Wallner et al. Epigenetics & Chromatin (2016) 9:33 DOI 10.1186/s13072-016-0079-z RESEARCH Epigenetic dynamics of monocyte- to-macrophage diferentiation Stefan Wallner 1 , Christopher Schröder 2 , Elsa Leitão 3 , Tea Berulava 3 , Claudia Haak 3 , Daniela Beißer 2 , Sven Rahmann 2 , Andreas S. Richter 4 , Thomas Manke 4 , Ulrike Bönisch 4 , Laura Arrigoni 4 , Sebastian Fröhler 5 , Filippos Klironomos 5 , Wei Chen 5 , Nikolaus Rajewsky 5 , Fabian Müller 6 , Peter Ebert 6 , Thomas Lengauer 6 , Matthias Barann 7 , Philip Rosenstiel 7 , Gilles Gasparoni 8 , Karl Nordström 8 , Jörn Walter 8 , Benedikt Brors 9 , Gideon Zipprich 9 , Bärbel Felder 9 , Ludger Klein-Hitpass 10 , Corinna Attenberger 11 , Gerd Schmitz 1 and Bernhard Horsthemke 3* Abstract Background: Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium. Results: Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers. These regions were unique for macrophages and associated with genes involved in the regulation of the actin cytoskeleton, phagocytosis and innate immune response. Conclusions: In summary, we have discovered a phagocytic gene network that is repressed by DNA methylation in monocytes and rapidly de-repressed after the onset of macrophage differentiation. Keywords: Monocyte, Macrophage, Epigenetics, Methylation, Enhancer, Next-generation sequencing, Ten eleven translocation methylcytosine dioxygenase, TET, DEEP, IHEC © 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background Te diferentiation of monocytes to macrophages is dependent on macrophage colony-stimulating fac- tor (CSF1/MCSF) and modulated by infammatory stimuli such as LPS, γ-IFN or TNFα. CSF1 promotes a resident-type macrophage phenotype with a role in tis- sue repair [1]. CSF1 binds to the extracellular domain of the CSF1 receptor (CSF1R) with downstream signal- ing via PI3K and MEK, to modulate diferentiation and survival. Although much progress has been made in the understanding of macrophage activation, polarization and function, the underlying processes are still not fully understood. A large transcriptomic data set of phagocyte diferen- tiation and activation [1], among numerous other cells and tissues, has recently been released by the FANTOM consortium [2, 3]. All phagocytes express a small num- ber of lineage-specifc transcription factors (TFs) and an array of known lineage-specifc genes [4]. Transcrip- tional changes are mainly mediated by the selection and establishment of enhancers (for review, see [5]). Based on mouse studies, it has been proposed that PU.1 and serum response factor (SRF) regulate cytoskeletal gene expres- sion in macrophages [6]. Furthermore, miRNA signatures were identifed in polarized macrophages that are difer- entially regulated during monocyte-to-macrophage dif- ferentiation and polarization [7]. Open Access Epigenetics & Chromatin *Correspondence: bernhard.horsthemke@uni-due.de 3 Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany Full list of author information is available at the end of the article