Nuclear structure and gene expression

We are studying structure/function relationships in mammalian cell nuclei, focussed on mechanisms of RNA processing, including alternative splicing of mRNA precursors and pre-rRNA processing in the nucleolus. Our major aim is to characterise the composition and function of subnuclear organelles and multiprotein complexes and to identify mechanisms regulating their assembly and turnover, particularly in human cells. The importance of understanding nuclear organisation is underlined by evidence showing that multiple human diseases, including inherited genetic disorders, malignancies and viral infections, modify or disrupt subnuclear bodies. Our studies employ a combination of quantitative techniques, including mass-spectrometry-based proteomics, fluorescence and electron microscopy and deep sequencing.

 
We are also taking a chemical biology approach to study RNA processing and nuclear organisation, involving our characterisation of novel small molecule modulators that affect RNA processing mechanisms and/or modify the structure and composition of subnuclear bodies. We have identified these chemical tools by screening libraries of drug-like small molecules, in collaboration with David Gray and colleagues in the SLS Drug Discovery Unit and have already identified protein targets for several of these small molecules. Work is underway to identify additional protein targets for our collection of novel small molecule modulators.

Another theme of our research is using quantitative, mass spectrometry-based proteomics to study stem cell biology. We have characterised protein expression across hundreds of independent iPSC lines derived from both healthy donors and from disease cohorts, which were generated in the HipSci consortium. Together with our collaborators we have linked protein expression levels with both genomic and transcriptome data from the same cell lines and mapped protein and peptide QTLs. We have identified that loss of X chromosome inactivation in iPSC lines derived from healthy female donors correlates strongly with loss of Xist RNA expression and discovered that this affects protein expression from many autosomal loci, as well as resulting in increased expression of both RNA and protein from genes on the reactivated X chromosome. We are continuing our studies on iPSC lines to determine how proteome expression varies between individuals across the human population and how this impacts on cell phenotypes, responses and disease mechanisms.