Markus Muckenhuber

Research Interest

The cytokine interferon beta (IFNβ) is a known signalling molecule involved in innate immune response, cellular differentiation and part of an anti-tumour defence. Via the classical JAK-STAT signaling cascade IFNβ can specifically activate a set of genes. However, the relation between epigenetic signals and corresponding chromatin states with gene expression response is poorly understood. We aim to address this issue by linking gene expression profiles from RNA-seq with chromatin feature maps from ChIP-seq, ATAC-seq of responding genes at various time points of IFNβ treatment in mouse embryonic stem cells. Furthermore, we will conduct a single cell sequencing analysis by RNA-seq and ATAC-seq to assess the heterogeneity of the cellular response to IFNβ. Moreover, the combination of various data sets will allow us also to identify enhancers that become activated upon IFNβ treatment and to characterize their functions in the response pathway. By integrating the data a genome-wide, multi-layered model of epigenetic regulation will be created that describes the function of chromatin features for gene activation upon cytokine-induce stimuli.


Scientific Background

  • Sine 09/2016                    PhD project on 'Cytokine-induced gene expression: dissecting the role of chromatin states on the cellular response' in the Research Group of PD Dr. Karsten Rippe 'Genome Organization & Function' at the German Cancer Research Center (DKFZ) and BioQuant, Heidelberg
  • 01/2015 – 09/2016           ‘Identifying Novel Epigenetic Regulators of Neuronal Development’; Institute of Molecular Biology (IMB), Mainz, Germany 

  • 09/2013 – 10/2014           Master’s project on ’The impact of Airn lncRNA expression on enhancer-promoter interactions‘; Research group of Dr. Denise P. Barlow; Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM) , Vienna, Austria

  • 05/2013 – 09/2013           Research project on ‘The role of post-transcriptional regulation in establishing specific miR expression pattern during embryonic development in C. elegans’; Research group of Dr. Luisa Cochella; Research Institute of Molecular Pathology (IMP), Vienna, Austria

  • 03/2013 – 05/2013           Research project on ‘Analysis of differences in imprinted expression in Igf2r cluster of murine embryonic and extra-embryonic tissues by qPCR’; Research group of Dr. Denise P. Barlow; Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria

  • 06/2011                            Bachelor Thesis ‘Optimisation of the electrotransfer of serum via SDS-PAGE and western blot onto a PVDF-membrane’; Research group of Univ. Prof. Dr. Kurt Herkner; Department of Pediatrics and Adolescent Medicine, General Hospital, Vienna, Austria

  • 11/2011 – 01/2015            Graduate studies (Master) of Molecular Biology with specialisation Molecular Cell Biology at the University of Vienna, Vienna, Austria

  • 10/2007 – 11/2011            Undergraduate studies (Bachelor) of Biology with specialisation Molecular Biology at the University of Vienna, Vienna, Austria


  • Annemarie Poustka Fellowship, German Cancer Research Center, 2016


Daniel Andergassen, Christoph P Dotter, Daniel Wenzel, Verena Sigl, Philipp C Bammer, Markus Muckenhuber, Daniela Mayer, Tomasz M Kulinski, Hans-Christian Theussl, Josef M Penninger, Christoph Bock, Denise P Barlow, Florian M Pauler, Quanah J Hudson; Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression. eLife 2017;6:e25125


Markus Muckenhuber

DKFZ & BioQuant Center

Division of Chromatin Networks

Im Neuenheimer Feld 267-BQ24

69120 Heidelberg


BioQuant room 623a

Tel.: +49-6221-54-51375

Fax: +49 6221 54 51487

e-mail: m.muckenhuber (at)