Determinants of nucleosome positioning and their influence on plant gene expression.
Identifieur interne : 001831 ( Main/Exploration ); précédent : 001830; suivant : 001832Determinants of nucleosome positioning and their influence on plant gene expression.
Auteurs : Ming-Jung Liu [États-Unis] ; Alexander E. Seddon [États-Unis] ; Zing Tsung-Yeh Tsai [États-Unis] ; Ian T. Major [États-Unis] ; Monique Floer [États-Unis] ; Gregg A. Howe [États-Unis] ; Shin-Han Shiu [États-Unis]Source :
- Genome research [ 1549-5469 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN des plantes (), ADN des plantes (métabolisme), Analyse de profil d'expression de gènes (), Arabidopsis (), Arabidopsis (génétique), Arabidopsis (métabolisme), Composition en bases nucléiques, Cyclopentanes (pharmacologie), Nucléosomes (), Nucléosomes (métabolisme), Oxylipines (pharmacologie), Régulation de l'expression des gènes végétaux (), Sites de fixation (), Éléments de régulation transcriptionnelle ().
- MESH :
- génétique : Arabidopsis.
- métabolisme : ADN des plantes, Arabidopsis, Nucléosomes.
- pharmacologie : Cyclopentanes, Oxylipines.
- ADN des plantes, Analyse de profil d'expression de gènes, Arabidopsis, Composition en bases nucléiques, Nucléosomes, Régulation de l'expression des gènes végétaux, Sites de fixation, Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- Arabidopsis (drug effects), Arabidopsis (genetics), Arabidopsis (metabolism), Base Composition, Binding Sites (drug effects), Cyclopentanes (pharmacology), DNA, Plant (chemistry), DNA, Plant (metabolism), Gene Expression Profiling (methods), Gene Expression Regulation, Plant (drug effects), Nucleosomes (chemistry), Nucleosomes (drug effects), Nucleosomes (metabolism), Oxylipins (pharmacology), Regulatory Elements, Transcriptional (drug effects).
- MESH :
- chemical , chemistry : DNA, Plant, Nucleosomes.
- chemical , drug effects : Nucleosomes.
- chemical , metabolism : DNA, Plant, Nucleosomes.
- chemical , pharmacology : Cyclopentanes, Oxylipins.
- drug effects : Arabidopsis, Binding Sites, Gene Expression Regulation, Plant, Regulatory Elements, Transcriptional.
- genetics : Arabidopsis.
- metabolism : Arabidopsis.
- methods : Gene Expression Profiling.
- Base Composition.
Abstract
Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.
DOI: 10.1101/gr.188680.114
PubMed: 26063739
Affiliations:
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Le document en format XML
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<term>Arabidopsis (genetics)</term>
<term>Arabidopsis (metabolism)</term>
<term>Base Composition</term>
<term>Binding Sites (drug effects)</term>
<term>Cyclopentanes (pharmacology)</term>
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<term>DNA, Plant (metabolism)</term>
<term>Gene Expression Profiling (methods)</term>
<term>Gene Expression Regulation, Plant (drug effects)</term>
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<term>Nucleosomes (drug effects)</term>
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<term>Analyse de profil d'expression de gènes ()</term>
<term>Arabidopsis ()</term>
<term>Arabidopsis (génétique)</term>
<term>Arabidopsis (métabolisme)</term>
<term>Composition en bases nucléiques</term>
<term>Cyclopentanes (pharmacologie)</term>
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<term>Oxylipines (pharmacologie)</term>
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<front><div type="abstract" xml:lang="en">Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits. </div>
</front>
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