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Castillo, Gabriel and Turck, Franziska and Leveugle, Magalie and Carbonero Zalduegui, Pilar and Coupland, George and Paz Ares, Javier and Oñate Sanchez, Luis (2011). Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors. "Plos One", v. 6 (n. 6); pp.. ISSN 1932-6203. https://doi.org/10.1371/journal.pone.0021524.
Title: | Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors |
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Author/s: |
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Item Type: | Article |
Título de Revista/Publicación: | Plos One |
Date: | June 2011 |
ISSN: | 1932-6203 |
Volume: | 6 |
Subjects: | |
Faculty: | E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM) |
Department: | Biotecnología - Biología Vegetal |
Creative Commons Licenses: | Recognition - No derivative works - Non commercial |
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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.
Item ID: | 53708 |
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DC Identifier: | https://oa.upm.es/53708/ |
OAI Identifier: | oai:oa.upm.es:53708 |
DOI: | 10.1371/journal.pone.0021524 |
Official URL: | https://journals.plos.org/plosone/article?id=10.13... |
Deposited by: | Biblioteca ETSI Agronómica, Alimentaria y de Biosistemas |
Deposited on: | 23 Jan 2019 10:08 |
Last Modified: | 23 Jan 2019 10:10 |