Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.

PLoS Biology
Mitchell P LevesquePhilip N Benfey

Abstract

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 me...Continue Reading

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Methods Mentioned

BETA
immunoprecipitation
PCR
transgenic
ChIP
dissection
fluorescence-activated cell sorting

Software Mentioned

Gibbs
Motif
Cluster
Linux
Microsoft Access
R
ImageJ
Photoshop
TreeView
SAS

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