Tissue-specific nuclear envelope transmembrane protein (NET) functions in spatial genome organisation, importance in development, and disruption in human disease

The nuclear envelope is linked to over 30 inherited diseases; however, these diseases present a conundrum because the genes mutated encode widely expressed nuclear envelope proteins, yet each generates a distinct tissue-specific pathology. The Schirmer lab proposed the hypothesis that tissue-specific partner nuclear envelope transmembrane proteins (NETs) direct the tissue-specificity of the pathologies. As the primary predicted mechanisms for pathology are disruption of mechanical stability and altered gene regulation, we performed screens for tissue-specific NETs that affect these processes, finding 12 affecting cytoskeletal organization and 11 affecting spatial genome organization or chromatin compaction and gene expression in muscle, fat, blood and liver systems. A PhD project would take a NET and perform a detailed characterization to elucidate the molecular mechanism underlying its effects. The lab is most interested in certain fat, muscle and blood NETs for which we already have DamID and Hi-C data for their effects on genome organisation and mouse models. The student will engage genome editing approaches to isolate and control particular genes independent of the NETs to determine how mechanistically their gene-tethering function affects gene expression. We found evidence for a "constrained diffusion" mechanism whereby not only do these tissue-specific NETs directly recruit genes to the periphery to better shut them down, but tethering of upstream and downstream genome regions can restrict the space a gene can sample in the nucleus to increase the probability of interactions with similarly constrained superenhancers. The student would develop skills for any of these projects in fluorescence in situ hybridisation (FISH), DamID, chromosome conformation capture (e.g. Hi-C) approaches, ChIP, RNA-Seq, super-resolution microscopy, and very likely mouse models. The lab has identified possible disease links for some of these NETs and thus candidate point mutations may also be tested to determine overall effects on muscle and fat physiology. The lab also has three other projects a student could join. 1) Tissue-specific NET regulation of nuclear size changes characteristic of particular tissue tumour types when they become more metastatic. This would involve studying the mechanism of nuclear size regulation and testing drugs a previous student found in a chemical library screen that can correct the nuclear size defects with a corresponding reduction in cell migration. 2) Herpesvirus egress through the nuclear envelope that requires not just lamin polymer disassembly, but also potentially NET involvement. Here a previous student found several vesicle fusion proteins in the nuclear envelope that when knocked down prevent virus particles from exiting the nucleus and one student is currently working out the mechanism for just one of several identified. 3) Biophysical characteristics of the nuclear lamin intermediate filament proteins that give them far greater tensile properties than other filament systems. Here a previous student used cross-linking mass spectrometry to find that intrinsically disordered linker regions in the lamin coiled coil use electrostatic interactions to fold individual coils over one another to shorten the lamin rod like a default unstretched spring that can then stretch by breaking these interactions under tension.

The Schirmer laboratory is located in the Wellcome Centre for Cell Biology in the Michael Swann building on the Kings Buildings Campus. e-mail: [Email Address Removed], Website: http://www.wcb.ed.ac.uk/research/schirmer