Current Research Projects:

Our research group has continued to focus on a number of projects related to Epigenetic dynamics and Genomic instability in the mouse and human genome:

1. Expression and function of endogenous retrotransposons in genomic instability.
With the completion of the human genome-sequencing project, the next major step in understanding genome function is to elucidate the precise molecular steps involved in the regulation of gene expression including long-term gene silencing within a chromatin context. This is crucial to understand the mechanisms that underpin genome instability, and to understand a number of disease states such as cancer and other syndromes involving chromosomal instability. Very little is known however, about the mechanisms by which chromatin structures are remodelled and transmit epigenetic information from one cell generation to the next, to establish stable epigenetic states which are the cell’s memory bank that restricts or permits gene activation. Our research activity over the last few years suggests that silencing histone markers such as H3 K9-3xMe and H2A.Z are enriched at a specific retrotransposon class, LINE L1 (The human genome is composed of 44% retrotransposons, 52% noncoding sequences and < 4% protein-coding sequences.). Our small scale sequencing of ~150 randomly picked ChIP DNA indicated that compared to histone H2A, the majority of H2A.Z clones (~30%) are LINE retrotransposons but not LTR elements. Strikingly, loss of this histone variant by RNAi produced a significant increase in the transcription of retrotransposable L1 elements. Therefore, our hypothesis is that the cell has utilised the ability of silencing histone marks to assemble condensed heterochromatic structures to prevent LINE transcription thus keeping them at bay. Clearly, the loss of LINE silencing would have a disastrous affect on genomic stability. The current research activity will test this novel hypothesis and provide new mechanistic information into the functions and expression of endogenous retroelements in human diseases.
Specific aims being investigated include:
a. Genome-wide organisation of retrotransposons by ChIP-on-ChIP using tiling arrays and elucidating the role of chromatin architecture in silencing retrotransposon activity.
b. Understand the role of RNAi-related machinery (RNAi, co-suppression or quelling) that can act to silence retrotransposons.
c. Investigate the role of chromatin remodelling complexes (SWR1) by siRNAi in activation and silencing of retrotransposition.
This study provides new insight into the role of histone components in silencing retrotransposons within the context of chromatin structure and further corroborates the emerging link between dysfunction of L1 activity and genomic instability in mammalian cells.

2. Genomic catastrophe and retrotransposon reactivation in cancer cell lines.
Maintaining the stability and integrity of the genome is critically essential for an organism’s survival. The molecular mechanisms that underpin genomic stability are, however, poorly understood. Retrotransposable elements, LINE-1, play an essential but undefined function in genome stability in particular cancers. Recently, we initiated a study in cancer cell-lines to discover mechanisms that underpin the role of LINE-1 elements in the context of cancer development. Given that genomic instability and altered expression of retrotransposon activity are intimately associated with many disease states including breast cancer, this research project will shed new light into how disease states arise and how the altered expression of retroelements regulate this process.
Specific aims being investigated include:
a. Role of aberrant histone and DNA methylation in unchecked LINE-1 activity in cancer cells
b. Understand the regulatory role of small RNAs and microRNAs pathways in global and gene-specific activation of LINE-1 elements.
c. Role of unchecked LINE-1 activity in cancer formation and cellular proliferation.
d. Explore the role of histones and DNA methylation machinery in cancer and tumour cell-lines.
e. Defining the link between retrotransposon activity and the genomic stability in cancer cell lines.
Unravelling the relationship between small regulatory RNAi components and DNA methylation in the development of cancers may provide new strategies for future therapeutic and diagnostic approaches.