Research description

Elsässer's research focuses on how human cells interpret their genetic blueprint to create the right embryonic structures at the right time, for example, during embryonic development. To do this, cells utilize both information from their past and signals from their current environment. Elsässer develops innovative methods and model systems to understand how cells process the diverse available information at the molecular level and thus, for example, determine their long-term differentiation direction. If cells 'forget' their original purpose, this can lead to diseses. Elsässer utilizes a broad spectrum of methods, from genomics and proteomics to synthetic biology, to get to the bottom of these molecular processes in human cells. He works on both fundamental questions and the translation of research findings into clinical applications.

Keywords

synthetic biology, genetic code expansion, epigenetics, epigenomics, stem cells, development, gene expression regulation, proteomics, sORFs, microproteins

Ten Most Important Publications

1. RNA transcripts regulate G-quadruplex landscapes through G-loop formation. Sato K., Lyu J., van den Berg J., Braat D., Cruz V., Navarro C., Schimmel J., Esteban-Jurado C., Alemany M., Dreyer J., Hendrikx A., Mattiroli F., van Oudenaarden A., Tijstermann M., Elsässer S.J., Knipscheer P. Science 2025; 388(6752):1225–1231; doi: 10.1126/science.adr0493, pubmed.ncbi.nlm.nih.gov.

2. Pooled overexpression screen identifies PIPPI as a novel microprotein involved in the ER stress response. Lafranchi L., Spinner A., Hornisch M., Schlesinger S., Navarro C., Brinkenstråhle L., Shao R., Piazza I., Elsässer S.J. Nucleic Acids Research2025; doi: 10.1101/2024.12.08.6274099, mdc-berlin.de.

3. A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function. Schlesinger S., Dirks C., Navarro C., Lafranchi L., Eirich J., Elsässer S.J. iScience2025; 28(3):111884; doi: 10.1016/j.isci.2025.111884, luzeenaraja.research.st.

4. Multiplexed chromatin immunoprecipitation-sequencing for quantitative study of histone modifications and chromatin factors. Kumar B., Navarro C., Yung P.Y.K., Lyu J., Salazar Mantero A., Katsori A.M., Schwämmle H., Martin M., Elsässer S.J. Nature Protocols2024; 20(3):779–809; doi: 10.1038/s41596-024-01058-z, pubmed.ncbi.nlm.nih.gov.

5. Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery. Meineke B., Heimgärtner J., Caridha R., Block M., Kimler K.J., Pires M., Landreh M., Elsässer S.J. Cell Reports Methods2023; 3(11):100626; doi: 10.1016/j.crmeth.2023.100626, pubmed.ncbi.nlm.nih.govpubmed.ncbi.nlm.nih.gov.

6. Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm and mesoderm differentiation. Kumar B., Navarro C., Winblad N., Schell J.P., Zhao C., Weltner J., Baqué-Vidal L., Salazar Mantero A., Petropoulos S., Lanner F., Elsässer S.J. Nature Cell Biology2022; 24(6):845–857; doi: 10.1038/s41556-022-00916-w, pubmed.ncbi.nlm.nih.gov.

7. Genome-wide mapping of G-quadruplex structures with CUT&Tag. Lyu J., Shao R., Yung P.Y.K., Elsässer S.J. Nucleic Acids Research2021; 50(3):e13; doi: 10.1093/nar/gkab1073, academic.oup.com.

8. An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility. Navarro C., Lyu J., Katsori A.M., Caridha R., Elsässer S.J. Nature Communications2020; 11:5095; doi: 10.1038/s41467-020-18863-1, pubmed.ncbi.nlm.nih.govpubmed.ncbi.nlm.nih.gov.

9. Universal single-residue terminal labels for fluorescent live cell imaging of microproteins. Lafranchi L., Schlesinger D., Kimler K.J., Elsässer S.J. Journal of the American Chemical Society2020; 142(47):20080–20087; doi: 10.1021/jacs.0c08239, pubmed.ncbi.nlm.nih.gov.

10. Site-specific incorporation of two noncanonical amino acids for two-color bioorthogonal labeling and chemical-controlled crosslinking of proteins on live mammalian cells. Meineke B., Heimgärtner J., Eirich J., Landreh M., Elsässer S.J. Cell Reports2020; 31(12):107811; doi: 10.1016/j.celrep.2020.107811