Dirk Schübeler

Group News

Jun 30, 2023
Zeroing in on how the ‘guardian of the genome’ works
Dec 5, 2022
How chemical modifications on DNA keep genes off
Sep 15, 2022
Elements of scientific success
Sep 6, 2021
Im Gespräch mit Dirk Schübeler, dem Direktor des FMI
Jul 7, 2021
Researchers identify missing ‘switch’ that controls essential genes
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Group Website

Dirk Schübeler

Gene regulation in chromatin

While it is apparent that eukaryotic gene activation occurs in the context of chromatin, the precise nature of "chromatin structure" associated with gene activation and silencing is not clear. A variety of measurable characteristics of a gene locus, such as covalent histone modifications, DNA methylation and the timing of DNA replication have been shown to correlate with transcriptional activity and are presumed to regulate gene expression. Our research is aimed at further understanding, at the level of individual gene loci and genome-wide, how these nuclear events influence the expression phenotype in higher eukaryotes and how they are propagated during cell division.

Dirk Schübeler

This is a list of selected publications from this group. For a full list of publications, please visit our Publications page and search by group name.

Luke Isbel, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S. Grand, Eric Hietter-Pfeiffer, Zuzanna Kozicka, Alicia K. Michael, Lukas Burger, Nicolas H. Thomä and Dirk Schübeler (2023) Readout of histone methylation by Trim24 locally restricts chromatin opening by p53

Nature Structural & Molecular Biology, Volume 30, 948-957

Kaluscha S, Domcke S, Wirbelauer C, Stadler MB, Durdu S, Burger L, Schübeler D (2022) Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation.

Nat Genet. 2022 Dec; 54(12):1895-1906

Ralph S. Grand*, Lukas Burger*, Cathrin Gräwe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, Vytautas Iesmantavicius, Sevi Durdu, Marco Pregnolato, Arnaud R. Krebs, Sébastien A. Smallwood, Nicolas Thomä, Michiel Vermeulen & Dirk Schübeler. (2021) BANP opens chromatin and activates CpG-island-regulated genes.

Nature 596, pages 133-137

Mario Iurlaro, Michael B. Stadler, Francesca Masoni, Zainab Jagani, Giorgio G. Galli and Dirk Schübeler (2021) Mammalian SWI/SNF continuously restores local accessibility to chromatin.

Nature Genetics 53, pages 279-287

Alicia K. Michael*, Ralph S. Grand*, Luke Isbel*, Simone Cavadini, Zuzanna Kozicka, Georg Kempf, Richard D. Bunker, Andreas D. Schenk, Alexandra Graff-Meyer, Ganesh R. Pathare, Joscha Weiss, Syota Matsumoto, Lukas Burger, Dirk Schübeler and Nicolas H. Thomä (2020) Mechanisms of OCT4-SOX2 motif readout on nucleosomes.

Science, Vol. 368, Issue 6498, pp. 1460-1465
* joint 1st authors

Paul Adrian Ginno, Dimos Gaidatzis, Angelika Feldmann, Leslie Hoerner, Dilek Imanci, Lukas Burger, Frederic Zilbermann, Antoine H. F. M. Peters, Frank Edenhofer, Sebastien Smallwood, Arnaud Krebs & Dirk Schübeler (2020) A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.

Nature Communications 11, 2680

Barisic D, Stadler MB, Iurlaro M, Schübeler D (2019) Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.

Nature. 2019 Apr 17

Hartl D, Krebs AR, Grand RS, Baubec T, Isbel L, Wirbelauer C, Burger L, Schübeler D (2019) CG dinucleotides enhance promoter activity independent of DNA methylation.

Genome Res. 2019 Apr;29(4):554-563

Isbel L, Schübeler D (2018) Non-mendelian Inheritance in Mammals Is Highly Constrained.

Cell. 2018 Nov 15;175(5):1179-1181

Ginno PA, Burger L, Seebacher J, Iesmantavicius V, Schübeler D (2018) Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape.

Nat Commun. 2018 Oct 2;9(1):4048

Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D (2017) Genome-wide single molecule footprinting quantifies steps of transcription initiation and reveals high RNA polymerase II turnover at paused promoters

Mol Cell 67:411-422.e4

Domcke S*, Bardet AF*, Ginno P, Hartl D, Burger L, Schübeler D (2015) Competition between DNA methylation and transcription factors determines binding of NRF1

Nature. 528:575-9
* joint 1st authors

Baubec T, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, Akalin A, Schübeler D (2015) Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

Nature. 520:243-8

Schübeler D (2015) Function and information content of DNA methylation

Nature. 517:321-6
Invited insight review

Krebs AR, Dessus-Babus S, Burger L, Schübeler D (2014) High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

Elife. 3:e04094

Baubec T, Ivanek R, Lienert F, Schübeler D (2013) Methylation-dependent and -independent genomic targeting principles of the MBD protein family

