Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway.
Levesque
Mitchell P
MP
Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA.
Vernoux
Teva
T
Busch
Wolfgang
W
Cui
Hongchang
H
Wang
Jean Y
JY
Blilou
Ikram
I
Hassan
Hala
H
Nakajima
Keiji
K
Matsumoto
Noritaka
N
Lohmann
Jan U
JU
Scheres
Ben
B
Benfey
Philip N
PN
D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018517:Plant Roots / Q000166:cytology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*
D029681:Arabidopsis Proteins; C100978:SCR protein, Arabidopsis; C410510:SHORT ROOT protein, Arabidopsis; D014157:Transcription Factors