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An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation

Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem c...

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Autores principales: Tian, Caihuan, Zhang, Xiaoni, He, Jun, Yu, Haopeng, Wang, Ying, Shi, Bihai, Han, Yingying, Wang, Guoxun, Feng, Xiaoming, Zhang, Cui, Wang, Jin, Qi, Jiyan, Yu, Rong, Jiao, Yuling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BlackWell Publishing Ltd 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299377/
https://www.ncbi.nlm.nih.gov/pubmed/25358340
http://dx.doi.org/10.15252/msb.20145470
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author Tian, Caihuan
Zhang, Xiaoni
He, Jun
Yu, Haopeng
Wang, Ying
Shi, Bihai
Han, Yingying
Wang, Guoxun
Feng, Xiaoming
Zhang, Cui
Wang, Jin
Qi, Jiyan
Yu, Rong
Jiao, Yuling
author_facet Tian, Caihuan
Zhang, Xiaoni
He, Jun
Yu, Haopeng
Wang, Ying
Shi, Bihai
Han, Yingying
Wang, Guoxun
Feng, Xiaoming
Zhang, Cui
Wang, Jin
Qi, Jiyan
Yu, Rong
Jiao, Yuling
author_sort Tian, Caihuan
collection PubMed
description Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellular-resolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein–DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process.
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spelling pubmed-42993772015-01-20 An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation Tian, Caihuan Zhang, Xiaoni He, Jun Yu, Haopeng Wang, Ying Shi, Bihai Han, Yingying Wang, Guoxun Feng, Xiaoming Zhang, Cui Wang, Jin Qi, Jiyan Yu, Rong Jiao, Yuling Mol Syst Biol Articles Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellular-resolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein–DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process. BlackWell Publishing Ltd 2014-10-30 /pmc/articles/PMC4299377/ /pubmed/25358340 http://dx.doi.org/10.15252/msb.20145470 Text en © 2014 The Authors. Published under the terms of the CC BY 4.0 license http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Tian, Caihuan
Zhang, Xiaoni
He, Jun
Yu, Haopeng
Wang, Ying
Shi, Bihai
Han, Yingying
Wang, Guoxun
Feng, Xiaoming
Zhang, Cui
Wang, Jin
Qi, Jiyan
Yu, Rong
Jiao, Yuling
An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title_full An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title_fullStr An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title_full_unstemmed An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title_short An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
title_sort organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299377/
https://www.ncbi.nlm.nih.gov/pubmed/25358340
http://dx.doi.org/10.15252/msb.20145470
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