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

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.

Description

Title: Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors
Author/s:
  • Castillo, Gabriel
  • Turck, Franziska
  • Leveugle, Magalie
  • Carbonero Zalduegui, Pilar
  • Coupland, George
  • Paz Ares, Javier
  • Oñate Sanchez, Luis
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

Full text

[img]
Preview
PDF - Requires a PDF viewer, such as GSview, Xpdf or Adobe Acrobat Reader
Download (1MB) | Preview

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

TypeCodeAcronymLeaderTitle
Government of SpainCONSOLIDER CSD2007-00057TRANSPLANTAJavier Paz-AresFunción y Potencial Biotecnológico de los Factores de Transcripción en Plantas
Government of SpainBIO2008-04715UnspecifiedJavier Paz-AresAproximaciones genéticas genómicas y proteómicas para el estudio de la ruta de señalización de la respuesta de ayuno de fosfato en plantas.
Government of SpainBFU2009-11809TRANSTRITPilar Carbonero ZaldueguiRedes transcripcionales en semillas de las TRITICEAE: comparación Hordeum vulgare y Brachypodium distachyon
Government of SpainBIO2010-17334UnspecifiedUnspecifiedEstudio de la señalización por giberelinas para mejorar la germinación de las semillas y la resistencia al estrés

More information

Item ID: 53708
DC Identifier: http://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=10.1371/journal.pone.0021524
Deposited by: Biblioteca ETSI Agrónomos
Deposited on: 23 Jan 2019 10:08
Last Modified: 23 Jan 2019 10:10
  • Logo InvestigaM (UPM)
  • Logo GEOUP4
  • Logo Open Access
  • Open Access
  • Logo Sherpa/Romeo
    Check whether the anglo-saxon journal in which you have published an article allows you to also publish it under open access.
  • Logo Dulcinea
    Check whether the spanish journal in which you have published an article allows you to also publish it under open access.
  • Logo de Recolecta
  • Logo del Observatorio I+D+i UPM
  • Logo de OpenCourseWare UPM