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 t...

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Autores principales:	Mitchell P Levesque, Teva Vernoux, Wolfgang Busch, Hongchang Cui, Jean Y Wang, Ikram Blilou, Hala Hassan, Keiji Nakajima, Noritaka Matsumoto, Jan U Lohmann, Ben Scheres, Philip N Benfey
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/60cf484e09db4c1ea74ba379863f37dc
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spelling	oai:doaj.org-article:60cf484e09db4c1ea74ba379863f37dc2021-11-25T05:33:10ZWhole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.1544-91731545-788510.1371/journal.pbio.0040143https://doaj.org/article/60cf484e09db4c1ea74ba379863f37dc2006-05-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.0040143https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Stem 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.Mitchell P LevesqueTeva VernouxWolfgang BuschHongchang CuiJean Y WangIkram BlilouHala HassanKeiji NakajimaNoritaka MatsumotoJan U LohmannBen ScheresPhilip N BenfeyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 4, Iss 5, p e143 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Mitchell P Levesque Teva Vernoux Wolfgang Busch Hongchang Cui Jean Y Wang Ikram Blilou Hala Hassan Keiji Nakajima Noritaka Matsumoto Jan U Lohmann Ben Scheres Philip N Benfey Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
description	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.
format	article
author	Mitchell P Levesque Teva Vernoux Wolfgang Busch Hongchang Cui Jean Y Wang Ikram Blilou Hala Hassan Keiji Nakajima Noritaka Matsumoto Jan U Lohmann Ben Scheres Philip N Benfey
author_facet	Mitchell P Levesque Teva Vernoux Wolfgang Busch Hongchang Cui Jean Y Wang Ikram Blilou Hala Hassan Keiji Nakajima Noritaka Matsumoto Jan U Lohmann Ben Scheres Philip N Benfey
author_sort	Mitchell P Levesque
title	Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
title_short	Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
title_full	Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
title_fullStr	Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
title_full_unstemmed	Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
title_sort	whole-genome analysis of the short-root developmental pathway in arabidopsis.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/60cf484e09db4c1ea74ba379863f37dc
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Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.

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