title: Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors.
abstract: Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. The number, position and interactions between cis-elements and transcription factors (TFs) determine the expression pattern of a gene. To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1) was used. As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element) that is sufficient to drive strong expression of a reporter gene in planta. A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs) was arrayed in a 96-well format (RR library) and a convenient mating based yeast one hybrid (Y1H) screening procedure was established. We constructed an episomal plasmid (pTUY1H) to clone the LIP1 element and used it as bait for Y1H screenings. A novel interaction with an HD-ZIP (AtML1) TF was identified and abolished by a 2 bp mutation in the LIP1 element. A role of this interaction in transcriptional regulation was confirmed in planta. In addition, we validated our strategy by reproducing the previously reported interaction between a MYB-CC (PHR1) TF, a central regulator of phosphate starvation responses, with a conserved promoter fragment (IPS1 element) containing its cognate binding sequence. Finally, we established that the LIP1 and IPS1 elements were differentially bound by HD-ZIP and MYB-CC family members in agreement with their genetic redundancy in planta. In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis- and trans-regulatory codes.
authors: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain.
authors: Gabriel
authors: G
authors: Castrillo
authors: Franziska
authors: F
authors: Turck
authors: Magalie
authors: M
authors: Leveugle
authors: Alain
authors: A
authors: Lecharny
authors: Pilar
authors: P
authors: Carbonero
authors: George
authors: G
authors: Coupland
authors: Javier
authors: J
authors: Paz-Ares
authors: Luis
authors: L
authors: Oñate-Sánchez
mesh_terms: D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D019607:Brassicaceae / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D030821:Plants, Genetically Modified / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D013466:Sulfurtransferases; D014157:Transcription Factors / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors; D013466:Sulfurtransferases; C116435:lipoic acid synthase