat in the development and progression of Huntington’s disease

We are currently examining the profiles of CAG expansion within defined anatomical and neurophysiological populations of cells with different regions of the HD brain with the aim of relating somatic expansion to cellular dysfunction.

The role of DNA damage, repair and replication in triplet expansion

We are examining the effects of cell-cell differences in various DNA repair pathways upon the rate and extent of expansion of CGG and CAG triplet repeats within populations of cells within the brain an din several cellular model systems.

The effects of CGG expansion upon chromosome biology

We are examining the relationship between CGG repeat structure, replication and recombination.

Mark Hirst
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Mail address Mail address:
Faculty of Science
Walton Hall
Milton Keynes

Telephone Telephone:
ext. 52147
+44 (0)1908 652147

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