Dirk Schübeler
Group News
Oct 1, 2024 Video: Uncovering the complex roles of transcription factors in gene regulation |
Sep 4, 2024 Video: Homing in on the role of chromatin organization in gene regulation |
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 |
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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.
Mario Iurlaro, Francesca Masoni, Ilya M. Flyamer, Christiane Wirbelauer, Murat Iskar, Lukas Burger, Luca Giorgetti & Dirk Schübeler (2024) Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Nature Genetics, volume 56, pages1203-1212Ralph Stefan Grand, Marco Pregnolato1, Lisa Baumgartner, Leslie Hoerner, Lukas Burger, Dirk Schübeler (2024) Genome access is transcription factor-specific and defined by nucleosome position
Molecular Cell, Volume 84, Issue 18Luke 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, 948-957Kaluscha 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):1895-1906Ralph 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 133-137Mario 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 279-287Alicia 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, 2680Barisic D, Stadler MB, Iurlaro M, Schübeler D (2019) Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.
Nature. 2019 Apr 17Hartl 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):554-563Isbel L, Schübeler D (2018) Non-mendelian Inheritance in Mammals Is Highly Constrained.
Cell. 2018 Nov 15;175(5):1179-1181Ginno 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):4048Krebs 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.e4Domcke 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. 520:243-8Schübeler D (2015) Function and information content of DNA methylation
Nature. 517:321-6Invited 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:e04094Baubec T, Ivanek R, Lienert F, Schübeler D (2013) Methylation-dependent and -independent genomic targeting principles of the MBD protein family
Cell. 153:480-492Arnold 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. 338:756-757Tippmann 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;8:593Tiwari 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. 480:490-495Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D. (2011) Identification of genetic elements that autonomously determine DNA methylation states
Nat Genet. 43:1091-7Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility
Nat Rev Genet. 12:554-64Bell 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. 17:894-900Mohn 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. 30:755-766Weber 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. 39:457-466Weber 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. 37:853-862Full list of publications
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