Nuclear matrix support of DNA replication and transcription

Background Visualization of the structure of nuclei has been the main method of cancer diagnosis since light microscopy allowed. However, very little is known about the underlying molecular alterations that give rise to aberrant nuclear architecture, or the effect these have on the organisation of nuclear processes. The epigenetic information inherent in nuclear organisation is also likely to be relevant to our understanding of nuclear decay during aging, and the onset of senescence.

Objectives Some proteins that are involved in the regulation of DNA replication are immobilized by attachment to the nuclear matrix in normal cells, but not in cancer cells (or in undifferentiated cells). This project will ask whether the same is true for proteins that regulate transcription, in order to test the extent to which published observations can be generalized beyond DNA replication. This will be important to test further the idea that part of the process of differentiation is to fix processes of DNA metabolism in nuclear space to enable pattern formation.

It will also look in detail at the CIZ1 protein to identify the proteins that it normally binds to in the nuclear matrix. Unlike the cytoskeleton, there is currently no consensus on the main protein components of the nuclear matrix.

Novelty and Timeliness CIZ1 has been implicated in several common human cancer types, as well as chronic age-related disorders, and is being developed as the basis for a blood test for cancer. Its interaction partners are likely to offer similar opportunities for exploitation either as markers of nuclear integrity (for application in regenerative medicine strategies or analysis of cancer cells), and might offer new opportunities for therapeutic drug targets. There are very few molecules that can be used for function-related studies of the nuclear matrix making this work both novel and timely.

The project combines mammalian cell biology with analytical biochemistry, and combines supervisors with related but complementary expertise in the two core process of DNA replication and transcription. Extensive evidence shows that the organization of DNA replication is intrinsically linked to template usage, making this collaboration one that could yield new insight into the mechanistic relevance of the nuclear matrix. The project will involve mammalian cell culture and synchrony techniques, sub-cellular fractionation and stability assays to isolate nuclear matrix fractions using a range of techniques, fluorescence microscopy and protein interaction studies, including 2D-LC-MS to identify new components of the nuclear matrix.

This is an excellent opportunity for a student to work across the cell biology/biochemistry interface on a potentially high impact project. The student will attend lab meetings in both labs as appropriate, and will therefore gain experience in presenting their work to audiences with different expertise/interests. There will also be joint lab meetings between the two groups, which are likely to trigger further collaborations and opportunities. Such approaches are becoming the norm and it is essential that early career scientists gain experience in this new way of working.