Eric Schirmer

Lab members

Avik Basu, Rafal Czapiewski, Charles Dixon, Jose de las Heras, Alexandr Makarov, Andrea Rizzotto, Aishwarya Sivakumar, Sylvain Tollis

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Nuclear envelope transmembrane protein regulation of tissuespecific genome organisation in differentiation and disease

Nuclear envelope transmembrane protein regulation of tissue- specific genome organisation in differentiation and disease 

Mutations in nuclear envelope (NE) proteins cause many diseases with tissue-specific pathologies including muscular dystrophies, lipodystrophies, neuropathy, dermopathy, and premature-aging syndromes. This presented a conundrum because mutations in the same widely expressed protein yielded distinct tissue-specific pathologies. We postulated that tissue-specific partners mediate pathology and identified candidate partners with proteomics. Strikingly, the majority of NE transmembrane proteins (NETs) are tissue-specific. The double membrane NE connects on the inside to chromatin and bulk chromatin organisation is disrupted in patient cells. Interestingly, screening these tissue-specific NETs identified several with functions in spatial genome organisation, perhaps explaining the NE-linked  diseases.

The laboratory is focused on understanding how tissue-specific NETs direct genome organisation and its consequences for gene regulation. We study the role of NETs in adipogenesis, myogenesis, liver and lymphocyte activation, finding for example that three muscle NETs that re-position genes during myogenesis together affect 37% of all myogenic genes. Their combined knockdown blocks myogenesis. These NETs direct genes to the NE that are needed early in differentiation, but subsequently become inhibitory and must be tightly shut down. 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 also investigated gene release from the NE, using DamID and Hi-C datasets to model our "constrained diffusion" hypothesis. Released genes that were flanked by unchanging NE- associated regions remained within <0.8 ?m from the NE, presumably because the flanking contacts restrict their diffusion. We showed that several genes and an enhancer up to 14Mb 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. 3) Testing the mechanism for another NET
that directs the nucleo-cytoplasmic redistribution of partners that activate innate immune responses. 4) investigating the interaction of herpesviruses with the NE, predicting that NET interactions will be crucial to this poorly studied phase of the virus life cycle.

Selected publications:

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(1), 81-97. PMID: 28045568

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(6), 834-847. PMID: 27264872

Czapiewski, R., Robson, M. I., and Schirmer, E. C. (2016) Anchoring a leviathan: how the nuclear membrane tethers the genome. Front. Genet. 7:82, doi: 10.3389/fgene.2016.00082. PMID: 27200088