Nuclear envelope transmembrane protein regulation of tissuespecific genome organisation in differentiation and disease
Mutations in widely expressed nuclear envelope (NE) proteins cause many distinct diseases with tissue-specific pathologies including muscular dystrophies, lipodystrophies, neuropathy, dermopathy, and premature-aging syndromes. This raised the question: how could mutations in the same ubiquitous protein cause distinct diseases affecting different tissues? Hypothesizing that tissue-specific partners mediate the tissue-specific pathologies, we identified candidate partners with proteomics. The NE connects on the inside to chromatin and genome organisation is disrupted in patient cells. If our hypothesis is correct, it follows that these tissue-specific NETs might direct tissue-specific patterns of genome organisation with consequences for gene expression and we have found this to be the case.
We found three muscle-specific NETs that re-position genes to the NE that are needed early in myogenesis, but subsequently become inhibitory and must be tightly shut down. Their combined knockdown blocks myogenesis. Thus, NE gene recruitment enables tighter regulatory control. Importantly, we found mutations in these muscle NETs in unlinked Emery-Dreifuss muscular dystrophy patients, further arguing the importance of this novel regulatory mechanism. We have found similar effects with a fat-specific NET in adipogenesis and found that mice lacking this protein have difficulty producing fat, become insensitive to insulin, have metabolic dysfunction and a general lipodystrophy phenotype (Fig. 1).
It appears that NE connections can also influence gene activities in the nuclear interior as during lymphocyte activation we found that released genes that were flanked by unchanging NE-associated regions remained within <0.8 µm from the NE, presumably because the flanking contacts restrict their diffusion and thus promote their association in chromosome compartments in what we call the "constrained diffusion" hypothesis. We showed that several genes and an enhancer up to 14 Mb away from one another are all released upon lymphocyte activation and associate in A2 sub-compartments. This type of regulation could contribute temporal control to lymphocyte activation.
Other lines of investigation include: 1) Studying the structure of intermediate filament lamins with the Rappsilber lab. 2) Investigating NET effects on nuclear size changes in several cancer types and screening for small molecules targeting this with the Auer and Tyers labs. Nuclear size changes mark increased disease severity and this is also tissue- specific. 3) Testing how another NET contributes to signaling of innate immune responses. 4) Investigating how herpesviruses escape through the NE, finding that vesicle fusion proteins in the NE are needed for efficient virus nuclear egress.
Robson, M.I., de las Heras, J.I., Czapiewski, R., Sivakumar, A., Kerr, A.R.W., and Schirmer, E.C. (2017). Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res 27, 1126-1138.
de las Heras, J.I., Zuleger, N., Batrakou, D.G., Czapiewski, R., Kerr, A.R.W. and Schirmer, E.C. (2017). Tissue-specific NETs alter genome organization and regulation even in a heterologous system. Nucleus 8, 81-97.
Robson, M.I., de las Heras, J.I., Czapiewski, R., Le Thanh, P., Booth, D.G., Kelly, D.A., Webb, S., Kerr, A.R.W., and Schirmer, E.C. (2016). Tissue-specific gene repositioning by muscle nuclear membrane proteins enhances repression of critical developmental genes during myogenesis. Mol. Cell 62, 834-847.