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A comprehensive and genome-wide analysis of Notch pathway regulation by in vivo RNAi and protein-protein interaction studies in Drosophila melanogaster

Applicant Merdes Gunter
Number 133097
Funding scheme Project funding (Div. I-III)
Research institution Computational Systems Biology Department of Biosystems, D-BSSE ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Embryology, Developmental Biology
Start/End 01.03.2011 - 31.08.2013
Approved amount 300'000.00
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All Disciplines (4)

Embryology, Developmental Biology
Molecular Biology

Keywords (14)

Notch signaling; Drosophila melanogaster; protein-protein interaction network; PcG-TrxG; ChIP-Seq; mass spectrometry; Systems Biology; RNAi; AP-MS; Notch; Drosophila; fruit fly; signaling; cancer

Lay Summary (English)

Lay summary
In all animals, the Notch signaling pathway plays a decisive role for the correct development from an egg to the adult, and miss-regulation leads to different human diseases and cancer. It is the short-term goal of this project, to deepen our understanding of this pathway and to make these results available for medical research. Accordingly, it will be the long-term goal to use the gained knowledge to manipulate the pathway during disease treatment and for tissue engineering (regenerative medicine).Proteins are not only required for the structural features of cells and the physical appearance of an animal but also play important roles in the decision making processes, which are underlying the development of a higher organism from the fertilized egg (single cell) to the adult (billions of cells). A very important aspect in this regard, are communication procedures between cells, which allow for the coordination of processes in large cell populations. For instance, a signal is emitted from one cell, received from the neighboring cell and translated into an action. This event is called signal transduction and requires the activity of a defined group of proteins. One can compare signal transduction with a chain of commands within a company, which leads to a certain action. In this scenario, proteins not only represent the involved personal but the hardware as well, and all proteins required for the chain of command form the signaling pathway. Several types of these pathways exist and are used repeatedly during the development of organisms as different as the fruit fly Drosophila and humans. Intriguingly, many of the most important signaling pathways have been discovered and analyzed in Drosophila, and only owing to these analyses their importance for the development of humans was detected subsequently. Thus, Drosophila is a wonderful tool to study the precise function of these pathways despite the obvious differences in physical appearance and structure between humans and flies.In the past years, we isolated a multitude of proteins that influence the Notch pathway and might play important roles for the development and progression of cancer in humans. Now, we will sort the identified proteins to certain positions within the chain of commands of the Notch signaling pathway, and determine precisely how the proteins interact with each other. In collaboration with clinicians, we will also try to evaluate if our results can be used to make prognosis for the development of tumors in individual patients and if this information can then be used to develop a more accurate treatment. However, these are long-term goals and will require sustained research efforts.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants



Stability of gene rankings from RNAi screens.
Siebourg Juliane, Merdes Gunter, Misselwitz Benjamin, Hardt Wolf-Dietrich, Beerenwinkel Niko (2012), Stability of gene rankings from RNAi screens., in Bioinformatics (Oxford, England), 28(12), 1612-8.


Group / person Country
Types of collaboration
Niko Beerenwinkel, D-BSSE, ETH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Alexander Schmidt, Biocenter, University of Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Ruedi Aebersold, IMSB, ETH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Matthias Gstaiger, IMSB, ETH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Notch Targeting in Cancer conference Talk given at a conference 27.06.2012 Mykonos, Greece Merdes Gunter;
1st International Conference on Systems Biology Talk given at a conference 24.10.2011 Basel, Switzerland Schwahn Alexander; Merdes Gunter;

Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Der Herr der Neuronen - NOTCH macht alles erst möglich German-speaking Switzerland 2012


The Notch pathway is a central and evolutionarily highly conserved signaling pathway coordinating cellular differentiation and proliferation programs during the development of multicellular organisms. The isolation of mutants with a notched wing started the molecular identification and characterization of the Notch transmembrane receptor in the fruit fly Drosophila melanogaster. In consequence, an apparently simple signal transduction mechanism was unraveled: Activation of Notch upon ligand binding results in its proteolytic cleavage and in the release of the Notch intracellular domain, which engages in transcriptional regulation. A number of Notch-interacting components have been identified in the meanwhile pinpointing to a complicated circuitry regulating Notch pathway activity, which is only poorly understood. Also in humans, Notch has a similarly important function in the control of cellular differentiation and stem cell formation, and its decisive role in a variety of human diseases including cancer is well established.Despite the biological importance of the Notch pathway and its increasing significance for medical research, single candidate approaches and labor intense genetic screens still dominate the attempts to identify the pathway components and to understand their interconnections. In this regard, systems biology can facilitate the identification of potential pathway components at a large and comprehensive scale. We have started such an approach by describing a first set of 353 validated novel Notch regulators we identified with a combination of high-throughput whole-genome ex vivo and in vivo RNAi screening techniques, and network analyses. With this data basis, and by the inclusion of new technologies and ideas, we plan to expand this Notch interaction network substantially and to link the Notch signaling cascade to selective target gene expression and growth control.To this end, we plan to examine the data obtained from the ex vivo RNAi screen with new computational tools to identify so far undetected Notch regulators. In parallel, our screening data and the initial network will serve as basis to establish a high-density protein-protein interaction landscape for the Notch signaling pathway by tandem affinity purification coupled with mass spectrometry (AP-MS), with the identified Notch pathway components being the baits and RNAi serving as in vivo validation tool. This analysis will be performed in collaboration with the laboratory of Professor Ruedi Aebersold (ETHZ, Switzerland). Mass spectrometry analyses will also be used to identify changes in post-translational modifications and in the abundance of Notch pathway components upon Notch activation (selective reaction monitoring, SRM), providing valuable insights into network dynamics. The obtained data sets will be complemented by in-depth analyses of the epigenetic gene regulators of the Polycomb-Trithorax groups (PcG-TrxG) of proteins, which we have identified as Notch regulators and which play important roles in cancer. Genome-wide binding profiles for the PcG-TrxG and other nuclear components of the Notch pathway will be determined before and after Notch activation in different cell types by chromatin immunoprecipitations coupled with massive parallel sequencing (ChIP-Seq). The analysis of the obtained data will enable us to gain insight into the mechanisms underlying the cell-type specific activation of Notch target genes and the role of Notch in growth control. Finally, we will combine all data in one comprehensive interaction network.In light of the evolutionary conservation of the pathway, our results will provide a unique resource for Notch-related and medical research in all animal models, and will allow us to model the pathway and its regulation in collaboration with computational biologists in the human system. This long-term goal can be expected to have a substantial impact on the exploitation of the Notch pathway for human tissue engineering and disease treatment.