Wellcome Trust PhD Programme for Clinicians at the University of Oxford: 'Investigation of the mechanism of chromatin looping between HS-40 and the alpha globin promoter in the humanised mouse model'. (360G-Wellcome-090188_Z_09_Z)

The control of mammalian gene expression in increasingly thought to depend on long-range interaction between distal regulatory elements and promoters. The mechanisms of such physical interactions are not understood, but two hypotheses exist. The first suggests that protein/DNA complexes at cis-regulatory elements are diffusible, with resulting random collision. Specific protein interactions may then allow the formation of stabilised chromatin loops. The second model proposes that a protein/DNA complex formed at one element may ?track? along a chromosome until it encounters a protein complex at its target element, with resulting chromatin looping. This project tests these hypotheses at the alpha globin locus, using recombineering in a humanised mouse model. We will alter the position of the major regulatory element HS-40 relative to upstream and downstream inserted promoters, driving reporter genes, to define the potential polarity of the interaction between the regulatory element and its promoter. If tracking occurs equally efficiently in both directions, of two identical promoters placed at a similar distance from the regulatory element the more proximal promoter should be preferentially transcribed, distinguishing this from the diffusion model. The project has fundamental implications for our understanding of how promoters are selected in a tissueand developmental stage-specific manner and of how the timing of gene expression is regulated.