The mechanism of DNA organisation mediated by cohesion and condensin

The DNA of all organisms must be compacted in order to store a large amount of genetic information in one cell. Compaction must be regulated to allow access of DNA replication or transcription machinery, but to enable suitable condensation for effective chromosome segregation into two daughter cells at mitosis. Defects in this process will impair genome integrity, which reduces cell viability and contributes to causing cancer. This study will investigate the mechanism of DNA condensation in Saccharomyces cerevisiae, a model organism providing powerful tools for genetic, biochemical, and cell biological analyses of conserved biological functions.

In S. cerevisiae, the repetitive ribosomal DNA array is highly condensed and has been a popular model for DNA condensation studies. Two related protein complexes, cohesin and condensin, are key players in the rDNA condensation. However, how cohesin and condensin organise the condensed DNA structures remains enigmatic.

The rDNA condensation mechanism involves interaction of the rDNA repeats within a single chromosome. A major challenge in DNA condensation research has been lack of techniques to study such intra-DNA interactions. To overcome this problem, we have constructed a novel yeast genetic system that uses a recombination system to convert the tandem repeats of rDNA into individual DNA circles. Interestingly, the majority of resulting rDNA circles exist in high molecular weight complexes consisting of 10-14 circularised rDNA molecule, reflecting that individual circularised rDNA molecules still remain biochemically condensed. The aim of this project is to examine how condensin and cohesin mediate interactions between experimentally generated rDNA circles, providing novel insights into the mechanism of DNA condensation. The student will take a three-part approach:-

1. Examine aggregation of rDNA circles generated from cells with different condensation status.
The rDNA condensation is tightly cell-cycle regulated, with chromosomes being less condensed in G1-phase and more condensed in G2/M-phase. The rDNA circles will be isolated from cells arrested in difference cell cycle stages and their aggregation examined, validating the biological information provided by the assay.

2. Examine roles of cohesin and condensin on establishment of circularised rDNA aggregation.
Since we know that cohesin and condensin regulate and maintain condensed rDNA morphology-loop structure in G2 cells, we expect these complexes are also required for aggregation of rDNA circles. We will test the effect of inactivating cohesin or condensin in vivo on the circularised rDNA aggregates.

3. Determine if cohesin and/or condensin are the protein linkers that hold circularised rDNA together.
We will test the important of condensin and cohesion by degrading them in vitro and examining disassembly of rDNA circle aggregates. Examining disassembly of circularised rDNAs complex upon in vitro cleavage of cohesin/condensin will reveal which complex holds rDNA repeats together in vivo.

This project exploits a pioneering approach to look at the important question of how cells achieve regulated chromosome condensation, investigating the role of the cohesion and condensin complexes that are conserved throughout eukaryotes. As a member of a new research team the student will benefit from individual attention, but also from the support of an extended group of laboratories at the Institute of Medical Sciences with considerable expertise in studying chromosome maintenance using yeast molecular genetics.

APPLICATION PROCEDURE:
This project is advertised in relation to the research areas of MEDICAL SCIENCES. Formal applications can be completed online: https://www.abdn.ac.uk/pgap/login.php. You should apply for Degree of Doctor of Philosophy in Medical Sciences, to ensure that your application is passed to the correct person for processing.

NOTE CLEARLY THE NAME OF THE SUPERVISOR AND EXACT PROJECT TITLE ON THE APPLICATION FORM. Applicants are limited to applying for a maximum of 3 applications for funded projects. Any further applications received will be automatically withdrawn.