A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development
- Claus Schertel1,4,
- Monica Albarca2,4,
- Claudia Rockel-Bauer1,
- Nicholas W. Kelley3,
- Johannes Bischof1,
- Korneel Hens2,5,
- Erik van Nimwegen3,
- Konrad Basler1 and
- Bart Deplancke2
- 1Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
- 2Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
- 3Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
- Corresponding authors: erik.vannimwegen{at}unibas.ch, konrad.basler{at}imls.uzh.ch, bart.deplancke{at}epfl.ch
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↵4 These authors contributed equally to this work.
Abstract
Transcription factors (TFs) are key regulators of cell fate. The estimated 755 genes that encode DNA binding domain-containing proteins comprise ∼5% of all Drosophila genes. However, the majority has remained uncharacterized so far due to the lack of proper genetic tools. We generated 594 site-directed transgenic Drosophila lines that contain integrations of individual UAS-TF constructs to facilitate spatiotemporally controlled misexpression in vivo. All transgenes were expressed in the developing wing, and two-thirds induced specific phenotypic defects. In vivo knockdown of the same genes yielded a phenotype for 50%, with both methods indicating a great potential for misexpression to characterize novel functions in wing growth, patterning, and development. Thus, our UAS-TF library provides an important addition to the genetic toolbox of Drosophila research, enabling the identification of several novel wing development-related TFs. In parallel, we established the chromatin landscape of wing imaginal discs by ChIP-seq analyses of five chromatin marks and RNA Pol II. Subsequent clustering revealed six distinct chromatin states, with two clusters showing enrichment for both active and repressive marks. TFs that carry such “bivalent” chromatin are highly enriched for causing misexpression phenotypes in the wing, and analysis of existing expression data shows that these TFs tend to be differentially expressed across the wing disc. Thus, bivalently marked chromatin can be used as a marker for spatially regulated TFs that are functionally relevant in a developing tissue.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.181305.114.
- Received July 11, 2014.
- Accepted January 7, 2015.
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