Epigenetics and Chromatin Biology Laboratory

Group Leader: Dr. Stephen Rea

Research interests

• Epigenetic regulation of gene expression.
• Histone modifications in normal development and disease.

The human genome comprises an estimated 20-25,000 genes which generate around 200 different cell types. These cells differ greatly in their structure and function yet the genetic material in each is identical. This remarkable diversity is made possible largely through the action of epigenetic mechanisms. These mechanisms act above the level of DNA, precisely controlling gene expression patterns and hence dictating the proper development of an organism. Various epigenetic mechanisms are now recognized and include; modification of the DNA, modifications of histone proteins and incorporation of histone variants.

Our Lab is particularly interested in histone acetylation. This is a reversible modification which is controlled by enzymes: histone acetyl-transferases (HATs), which add acetyl groups to proteins and histone de-acetylases (HDACs), which remove them. Histone acetylation is generally regarded as a transcriptional activating modification. However, it has also been associated with gene repression, DNA repair, DNA replication, and recombination. Considering the involvement of histone acetylation in such fundamental processes, it is not surprising that disruption of the normal acetylation status has been implicated in cancer.

To better understand epigenetic mechanisms, in particular, the role of histone acetylation in the regulation of gene expression, we are studying the human MOF complex. hMOF is a HAT that is responsible for the acetylation of histone H4 at lysine 16. In the fruitfly, Drosophila melanogaster, this H4K16Ac mediated by dMOF correlates with a two-fold upregulation of transcription required for dosage compensation. The purification of MOF-interacting proteins in both the fruitfly and human cells revealed a number of conserved interacting proteins, suggesting that the function of these complexes is maintained through evolution. More recently, it was found that loss of hMOF and also reduction in H4K16 acetylation levels are frequent occurrences in various human cancers. Thus, studying hMOF and H4K16Ac allows us to investigate the involvement of this particular modification in the development of an important human disease.

hMOF is responsible for bulk H4K16Ac. Cells where hMOF has been depleted, using specific siRNAs, display a major decrease in the level of H4K16 acetylation. In addition to other phenotypes (not shown), this causes an as-yet unexplained nuclear morphological defect-polylobulation. From Taipale, M. et al., (2005): Mol Cell Biol 25, 6798-6810.

Goals of Research

The main aims of our group are to understand how hMOF regulates gene expression and to determine the functional significance of hMOF in tumour progression.

Schematic depiction of the potential roles of hMOF in the cell. Acetylation of histone H4 at K16 by hMOF could: (A) facilitate a decrease in either the affinity of histones for DNA or in inter-nucleosomal interactions thus opening up the chromatin structure. (B) act as a binding site for specific proteins that can further modify chromatin, such as transcriptional coactivators or DNA repair proteins. (C) inhibit binding of specific factors such as transcriptional repressive complexes. (D) hMOF could modify a protein(s) important for nuclear stability. This target could be either a  nuclear pore or a nuclear membrane associated protein. Following DNA damage: (E) hMOF can activate ATM, one of the cell’s main repair pathways. The mechanism for this activation is unknown but may involve increased acetylation around the sites of damage. (F) the tumor suppressor p53 can be acetylated by hMOF resulting in a decision favouring programmed cell death as opposed to cell cycle arrest. Adapted from Rea, S., Xouri, G., Akhtar, A., (2007) Oncogene 26 (37), 5385-94.

• hMOF and gene expression

In Drosophila H4K16 acetylation mediated by dMOF, as part of the MSL complex, was shown to correlate with increased transcription. Depletion of hMOF in human cells has also been shown to affect the expression level of certain genes. However, the exact role of hMOF and H4K16Ac in transcriptional regulation and the mechanism behind this regulation in mammals is not clear. We plan to take in vitro and in vivo approaches to: 1) Determine whether hMOF regulates transcription. 2) Elucidate how hMOF regulates transcription. 3) Explain how hMOF HAT activity is regulated

• hMOF in tumour progression

It is now widely accepted that cancer is both a genetic and an epigenetic disease. Perturbations in epigenetic mechanisms such as DNA methylation, histone modifications and chromatin remodeling have been implicated in tumorigenesis. It has recently been shown that both hMOF and H4K16 acetylation levels are frequently reduced in various cancers. However, at the moment, it is unclear whether this loss is a cause or consequence of cell transformation. A second project in the lab will address whether loss of hMOF/H4K16 acetylation plays a functional role in the path to tumorigenesis. We also hope to evaluate the feasibility of hMOF as a biomarker or therapeutic target in various cancers.

hMOF expression and H4K16 acetylation in normal tissue and breast carcinoma. Immunohistological analysis shows that hMOF is highly expressed in most healthy tissues and that this correlates with H4K16 acetylation status (brown staining). hMOF expression is frequently lost/reduced in many tumors (breast carcinoma 18%, fig-bottom left; medulloblastoma 40%) and this reduction correlates with a decrease in H4K16 acetylation. Adapted from Pfister, S., et al., (2007) Int J Can 122, 1207-1213.

Group members

Jennifer Chubb, Ph.D.

I attended Trinity College Dublin, from 1998 until 2002 where I obtained a BA (mod) honours degree in Genetics. Following this I undertook a four year Wellcome Trust funded PhD in the cellular and molecular basis of disease at the University of Edinburgh. After my first year I graduated with a M.Sc. degree in the Life Sciences which led on to my three year PhD project in the area of psychiatric genetics. My PhD research involved characterization of two schizophrenia candidate genes disrupted by a balanced chromosomal translocation in a large Scottish family. I completed my PhD in 2007 and subsequently joined the Centre for Chromosome Biology at NUI Galway to continue my research into the cellular and molecular basis of complex illnesses.

My postdoctoral research will investigate the role of the histone acetyltransferase, hMOF, in tumorigenesis using mammalian primary and established cell lines as a model system.

Sandra Clasen, M.Sc.

I joined Dr Rea’s new group in April 2008 as a PhD student. Originally from Germany, I graduated with a Bachelor of Science from both, the FH Bonn-Rhein-Sieg, Germany and the Murdoch University in Perth, Australia in 2006. Immediately after, I started an M.Sc. in Biomolecular Science at the VU Amsterdam. During my Master studies I completed two epigenetics-related research projects in Amsterdam (with Dr. Kooter) and at the MRC Clinical Science Centre in London (with Prof. Festenstein).

My research interest is the epigenetic regulation of gene expression, especially by the modifications of histones. During my PhD I will characterize the functions of the human MOF enzyme in the regulation of gene expression.

Funding

Work in the lab is funded by a President of Ireland Young Researcher Award from Science Foundation Ireland.  

Positions available

Openings for postdoctoral fellows & PhD students with relevant interests/ experience in epigenetics/chromatin and cancer biology arise sporadically. Please contact Stephen Rea by email: stephen.reanuigalway.ie for further details.

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