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Heidelberg, Germany

Sancar G.,University of Heidelberg | Sancar C.,University of Heidelberg | Brugger B.,University of Heidelberg | Ha N.,BioQuant Center | And 8 more authors.
Molecular Cell | Year: 2011

The white-collar complex (WCC), the core transcription factor of the circadian clock of Neurospora, activates morning-specific expression of the transcription repressor CSP1. Newly synthesized CSP1 exists in a transient complex with the corepressor RCM1/RCO1 and the ubiquitin ligase UBR1. CSP1 is rapidly hyperphosphorylated and degraded via UBR1 and its ubiquitin conjugase RAD6. Genes controlled by CSP1 are rhythmically expressed and peak in the evening (i.e., in antiphase to morning-specific genes directly controlled by WCC). Rhythmic expression of these second-tier genes depends crucially on phosphorylation and rapid turnover of CSP1, which ensures tight coupling of CSP1 abundance and function to the circadian activity of WCC. Negative feedback of CSP1 on its own transcription buffers the amplitude of CSP1-dependent oscillations against fluctuations of WCC activity. CSP1 predominantly regulates genes involved in metabolism. It controls ergosterol synthesis and fatty acid desaturases and thereby modulates the lipid composition of membranes. © 2011 Elsevier Inc.

Mallm J.-P.,German Cancer Research Center | Mallm J.-P.,BioQuant Center | Rippe K.,German Cancer Research Center | Rippe K.,BioQuant Center
Cell Reports | Year: 2015

Non-coding RNAs can modulate histone modifications that, at the same time, affect transcript expression levels. Here, we dissect such a network in mouse embryonic stem cells (ESCs). It regulates the activity of the reverse transcriptase telomerase, which synthesizes telomeric repeats at the chromosome ends. We find that histone H3 serine 10 phosphorylation set by Aurora kinase B (AURKB) in ESCs during the S phase of the cell cycle at centromeric and (sub)telomeric loci promotes the expression of non-coding minor satellite RNA (. cenRNA). Inhibition of AURKB induces silencing of cenRNA transcription and establishment of a repressive chromatin state with histone H3 lysine 9 trimethylation and heterochromatin protein 1 accumulation. This process results in a continuous shortening of telomeres. We further show that AURKB interacts with both telomerase and cenRNA and activates telomerase in trans. Thus, in mouse ESCs, telomere maintenance is regulated via expression of cenRNA in a cell-cycle-dependent manner. Mallm and Rippe find that AURKB kinase and centromeric RNA regulate telomerase activity. AURKB phosphorylates serine 10 of histone H3 at chromosome p-arms during S phase in embryonic stem cells to induce centromere repeat transcription. Together, AURKB and centromere transcripts activate telomerase and ensure telomere maintenance. © 2015 The Authors.

Luijsterburg M.S.,University of Amsterdam | Luijsterburg M.S.,Netherlands Institute for Systems Biology | Luijsterburg M.S.,Max Delbruck Center for Molecular Medicine | Von Bornstaedt G.,German Cancer Research Center | And 13 more authors.
Journal of Cell Biology | Year: 2010

To understand how multiprotein complexes assemble and function on chromatin, we combined quantitative analysis of the mammalian nucleotide excision DNA repair (NER) machinery in living cells with computational modeling. We found that individual NER components exchange within tens of seconds between the bound state in repair complexes and the diffusive state in the nucleoplasm, whereas their net accumulation at repair sites evolves over several hours. Based on these in vivo data, we developed a predictive kinetic model for the assembly and function of repair complexes. DNA repair is orchestrated by the interplay of reversible protein-binding events and progressive enzymatic modifications of the chromatin substrate. We demonstrate that faithful recognition of DNA lesions is time consuming, whereas subsequently, repair complexes form rapidly through random and reversible assembly of NER proteins. Our kinetic analysis of the NER system reveals a fundamental conflict between specificity and efficiency of chromatin-associated protein machineries and shows how a trade off is negotiated through reversibility of protein binding. © 2010 Luijsterburg et al.

Mariani L.,German Cancer Research Center | Mariani L.,Humboldt University of Berlin | Mariani L.,German Rheumatism Research Center | Schulz E.G.,German Cancer Research Center | And 13 more authors.
Molecular Systems Biology | Year: 2010

Although cell-to-cell variability has been recognized as an unavoidable consequence of stochasticity in gene expression, it may also serve a functional role for tuning physiological responses within a cell population. In the immune system, remarkably large variability in the expression of cytokine genes has been observed in homogeneous populations of lymphocytes, but the underlying molecular mechanisms are incompletely understood. Here, we study the interleukin-4 gene (il4) in T-helper lymphocytes, combining mathematical modeling with the experimental quantification of expression variability and critical parameters. We show that a stochastic rate-limiting step upstream of transcription initiation, but acting at the level of an individual allele, controls il4 expression. Only a fraction of cells reaches an active, transcription-competent state in the transient time window determined by antigen stimulation. We support this finding by experimental evidence of a previously unknown short-term memory that was predicted by the model to arise from the long lifetime of the active state. Our analysis shows how a stochastic mechanism acting at the chromatin level can be integrated with transcriptional regulation to quantitatively control cell-to-cell variability. © 2010 EMBO and Macmillan Publishers Limited.

Bingen P.,German Cancer Research Center | Bingen P.,BioQuant Center | Reuss M.,German Cancer Research Center | Reuss M.,BioQuant Center | And 5 more authors.
Optics Express | Year: 2011

We introduce a parallelized STED microscope featuring m = 4 pairs of scanning excitation and STED beams, providing m-fold increased imaging speed of a given sample area, while maintaining basically all of the advantages of single beam scanning. Requiring only a single laser source and fiber input, the setup is inherently aligned both spatially and temporally. Given enough laser power, the design is readily scalable to higher degrees of parallelization m. © 2011 Optical Society of America.

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