Cell. 153:480-492

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jorgensen H, Stadler MB, van Nimwegen E*, Schübeler D* (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Genome Res. 23:60-73
* corresponding authors

Schübeler D (2012) Epigenetic islands in a genetic ocean

Science. 338:756-757

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D (2012) Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA level

Mol Syst Biol. 17;8:593

Tiwari VK, Stadler MB*, Wirbelauer C, Paro R, Schübeler D*, Beisel C (2012) A chromatin-modifying function for JNK at NF-Y bound Promoters during Stem Cell Differentiation

Nature Genet. 44:94-100
* corresponding authors

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D (2011) DNA binding factors shape the mouse methylome at distal regulatory regions

Nature. 480:490-495

Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D. (2011) Identification of genetic elements that autonomously determine DNA methylation states

Nat Genet. 43:1091-7

Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility

Nat Rev Genet. 12:554-64

Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schübeler D (2010) DNA accessibility discriminates sites of PcG repression, H4K16 acetylation and replication initiation throughout the genome

Nat Struct Mol Biol. 17:894-900

Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D (2008) Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors

Molecular Cell. 30:755-766

Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

Nature Genet. 39:457-466

Weber M, Davies J, Wittig D, Oakeley E, Haase M, Lam WL, Schübeler D (2005) Chromosome-wide and promoter-specific analyses reveal sites of differential DNA methylation in normal and transformed human cells

Nature Genet. 37:853-862

Full list of publications
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Group leader

In current position since 2020
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PhD students

In current position since 2019
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In current position since 2021
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Postdoctoral fellows

In current position since 2023
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In current position since 2020
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In current position since 2023
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In current position since 2020
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In current position since 2020
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In current position since 2023
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Technical/Research associates

In current position since 2018
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In current position since 2008
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In current position since 2023
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In current position since 2003
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PhD students

Marlena Luebke (2018-2023)
Marco Pregnolato (2017-2023)
Sebastian Kaluscha (2016-2021)
Dominik Hartl (2013-2018)
Silvia Domcke (2013-2017)
Darko Barisic (2012-2017)
Daniele Colombo (2012-2017)
Juliane Schmidt (2011-2016)
Angelika Feldmann (2009-2014)
Philip Jermann (2009-2014)
Anne Schoeler (2008-2012)
Sylvia Tippmann (2008-2012)
Florian Lienert (2007-2011)
Fabio Mohn (2005-2009)
Michaela Schwaiger (2004-2009)
Oliver Bell (2003-2008)

Postdoctoral fellows

Marlena Luebke (2023)
Marco Pregnolato (2023)
Luke Isbel (2016-2023)
Mario Iurlaro (2017-2023)
Sebastian Kaluscha (2021-2022)
Ralph Grand (2015-2021)
Sevi Durdu (2017-2020)
Paul Ginno (2012-2020)
Lukas Burger (2015-2018)
Arnaud Krebs (2011-2017)
Juliane Schmidt (2016-2017)
Anaïs Bardet (2013-2016)
Tuncay Baubec (2009-2015)
Rabih Murr (2008-2014)
Altuna Akalin (2013-2014)
Robert Ivanek (2009-2012)
Vijay Tiwari (2008-2012)
Fabio Mohn (2009-2010)
Tim Roloff (2006-2009)
Oliver Bell (2008)
Michael Weber (2003-2007)

Technical/Research associates

Dilek Imanci (2016-2017)


Maria Eleni Vathi (2023)
Fumiya Moribe (2020)
Anna-Karina Felder (2018-2019)
Fotios Gkountromichos (2017-2018)
Eduard Anselm (2012)
Johannes Kaut (2009)
Bjoern Gaertner (2007-2008)
Elena Aritonovska (2005-2006)
David Wittig (2004-2005)
Ozren Bogdanovic (2003-2004)

Visiting scientists

Cathrin Graewe (2021)
Sevi Durdu (2020)
Daniele Colombo (2017)
Sarah Elgin (2011)
Andrea Corsinotti (2007-2008)


PhD, Technical University, Braunschweig, Germany
MSc, Technical University, Braunschweig, Germany

Positions held

Full Professor, Molecular Biology, University of Basel
Director FMI
Co-Director FMI
Adjunct Professor, University of Basel
Privatdozent, University of Basel
Senior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel
Junior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel
Postdoctoral Fellow, Fred Hutchinson Cancer Research Center, Seattle


European Research Council Advanced Grant
European Research Council Advanced Grant
ESCI Award for Excellence in Basic/Translational Research
Election to Academia Europaea
VIVA Leading Scientist Award
Member, EMBO
European Research Council Starting Grant
Friedrich Miescher Prize, Swiss Society for Biochemistry
Member, Epigenome Network of Excellence
EMBO Young Investigator Award
Postdoctoral Fellowship, Rett Syndrome Research Foundation
Postdoctoral Fellowship, Deutsche Forschungsgemeinschaft
Thesis award, GBF Förderpreis
Graduate Fellowship, Foundation of the German Chemical Industry