The effect on genome behaviour of growing cells in 3D matricies

There has been a small amount of evidence in the literature that growing cells in 3D scaffolds instead of 2D monolayers alters genome behaviour and organisation such that nuclear structure is altered and consequently chromosome behaviour. Understanding such changes i.e. chromosome and gene position, nuclear structure organisation and function, chromatin movement and chromatin modification (epigenome) will provide greatly needed data to the cell biology field on whether to change their cell culture habits.

The project will involve growing young and aged cells in different 3D matricies to ask whether chromosome and gene position is altered, is the epigenome and the transcriptome affected and what happens to nuclear structures that anchor and influence chromosomes such as nucleoli, nuclear lamins, the LINC complex, the nucleoskeleton and how genes and chromosomes are moved after external stimuli such as changes to temperature and availability of nutrients. A range of techniques will be used such as super-resolution bioimaging, real-time imaging, fluorescence in situ hybridisation, real-time PCR, chromatin immuno-precipitation and sequencing.

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