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Chromatin Networks

Prof. Dr. Karsten Rippe

The Chromatin Networks Group works towards merging biology and biophysics to quantify dynamic genome organization's links to gene expression and cell states.
Our interdisciplinary research team studies nuclear organization, phase separation, cytokine-driven epigenetics, aberrant cancer gene expression, and telomere maintenance and combines molecular and cell biology and biophysics to develop quantitative descriptions that relate the dynamic organization of the epigenome with gene expression programs and functional cell states. Our main research areas comprise nuclear organization, transcription regulation, tumor heterogeneity, and telomere maintenance in cancer. Approaches encompass quantitative microscopy, single-cell omics, chromatin editing, and biophysical modeling for comprehensive biomedical insights.

Research Strategy

The Division of Chromatin Networks is an interdisciplinary research team that combines molecular/cell biology and biophysics to develop quantitative descriptions that relate the dynamic organization of the (epi)genome with gene expression programs and functional cell states. Our main research areas comprise nuclear organization with a focus on the contribution of phase separation mechanisms, epigenetic regulation in response to external cytokine stimuli as well as deregulated gene expression and telomere maintenance in cancer. To address the associated biomedical questions, we apply a set of complementary methods that center around: 

  1. Quantitative fluorescence microscopy to analyze chromatin organization, transcription activation/silencing as well as protein dynamics/interactions

  2. Single cell omics to map transcriptome, open chromatin, surface proteins and B/T cell receptor profiles)

  3. Chromatin editing including light-induced effector recruitment

  4. Bioinformatic data analysis and biophysical modeling of the underlying regulatory networks.

Project Leader

Rippe SW
Prof. Dr. Karsten Rippe

Phone:  +49 62215451450

Email:  karsten.rippe@dkfz.de

Site:  https://malone.bioquant.uni-heidelberg.de/

Selected Publications

ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats >

Lukas Frank, Anne Rademacher, Norbert Mücke, Stephan M Tirier, Emma Koeleman, Caroline Knotz, Sabrina Schumacher, Sabine A Stainczyk, Frank Westermann, Stefan Fröhling, Priya Chudasama, Karsten Rippe 

Nucleic Acids Res.2022 Jun 24;50(11):e61. 

Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single‐cell transcriptomics 

Stephan M. Tirier, Jan-Philipp Mallm, Simon Steiger, Alexandra M. Poos, Mohamed H. S. Awwad, Nicola Giesen, Nicola Casiraghi, Hana Susak, Katharina Bauer, Anja Baumann, Lukas John, Anja Seckinger, Dirk Hose, Carsten Müller-Tidow, Hartmut Goldschmidt, Oliver Stegle, Michael Hundemer, Niels Weinhold, Marc S. Raab & Karsten Rippe 

Nature Communications volume 12, Article number: 6960 (2021) 

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation 

Fabian Erdel, Anne Rademacher, Rifka Vlijm, Jana Tünnermann, Lukas Frank, Robin Weinmann, Elisabeth Schweigert, Klaus Yserentant, Johan Hummert, Caroline Bauer, Sabrina Schumacher, Ahmad Al Alwash, Christophe Normand, Dirk-Peter Herten, Johann Engelhardt, Karsten Rippe

Mol Cell.2020 Apr 16;78(2):236-249.e7.