Simon Elsässer

Dr. Simon Elsässer

Simon Elsässer is an Associate Professor at the department of Medical Biochemistry and Biophysics, Karolinska Institutet. He has been studying epigenetic gene regulation in embryonic stem cells during his doctoral and postdoctoral work. He has more recently developed novel synthetic biology tools for elucidating the function of proteins inside of living cells and is now establishing a research focus on the small proteome. Short peptides encoded by short open reading frames (sPEPs) are translated abundantly in prokaryotic and eukarytic cells, yet their functions remain mysterious. While examples of such peptides performing essential functions in human tissues are known for over a decade, the breadth and universal relevance of peptides encoded in short open reading frames is only beginning to be explored. Exemplary studies suggest that sPEPs provide a means of intracellular signalling as well as communication between cells within a tissue or between organs in a living animal. Understanding the function of sPEPs may bolster our ability to orchestrate cellular reprogramming or organ development as they could be easily mimicked in vitro. Simon’s research will focus on elucidating the interactomes and functions of sPEPs with respect to their role in intra- and inter-tissue communication. Translational aspects of his research aim to identify new biomarkers, drug targets or blueprints for novel drugs in the small proteome. Through the Ming Wai Lau Center collaborative research environment, Simon aims to elucidate the role of sPEPs in stem cell biology and lineage specification.

Selected Publications

Chromatin Biology

Navarro, C., Lyu, J., Katsori, A.-M., Caridha, R., & Elsässer, S. J. (2020). An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility. Nature Communications, 11(1), 5095.

Kumar, B., & Elsässer, S. (2019). Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells. Cell Reports.

Elsässer, S. J., Ernst, R. J., Walker, O. S., & Chin, J. W. (2016). Genetic code expansion in stable cell lines enables encoded chromatin modification. Nature Methods, 13(2), 158–164.

Elsässer, S. J., Noh, K. M., Diaz, N., Allis, C. D., & Banaszynski, L. A. (2015). Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature.


Lafranchi, L., Schlesinger, D., Kimler, K. J., & Elsässer, S. J. (2020). Universal Single-Residue Terminal Labels for Fluorescent Live Cell Imaging of Microproteins. Journal of the American Chemical Society, jacs.0c09574.

Synthetic Biology

Meineke, B., Heimgärtner, J., Eirich, J., Landreh, M., & Elsässer, S. J. (2020). Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells. Cell Reports, 31(12), 107811.

van Husen, L. S., Schedin-Weiss, S., Trung, M. N., Kazmi, M. A., Winblad, B., Sakmar, T. P., Elsässer, S. J., & Tjernberg, L. O. (2019). Dual Bioorthogonal Labeling of the Amyloid-β Protein Precursor Facilitates Simultaneous Visualization of the Protein and Its Cleavage Products. Journal of Alzheimer’s Disease, 72(2), 537–548.

Elsässer, S. J. (2018). Generation of Stable Amber Suppression Cell Lines. In Methods in Molecular Biology (pp. 237–245).

Meineke, B., Heimgärtner, J., Lafranchi, L., & Elsässer, S. J. (2018). Methanomethylophilus alvus Mx1201 Provides Basis for Mutual Orthogonal Pyrrolysyl tRNA/Aminoacyl-tRNA Synthetase Pairs in Mammalian Cells. ACS Chemical Biology, 13(11), 3087–3096.

Science Policy

Pesic, M., Egamberdieva, D., Kolodziejczyk, B., Elsässer, S. J., Neergheen, V. S., & Kagansky, A. (2020). Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being. Biologia Futura.

Neergheen-Bhujun, V., Awan, A. T., Baran, Y., Bunnefeld, N., Chan, K., dela Cruz, T. E., Egamberdieva, D., Elsässer, S., Johnson, M. V., Komai, S., Konevega, A. L., Malone, J. H., Mason, P., Nguon, R., Piper, R., Shrestha, U. B., Pešić, M., & Kagansky, A. (2017). Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action. Journal of Global Health, 7(2).