Publications - Published papers

Please find below publications of our group. Currently, we list 53 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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The CHR site: definition and genome-wide identification of a cell cycle transcriptional element

Gerd A. Müller, Axel Wintsche, Konstanze Stangner, Sonja J. Prohaska, Peter F. Stadler, and Kurt Engeland


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Nucl. Acids Res. (2014)


The cell cycle genes homology region (CHR) has been identified as a DNA element with an important role in transcriptional regulation of late cell cycle genes. It has been shown that DREAM and MMB protein complexes as well as the FOXM1-MuvB complex can contact DNA via CHR sites. However, it has not been elucidated which CHR sequence variations from the canonical TTTGAA are functional and how frequent CHR-based regulation is utilized in mammalian genomes. Here, we define the spectrum of functional CHR elements in the human genome. As the basis for a computational meta-analysis, we identify new CHR sequences and compile phylogenetic motif conservation as well as genome-wide protein-DNA binding and gene expression data. We identify CHR elements in most late cell cycle genes which bind DREAM, MMB, or FOXM1-MuvB. Moreover, binding sites for E2F transcription factors are detected in many early cell cycle genes bound by DREAM. In contrast, Myb and forkhead binding sites are not enriched in late cell cycle genes. Our findings lead to a general mechanism: Sequential binding of DREAM, MMB, and FOXM1-MuvB complexes to such genes requires CHR elements. Taken together, we define the group of CHR-regulated genes in mammalian genomes and provide evidence that the CHR is the central promoter element in transcriptional regulation of late cell cycle genes by DREAM, MMB, and FOXM1-MuvB.