Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Identifieur interne : 003855 ( Main/Exploration ); précédent : 003854; suivant : 003856Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Auteurs : Todd P. Michael [États-Unis] ; Todd C. Mockler ; Ghislain Breton ; Connor Mcentee ; Amanda Byer ; Jonathan D. Trout ; Samuel P. Hazen ; Rongkun Shen ; Henry D. Priest ; Christopher M. Sullivan ; Scott A. Givan ; Marcelo Yanovsky ; Fangxin Hong ; Steve A. Kay ; Joanne ChorySource :
- PLoS genetics [ 1553-7404 ] ; 2008.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Arabidopsis (physiologie), Bases de données génétiques (MeSH), Facteurs de transcription (génétique), Gènes de plante (MeSH), Gènes rapporteurs (MeSH), Génome végétal (MeSH), Luciferases (génétique), Modèles génétiques (MeSH), Oryza (génétique), Oryza (physiologie), Photopériode (MeSH), Populus (génétique), Populus (physiologie), Protéines d'Arabidopsis (biosynthèse), Protéines d'Arabidopsis (génétique), Protéines de liaison à l'ADN (génétique), Rythme circadien (génétique), Rythme circadien (physiologie), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'espèce (MeSH), Séquençage par oligonucléotides en batterie (MeSH), Température (MeSH), Végétaux génétiquement modifiés (MeSH).
- MESH :
- biosynthèse : Protéines d'Arabidopsis.
- génétique : Arabidopsis, Facteurs de transcription, Luciferases, Oryza, Populus, Protéines d'Arabidopsis, Protéines de liaison à l'ADN, Rythme circadien.
- physiologie : Arabidopsis, Oryza, Populus, Rythme circadien.
- Analyse de profil d'expression de gènes, Bases de données génétiques, Gènes de plante, Gènes rapporteurs, Génome végétal, Modèles génétiques, Photopériode, Régulation de l'expression des gènes végétaux, Spécificité d'espèce, Séquençage par oligonucléotides en batterie, Température, Végétaux génétiquement modifiés.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Arabidopsis (physiology), Arabidopsis Proteins (biosynthesis), Arabidopsis Proteins (genetics), Circadian Rhythm (genetics), Circadian Rhythm (physiology), DNA-Binding Proteins (genetics), Databases, Genetic (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Genes, Reporter (MeSH), Genome, Plant (MeSH), Luciferases (genetics), Models, Genetic (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Oryza (genetics), Oryza (physiology), Photoperiod (MeSH), Plants, Genetically Modified (MeSH), Populus (genetics), Populus (physiology), Species Specificity (MeSH), Temperature (MeSH), Transcription Factors (genetics).
- MESH :
- chemical , biosynthesis : Arabidopsis Proteins.
- genetics : Arabidopsis, Arabidopsis Proteins, Circadian Rhythm, DNA-Binding Proteins, Luciferases, Oryza, Populus, Transcription Factors.
- physiology : Arabidopsis, Circadian Rhythm, Oryza, Populus.
- Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Genes, Reporter, Genome, Plant, Models, Genetic, Oligonucleotide Array Sequence Analysis, Photoperiod, Plants, Genetically Modified, Species Specificity, Temperature.
Abstract
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.
DOI: 10.1371/journal.pgen.0040014
PubMed: 18248097
PubMed Central: PMC2222925
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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<front><div type="abstract" xml:lang="en">Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.</div>
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<Abstract><AbstractText>Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.</AbstractText>
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