Design and Function of Transcription Factors in the Chromatin Environment
In collaboration with Dr. Andrew Flaus, at the NUI Galway Chromosome Biology Group
Nucleosomes are the fundamental organising units of eukaryotic genomes. They control the packaging of DNA as chromatin and play keys role in transcription, replication and repair. The importance of the nucleosomal compaction to the function of the cell nucleus has stimulated a revolution in our understanding of cancer and many genetic diseases.
Nucleosome organisation in fungi, plants and animals, including the human genome, can be mapped by isolating nucleosomes then reading out the associated DNA sequences (.ChIP-chip. and .ChIP-seq.). In some parts of genomes it is observed that packaging into nucleosomes appears to be almost random whereas in other regions, such as upstream and downstream of certain genes, tightly positioned nucleosomes and nucleosome-free regions are critical for the control of transcription. High resolution maps of nucleosome positions have enabled investigation of the role nucleosomes play in controlling access to DNA by transcription factors. Conserved binding sites for transcription factors in yeast tend to be clustered towards the borders of nucleosomes facing away from the packaged surface.
We wish to characterise the quantitative relationship between nucleosome positioning, transcription factor binding sites, and the rate of transcription. In the first instance, the project will use public nucleosome map data for the yeast and human genomes to determine the positional distribution of transcription factor binding sites with respect to well mapped nucleosomes. This will be correlated with the rate of initiation of transcription using public gene expression data. Our hypothesis is that binding sites for different transcription factors have distinct positional preferences relative to the nucleosome and that nucleosome maps can therefore enhance the identification of functional transcription factor binding sites.
Subsequently, the project will focus on the links between nucleosome positioning and binding sites for zinc finger transcription factors (ZnTFs). Methods are now available to efficiently design site-specific ZnTFs and these have been proposed as novel agents for controlling transcription. Novel datasets of nucleosome positioning around engineered ZnTF binding sites will therefore be collected and analysed in detail. This has the potential to enhance the design of functional synthetic transcription factors and these have many applications in biotechnology and biomedicine.
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