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Exploring ubiquitin signaling with dedicated PIQOR Ubiquitin-PS microarrays
Hartmut Scheel, Corinna B. Scholz, Kay Hofmann
Bioinformatics Group, Miltenyi Biotec GmbH, MACSmolecular Business Unit,
Stöckheimer Weg 1, D-50829 Köln, Germany. E-mail: kay.hofmann@miltenyibiotec.de
The MACSmolecluar business unit of Miltenyi Biotec offers smart products and services for
molecular biology research and gene expression analysis via the proprietary PIQOR
Microarray platform for topic-defined or custom expression profiling solutions.
Here, we introduce the PIQOR Ubiquitin-PS microarray with a focus on the ubiquitinproteasome
system (UPS). By developing this microarray, we are addressing the growing
need for a deeper understanding of the UPS and a comprehensive monitoring of its
components. It has become clear in the recent years that ubiquitylation plays a key role in
processes like cell cycle progression, protein quality control, DNA repair, stress response,
apoptosis and regulation of signaling.
The importance of the UPS for signal transduction is not restricted to its well-known role in
the selective degradation of regulatory proteins. Equally important is the role of ubiquitin
modification as a signal by itself. The high complexity of the UPS is underscored by the large
number of components involved in ubiquitin attachment, removal and recognition, all similar
to the numbers known for phosphorylation signaling. A deregulation of the UPS is associated
with a multitude of diseases, including cancer, catabolic diseases, inflammation and
neurodegeneration. Therefore, the UPS becomes more and more a rich source for discoveries
with therapeutic impact and ubiquitin research increases steadily.
A hallmark of the UPS is that most proteins involved belong to a limited number of protein
families characterized by common homology domains. The bioinformatics group of Miltenyi
MACSmolecular possesses appropriate tools like the profile technique to mine sequence
databases for proteins with a given homology domain. In a systematic UPS analysis
programme applying this technique, a list of ~1200 genes was generated covering all aspects
of the UPS and including many unpublished candidate genes, e.g. approximately 600 E3
ligases were identified. With this catalogue of genes at hand, a new microarray was designed,
which allows the systematic detection of mRNA expression changes in the entire UPS. This
new microarray fits nicely into the portfolio of other topic-defined microarrays offered by
Miltenyi Biotec, which already includes microarrays designed for oncology and immunology.
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