title: A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila.
abstract: Understanding eukaryotic transcriptional regulation and its role in development and pattern formation is one of the big challenges in biology today. Most attempts at tackling this problem either focus on the molecular details of transcription factor binding, or aim at genome-wide prediction of expression patterns from sequence through bioinformatics and mathematical modelling. Here we bridge the gap between these two complementary approaches by providing an integrative model of cis-regulatory elements governing the expression of the gap gene giant (gt) in the blastoderm embryo of Drosophila melanogaster. We use a reverse-engineering method, where mathematical models are fit to quantitative spatio-temporal reporter gene expression data to infer the regulatory mechanisms underlying gt expression in its anterior and posterior domains. These models are validated through prediction of gene expression in mutant backgrounds. A detailed analysis of our data and models reveals that gt is regulated by domain-specific CREs at early stages, while a late element drives expression in both the anterior and the posterior domains. Initial gt expression depends exclusively on inputs from maternal factors. Later, gap gene cross-repression and gt auto-activation become increasingly important. We show that auto-regulation creates a positive feedback, which mediates the transition from early to late stages of regulation. We confirm the existence and role of gt auto-activation through targeted mutagenesis of Gt transcription factor binding sites. In summary, our analysis provides a comprehensive picture of spatio-temporal gene regulation by different interacting enhancer elements for an important developmental regulator.
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Astrid
authors.initials: A
authors.lastname: Hoermann
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Damjan
authors.initials: D
authors.lastname: Cicin-Sain
authors.affiliation: EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain. Electronic address: yogi.jaeger@crg.eu.
authors.forename: Johannes
authors.initials: J
authors.lastname: Jaeger
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000235:genetics* / Q000502:physiology*; D004331:Drosophila melanogaster / Q000235:genetics*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D017930:Genes, Reporter; D005818:Genetic Engineering; D018398:Homeodomain Proteins / Q000502:physiology; D017404:In Situ Hybridization, Fluorescence; D008962:Models, Theoretical; D016296:Mutagenesis; D009154:Mutation; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000235:genetics* / Q000502:physiology*
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D012097:Repressor Proteins; C118475:gt protein, Drosophila
keywords: Auto-activation; Cis-regulatory elements (CREs); Drosophila melanogaster; Gene expression dynamics; Mathematical modelling; Reverse engineering