Our Research

We aim to understand fundamental principles of gene regulation.

Regulatory mechanisms that modify chromatin structure are an integral part of this process. These include reversible modification of histones, DNA methylation and chromatin remodeling. How these function, crosstalk to transcription factors and depend on the underlying DNA sequence is of particular interest for us.

We want to understand how chromatin states are generated and how they are involved in the information flow towards transcription. Mammalian cells serve as model system enabling us to combine molecular biology approaches with genome-wide experimental readouts. We generate comprehensive datasets of the genomic distribution of epigenome variables in combination with targeted analysis of individual sequences. From the resulting datasets we derive and test regulatory models with the ultimate goal to implement epigenetic regulation into current models of transcriptional regulation.

 

Current research themes and selected publications:

Regulation of DNA methylation and CHromatin organization

Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape
PA Ginno, L Burger, J Seebacher, V Iesmantavicius, D Schübeler
Nature Communications 9 (1), 4048

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
DF Colombo, L Burger, T Baubec, D Schübeler
PLoS Genetics 13 (12), e1007102

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation
T Baubec, DF Colombo, C Wirbelauer, J Schmidt, L Burger, AR Krebs, A Akalin, D Schübeler
Nature 520 (7546), 243

Methylation-dependent and-independent genomic targeting principles of the MBD protein family
T Baubec, R Ivánek, F Lienert, D Schübeler
Cell 153 (2), 480-492


transcription factors as sensors and modifiers of chromatin

Competition between DNA methylation and transcription factors determines binding of NRF1
S Domcke, AF Bardet, PA Ginno, D Hartl, L Burger, D Schübeler
Nature 528 (7583), 575

Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
A Feldmann, R Ivanek, R Murr, D Gaidatzis, L Burger, D Schübeler
PLoS Genetics 9 (12), e1003994

DNA-binding factors shape the mouse methylome at distal regulatory regions
MB Stadler, R Murr, L Burger, R Ivanek, F Lienert, A Schöler, E van Nimwegen, C Wirbelauer, EJ Oakeley, D Gaidatzis, VK Tiwari, D Schübeler
Nature 480, 490–495


DNA sequence determinants of epigenetic states

Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters
AR Krebs, D Imanci, L Hoerner, D Gaidatzis, L Burger, D Schübeler
Molecular Cell 67 (3), 411-422. e4

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
AR Krebs, S Dessus-Babus, L Burger, D Schübeler
eLife 3, e04094

Identification of genetic elements that autonomously determine DNA methylation states
F Lienert, C Wirbelauer, I Som, A Dean, F Mohn, D Schübeler
Nature Genetics 43 (11), 1091