Dirk Schübeler

Group News

Apr 17, 2019
Making room for genome regulation
Mar 7, 2019
Transfer of FMI Directorship: Silvia Arber and Dirk Schübeler to be co-directors
Feb 5, 2019
Fine-tuning gene regulation by CG dinucleotides
Oct 9, 2018
Retention of the regulatory landscape in mitosis
Oct 5, 2018
Congratulations to the FMI Prize winners 2018
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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.

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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.


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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Members

Group leader


PhD students


Postdoctoral fellows


Technical/Research associates


Alumni

PhD students

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

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)

Undergraduates

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

Daniele Colombo (2017)
Sarah Elgin (2011)
Andrea Corsinotti (2007-2008)

Education

1998
PhD, Technical University, Braunschweig, Germany
1995
MSc, Technical University, Braunschweig, Germany

Positions held

2019-
Co-Director FMI
2008-
Senior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel
2003-2007
Junior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel
1998-2003
Postdoctoral Fellow, Fred Hutchinson Cancer Research Center, Seattle

Honors

2015
European Research Council Advanced Grant
2014
ESCI Award for Excellence in Basic/Translational Research
2012
Election to Academia Europaea
2011
VIVA Leading Scientist Award
2011
Adjunct Professor, University of Basel
2009
Member, EMBO
2009
Privatdozent, University of Basel
2008
European Research Council Starting Grant
2007
Friedrich Miescher Prize, Swiss Society for Biochemistry
2006
Member, Epigenome Network of Excellence
2006
EMBO Young Investigator Award
2000-2002
Postdoctoral Fellowship, Rett Syndrome Research Foundation
1998-2000
Postdoctoral Fellowship, Deutsche Forschungsgemeinschaft
1997
Thesis award, GBF Förderpreis
1995-1998
Graduate Fellowship, Foundation of the German Chemical Industry