Reference : Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcr...
Scientific journals : Article
Life sciences : Genetics & genetic processes
http://hdl.handle.net/2268/178798
Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference
English
Potier, Delphine [University of Leuven > Center for Human Genetics > Laboratory of Computational Biology > >]
Davie, Kristofer [University of Leuven > Center for Human Genetics > Laboratory of Computational Biology > >]
Hulselmans, Gert [University of Leuven > Center for Human Genetics > Laboratory of Computational Biology > >]
Naval Sanchez, Marina [Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology > >]
Haagen, Lotte [Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology > >]
Huynh-Thu, Vân Anh mailto [Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
Koldere, Duygu [Bogazici University > Department of Molecular Biology and Genetics > > >]
Celik, Azu [Bogazici University > Department of Molecular Biology and Genetics > > >]
Geurts, Pierre mailto [Université de Liège - ULg > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique >]
Christiaens, Valérie [Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology > >]
Aerts, Stein [Katholieke Universiteit Leuven - KUL > Center for Human Genetics > Laboratory of Computational Biology > >]
18-Dec-2014
Cell Reports
Elsevier
9
6
2290-2303
Yes (verified by ORBi)
International
2211-1247
[en] Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRNs). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse engineer the GRNs of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types and inferred a coexpression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5,632 direct target genes through 24,926 enhancers. Using this network, we found network motifs, cis-regulatory codes, and regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions.
http://hdl.handle.net/2268/178798
also: http://hdl.handle.net/2268/182039
10.1016/j.celrep.2014.11.038

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