Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis.
Abstract
SHORT-ROOT (SHR) is a key regulator of root growth and development in Arabidopsis
(Arabidopsis thaliana). Made in the stele, the SHR protein moves into an adjacent
cell layer, where it specifies endodermal cell fate; it is also essential for apical
meristem maintenance, ground tissue patterning, vascular differentiation, and lateral
root formation. Much has been learned about the mechanism by which SHR controls radial
patterning, but how it regulates other aspects of root morphogenesis is still unclear.
To dissect the SHR developmental pathway, we have determined the genome-wide locations
of SHR direct targets using a chromatin immunoprecipitation followed by microarray
analysis method. K-means clustering analysis not only identified additional quiescent
center-specific SHR targets but also revealed a direct role for SHR in gene regulation
in the pericycle and xylem. Using cell type-specific markers, we showed that in shr,
the phloem and the phloem-associated pericycle expanded, whereas the xylem and xylem-associated
pericycle diminished. Interestingly, we found that cytokinin level was elevated in
shr and that exogenous cytokinin conferred a shr-like vascular patterning phenotype
in wild-type root. By chromatin immunoprecipitation-polymerase chain reaction and
reverse transcription-polymerase chain reaction assays, we showed that SHR regulates
cytokinin homeostasis by directly controlling the transcription of cytokinin oxidase
3, a cytokinin catabolism enzyme preferentially expressed in the stele. Finally, overexpression
of a cytokinin oxidase in shr alleviated its vascular patterning defect. On the basis
of these results, we suggest that one mechanism by which SHR controls vascular patterning
is the regulation of cytokinin homeostasis.
Type
Journal articleSubject
ArabidopsisArabidopsis Proteins
Body Patterning
Chromatin Immunoprecipitation
Cluster Analysis
Cytokinins
Gene Expression Regulation, Plant
Genome, Plant
Green Fluorescent Proteins
Homeostasis
Microscopy, Confocal
Mutation
Oligonucleotide Array Sequence Analysis
Phenotype
Phloem
Plant Vascular Bundle
Transcription Factors
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https://hdl.handle.net/10161/14887Published Version (Please cite this version)
10.1104/pp.111.183178Publication Info
Cui, Hongchang; Hao, Yueling; Kovtun, Mikhail; Stolc, Viktor; Deng, Xing-Wang; Sakakibara,
Hitoshi; & Kojima, Mikiko (2011). Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular
patterning through cytokinin homeostasis. Plant Physiol, 157(3). pp. 1221-1231. 10.1104/pp.111.183178. Retrieved from https://hdl.handle.net/10161/14887.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Mikhail Kovtun
Biostatistician III

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