title: A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.
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.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Claus
authors.initials: C
authors.lastname: Schertel
authors.affiliation: Laboratory 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;
authors.forename: Monica
authors.initials: M
authors.lastname: Albarca
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Claudia
authors.initials: C
authors.lastname: Rockel-Bauer
authors.affiliation: Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland.
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Kelley
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
authors.forename: Johannes
authors.initials: J
authors.lastname: Bischof
authors.affiliation: Laboratory 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;
authors.forename: Korneel
authors.initials: K
authors.lastname: Hens
authors.affiliation: Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland erik.vannimwegen@unibas.ch konrad.basler@imls.uzh.ch bart.deplancke@epfl.ch.
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; erik.vannimwegen@unibas.ch konrad.basler@imls.uzh.ch bart.deplancke@epfl.ch.
authors.forename: Konrad
authors.initials: K
authors.lastname: Basler
authors.affiliation: Laboratory 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; erik.vannimwegen@unibas.ch konrad.basler@imls.uzh.ch bart.deplancke@epfl.ch.
authors.forename: Bart
authors.initials: B
authors.lastname: Deplancke
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D019521:Body Patterning / Q000235:genetics*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D006657:Histones / Q000235:genetics; D060227:Imaginal Discs / Q000196:embryology*; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D034622:RNA Interference; D012319:RNA Polymerase II / Q000235:genetics; D034741:RNA, Small Interfering; D014157:Transcription Factors / Q000235:genetics*; D014921:Wings, Animal / Q000196:embryology*
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D006657:Histones; D034741:RNA, Small Interfering; D014157:Transcription Factors; D012319:RNA Polymerase II