Phase Separation driven Heterochromatin Formation as a Regulatory Mechanism for Repeat Silencing and Cellular Differentiation

Pericentric heterochromatin in mouse and Drosophila assembles via heterochromatin protein 1 (HP1) in a self-organizing manner into distinct nuclear subcompartments that are called chromocenters. During development chromocenters change their structure and protein compositions in dependence of their protein composition and posttranslational modifications. This process is important for the silencing of transcription from repeat sequences within chromocenters. We are investigating the role of phase separation processes for chromocenter establishment and function to reveal structure-function relationship as well as their changes in dependence of the developmental stage.

About us

The Imhof group studies the proteomic composition of distinct chromatin domains, the mechanisms that operate to maintain the composition of histone modifications and the associated proteins at a given DNA locus. We are interested in the effect of the concentration of key metabolites on the activity of enzymes that establish a specific chromatin structure and investigate how the modification patterns of changes upon physiological challenges such as memory formation or ageing. Our main model system is the fruit fly Drosophila melanogaster. It is also an excellent system to investigate the role of genomic conflict in the formation of species, which is mediated by incompatible chromatin and is another big interest of the lab.


Axel Imhof
Ludwig-Maximilians-Universität München
Zentrallabor für Proteinanalytik (Protein Analysis Unit)
Großhadernerstr. 9 / Raum NC01.043
82152 Planegg-Martinsried
Phone: +49 89 2180 75420



The Rippe lab has a long-standing interest to reveal structure-function relationships of chromatin subcompartments and underlying assembly mechanisms. Within this are of our research we are studying dense heterochromatin foci (chromocenters) involved in silencing of repeat transcription, the nucleolus and RNA polymerase II subcompartments as site of active transcription and complexes of PML nuclear bodies at telomeres. The functional properties of these macromolecular assemblies are dissected by fluorescence microscopy based methods in conjunction with deep sequencing techniques at the single cell level.


Karsten Rippe
Deutsches Krebsforschungszentrum & BioQuant
Division of Chromatin Networks
Phone: +49 6221 54 51376 (office, BioQuant room 645) / +49-6221-54-51372 (lab, BioQuant room 622)




Trojanowski J, Frank L, Rademacher A, Grigaitis P, Rippe K (2021) Transcription activation is enhanced by multivalent interactions independent of liquid-liquid phase separation. bioRxiv: 2021.2001.2027.428421


Lukacs A, Thomae AW, Krueger P, Schauer T, Venkatasubramani AV, Kochanova NY, Aftab W, Choudhury R, Forne I, Imhof A (2021) The Integrity of the Speciation Core Complex is necessary for centromeric binding and reproductive isolation in Drosophila. bioRxiv: 2021.2002.2005.429932


Frank L, Weinmann R, Erdel F, Trojanowski J, Rippe K (2021) Transcriptional activation of heterochromatin by recruitment of dCas9 activators. In Enhancers and Promoters: Methods and Protocols, Borggrefe T, Giaimo BD (eds), in press. New York: Springer Nature


Kochanova NY, Schauer T, Mathias GP, Lukacs A, Schmidt A, Flatley A, Schepers A, Thomae AW, Imhof A (2020) A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation. Nucleic Acids Res 48: 4161-4178


Frank L, Rippe K (2020) Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 432: 4270-4286


Erdel F, Rademacher A, Vlijm R, Tunnermann J, Frank L, Weinmann R, Schweigert E, Yserentant K, Hummert J, Bauer C, Schumacher S, Al Alwash A, Normand C, Herten DP, Engelhardt J, Rippe K (2020) Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation. Mol Cell 78: 236-249 e237