A stele-enriched gene regulatory network in the Arabidopsis root

被引:119
作者
Brady, Siobhan M. [2 ,3 ,4 ,5 ]
Zhang, Lifang [1 ]
Megraw, Molly [6 ]
Martinez, Natalia J. [7 ,8 ]
Jiang, Eric [2 ,3 ]
Yi, Charles S. [2 ,3 ]
Liu, Weilin [2 ,3 ]
Zeng, Anna [4 ,5 ]
Taylor-Teeples, Mallorie [4 ,5 ]
Kim, Dahae [4 ,5 ]
Ahnert, Sebastian [9 ]
Ohler, Uwe [6 ]
Ware, Doreen [1 ,10 ]
Walhout, Albertha J. M. [7 ,8 ]
Benfey, Philip N. [2 ,3 ]
机构
[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
[2] Duke Univ, Dept Biol, Durham, NC 27708 USA
[3] Duke Univ, IGSP Ctr Syst Biol, Durham, NC 27708 USA
[4] UC Davis, Dept Plant Biol, Davis, CA USA
[5] UC Davis, Genome Ctr, Davis, CA USA
[6] Duke Univ, Inst Genome Sci & Policy, Durham, NC 27708 USA
[7] Univ Massachusetts, Sch Med, Program Gene Funct & Express, Worcester, MA 01605 USA
[8] Univ Massachusetts, Sch Med, Program Mol Med, Worcester, MA 01605 USA
[9] Univ Cambridge, Cavendish Lab, Condensed Matter Theory Grp, Cambridge CB3 0HE, England
[10] ARS, USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY USA
基金
美国国家科学基金会; 加拿大自然科学与工程研究理事会;
关键词
Arabidopsis; gene regulatory network; miRNA; transcription factor; DNA INTERACTION NETWORK; TRANSCRIPTION FACTORS; EXPRESSION; ELEGANS; YEAST; PROTEINS; SYSTEM; PLANTS; ASSAYS; MAP;
D O I
10.1038/msb.2010.114
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered. Molecular Systems Biology 7: 459; published online 18 January 2011; doi:10.1038/msb.2010.114
引用
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页数:9
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