brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana

Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chrom...

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Published in:The Plant journal : for cell and molecular biology Vol. 65; no. 4; pp. 634 - 646
Main Authors: Yu, Xiaofei, Li, Lei, Zola, Jaroslaw, Aluru, Maneesha, Ye, Huaxun, Foudree, Andrew, Guo, Hongqing, Anderson, Sarah, Aluru, Srinivas, Liu, Peng, Rodermel, Steve, Yin, Yanhai
Format: Journal Article
Language:English
Published: Oxford, UK Blackwell Publishing Ltd 01.02.2011
Subjects:
Algorithms
Arabidopsis
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis Proteins
Arabidopsis Proteins - genetics
Arabidopsis Proteins - metabolism
Arabidopsis thaliana
Binding Sites
brassinosteroid
Brassinosteroids
ChIP‐chip
Chloroplasts
Chromatin
Chromatin Immunoprecipitation
Computational Biology
Computer applications
Data processing
Flowers & plants
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Plant
gene regulatory network
Gene Regulatory Networks
gene targeting
genetics
Genome, Plant
Genomics
Immunoprecipitation
Light effects
metabolism
microarray
mutants
Nuclear Proteins
Nuclear Proteins - genetics
Nuclear Proteins - metabolism
Plant biology
plant development
Plant growth
Plant Growth Regulators
Plant Growth Regulators - metabolism
plant hormone
regulator genes
Signal transduction
Steroids
Steroids - metabolism
Transcription factors
Transcription Factors - genetics
Transcription Factors - metabolism
ISSN:0960-7412, 1365-313X, 1365-313X
Online Access:Get full text
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Summary:Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling arrays (ChIP-chip) and gene expression studies, we have identified 1609 putative BES1 target genes, 404 of which are regulated by BRs and/or in gain-of-function bes1-D mutant. BES1 targets contribute to BR responses and interactions with other hormonal or light signaling pathways. Computational modeling of gene expression data using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) reveals that BES1-targeted transcriptional factors form a gene regulatory network (GRN). Mutants of many genes in the network displayed defects in BR responses. Moreover, we found that BES1 functions to inhibit chloroplast development by repressing the expression of GLK1 and GLK2 transcription factors, confirming a hypothesis generated from the GRN. Our results thus provide a global view of BR regulated gene expression and a GRN that guides future studies in understanding BR-regulated plant growth.
Bibliography:http://dx.doi.org/10.1111/j.1365-313X.2010.04449.x
Present address: Department of Immunology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390.
Present address: Department of Genetics, Harvard Medical School, 185 Cambridge St, CPZN7250, Boston MA 02114‐2790.
These authors contributed equally to the work.
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ISSN:0960-7412
1365-313X
1365-313X
DOI:10.1111/j.1365-313X.2010.04449.x