Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors

Castillo, Gabriel, Turck, Franziska, Leveugle, Magalie, Carbonero Zalduegui, Pilar ORCID: https://orcid.org/0000-0002-4949-3577, Coupland, George, Paz Ares, Javier and Oñate Sanchez, Luis ORCID: https://orcid.org/0000-0001-7047-5739 (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.

Description

Title: Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors
Author/s:
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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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.

Funding Projects

Type
Code
Acronym
Leader
Title
Government of Spain
CONSOLIDER CSD2007-00057
TRANSPLANTA
Javier Paz-Ares
Función y Potencial Biotecnológico de los Factores de Transcripción en Plantas
Government of Spain
BIO2008-04715
Unspecified
Javier Paz-Ares
Aproximaciones genéticas genómicas y proteómicas para el estudio de la ruta de señalización de la respuesta de ayuno de fosfato en plantas.
Government of Spain
BFU2009-11809
TRANSTRIT
Pilar Carbonero Zalduegui
Redes transcripcionales en semillas de las TRITICEAE: comparación Hordeum vulgare y Brachypodium distachyon
Government of Spain
BIO2010-17334
Unspecified
Unspecified
Estudio de la señalización por giberelinas para mejorar la germinación de las semillas y la resistencia al estrés

More information

Item ID: 53708
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
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