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Decoding the regulatory logic of the Drosophila male stem cell system

Fani Papagiannouli, Srividya Tamirisa, Eugen Rempel, Olga Ermakova, Nils Trost, Jun Zhou, Juliane Mundorf, Samantha Brunel, Naima Ruhland, Michael Boutros, Jan U. Lohmann, Ingrid Lohmann
doi: https://doi.org/10.1101/227876
Fani Papagiannouli
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
2Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, CA 94305-5329, Stanford, USA
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Srividya Tamirisa
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Eugen Rempel
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Olga Ermakova
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Nils Trost
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Jun Zhou
3German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and University of Heidelberg, Dept. of Cell and Molecular Biology, D-69120 Heidelberg, Germany
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Juliane Mundorf
4Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
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Samantha Brunel
5Institut Jacques Monod, University Paris-Diderot, 75205 Paris, France
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Naima Ruhland
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Michael Boutros
3German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and University of Heidelberg, Dept. of Cell and Molecular Biology, D-69120 Heidelberg, Germany
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Jan U. Lohmann
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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Ingrid Lohmann
1Centre for Organismal Studies (COS) Heidelberg, 69120, Heidelberg, Germany
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  • For correspondence: ingrid.lohmann@cos.uni-heidelberg.de
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ABSTRACT

In the past decade, the importance of the niche to provide regulatory inputs to balance stem cell self-renewal and differentiation has become clear. However, the regulatory interplay between stem cells and their niche at the whole genome level is still poorly understood. To elucidate the mechanisms controlling stem cells and their progenies as they progress through their developmental program at the transcriptional level, we recorded the regulatory program of two independent cell lineages in the Drosophila testis stem cell model. To this end, we identified genes active in the soma or germline as well as genome-wide binding profiles of two essential transcription factors, Zfh-1 and Abd-A, expressed in somatic support cells and crucial for fate acquisition of both cell lineages. Our data identified key roles for TOR signalling, signal processing V-ATPase proton pumps and the nuclear transport engaged nucleoporins and we demonstrate their importance in controlling germline maintenance, proliferation and differentiation from the support side. To make our dataset publicly available and support quick and intuitive data mining, we generated an interactive online analysis tool. Applying our tool for comparative analysis, we uncovered conserved core gene sets of adult stem cells across species boundaries. We have tested the functional relevance of these genes in the Drosophila testis and intestine and find a striking overrepresentation of stem cell defects when the corresponding genes were depleted. In summary, our dataset and interactive platform represents a versatile tool for identifying novel gene networks active in diverse stem cell types and provides a valuable resource for elucidating the multifaceted regulatory inputs required to guide proper stem cell behaviour.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 02, 2017.
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Decoding the regulatory logic of the Drosophila male stem cell system
Fani Papagiannouli, Srividya Tamirisa, Eugen Rempel, Olga Ermakova, Nils Trost, Jun Zhou, Juliane Mundorf, Samantha Brunel, Naima Ruhland, Michael Boutros, Jan U. Lohmann, Ingrid Lohmann
bioRxiv 227876; doi: https://doi.org/10.1101/227876
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Decoding the regulatory logic of the Drosophila male stem cell system
Fani Papagiannouli, Srividya Tamirisa, Eugen Rempel, Olga Ermakova, Nils Trost, Jun Zhou, Juliane Mundorf, Samantha Brunel, Naima Ruhland, Michael Boutros, Jan U. Lohmann, Ingrid Lohmann
bioRxiv 227876; doi: https://doi.org/10.1101/227876

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