Dr. Gerhard Mittler
Our research facility is specialized in functional proteomics, which is concerned with correlating physiological changes at the cellular level with alterations in protein composition and protein modifications as a major discovery and hypothesis generating tool. To pursue this we employ metabolic labeling using stable isotopes (SILAC) in order to not only achieve a comprehensive qualitative but also a quantitative description of subproteomes using state-of-the-art nanoLC-MS technology. We have been successfully studying rather complex proteomes, like subcellular structures (e.g. nuclear matrix) and interactomes (Cdk9 interactome). In addition we are especially interested in the characterization of macromolecular complexes (DNA/RNA-protein and protein-protein complexes), which can be isolated by means of classical biochemical purification methodologies.
Biologically, we have a long term interest in studying metazoan gene regulation in the context of transcription factors and epigenetics (e.g. protein methylation) [1, 2]. To further our understanding of the gene regulatory code we have pioneered a quantitative proteomics approach termed SILAC DNA-protein interaction screening  that is complementary to the classical chromatin immunoprecipitation (ChIP) method since our technology reveals proteins that are able to specifically interact with any cis-regulatory element of interest. Studying a novel evolutionary highly conserved core promoter-associated cis-element termed M4 , we could recently demonstrate that our methodology has the capacity to uncover novel biologically important and physiologically relevant TF DNA interactions.
We are now in the process of streamlining the technology for higher sensitivity, stringency and efficiency. We have also started to transfer the technology to living cells to reach our final goal of establishing a bona fide ‘reversed ChIP’  approach.
 Mittler, G. et al., 2009. Genome Res. 19, 284-293
 Ong, S.E. et al., 2004, Nat. Methods 1, 119-126
 Xie, X. et al., 2005, Nature 434, 338-345
 Rusk, N., 2009. Nat. Methods 6, 187
10 selected publications:
- Ubc9 Sumoylation controls SUMO chain formation and meiotic synapsis in Saccharomyces cerevisiae.
Klug, H., Xaver, M., Chaugule, V.K., Koidl, S., Mittler, G., Klein, F., Pichler, A. (2013)
Mol. Cell 50, 625-636
- Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer.
Tropberger, P., Pott, S., Keller, C., Kamieniarz-Gdula, K., Caron, M., Richter, F., Li, G., Mittler, G., Liu, E.T., Bühler, M., Margueron, R., Schneider, R. (2013)
Cell 152, 859-872
- RNA helicase DDX5 and the noncoding RNA SRA act as coactivators in the Notch signaling pathway.
Jung, C., Mittler, G., Oswald, F., Borggrefe, T. (2013)
Biochim. Biophys. Acta 1833, 1180-1189
- The Prdm3 and Prdm16 H3K9me1 methyltransferases initiate and maintain mammalian heterochromatin organization.
Pinheiro, I., Margueron, R., Eisold, M., Fritzsch, C., Shukeir, N., Richter, F.M., Mittler, G., Genoud, C., Son, J., Reinberg, D., Lachner, M., Jenuwein, T. (2012)
Cell 150, 948-960
- Methylation of H2AR29 is a novel repressive PRMT6 target.
Waldmann, T., Izzo, A., Kamieniarz, K., Richter, F., Vogler, C., Sarg, B., Lindner, H., Young, N.L., Mittler, G., Garcia, B.A., Schneider, R. (2011)
Epigenetics Chromatin 4:11
- Mzb1 (pERp1) regulates calcium homeostasis, antibody secretion and integrin activation in innate-like B cells.
Flach H, Rosenbaum M, Duchniewicz M, Kim S, Zhang SL, Cahalan MD, Mittler G, Grosschedl R (2010).
Immunity, 33, 723-725.
- Histone demethylase KDM5A is an integral part of the core Notch-RBP-J repressor complex.
Liefke R, Oswald F, Alvarado C, Ferres-Marco D, Mittler G, Rodriguez P, Dominguez, M., Borggrefe, T. (2010).
Genes Dev 24, 590-601.
- A SILAC-based DNA-protein interaction screen that identifies candidate binding proteins to functional DNA elements.
Mittler G, Butter F, Mann M (2009).
Genome Res. 19, 284-293
- Identifying and quantifying in vivo methylation sites by heavy methyl SILAC.
Ong SE, Mittler G*, Mann M* (2004).
Nature Methods 1, 119-126 (* shared corresponding authors).
- VaCID a novel protein that is critical for the activity of the Herpes simplex virus transactivator VP16 functions through the recruitment of human Mediator.
Mittler G, Stühler T, Santolin L, Uhlmann T, Kremmer E, Lottspeich F, Berti L, Meisterernst M (2003).
EMBO Journal 22, 6494-6504.