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Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana.

Pontvianne F, Abou-Ellail M, Douet J, Comella P, Matia I, Chandrasekhara C, Debures A, Blevins T, Cooke R, Medina FJ, Tourmente S, Pikaard CS, Sáez-Vásquez J - PLoS Genet. (2010)

Bottom Line: We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately.Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes.Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.

View Article: PubMed Central - PubMed

Affiliation: UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France.

ABSTRACT
In eukaryotes, 45S rRNA genes are arranged in tandem arrays in copy numbers ranging from several hundred to several thousand in plants. Although it is clear that not all copies are transcribed under normal growth conditions, the molecular basis controlling the expression of specific sets of rRNA genes remains unclear. Here, we report four major rRNA gene variants in Arabidopsis thaliana. Interestingly, while transcription of one of these rRNA variants is induced, the others are either repressed or remain unaltered in A. thaliana plants with a disrupted nucleolin-like protein gene (Atnuc-L1). Remarkably, the most highly represented rRNA gene variant, which is inactive in WT plants, is reactivated in Atnuc-L1 mutants. We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately. Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes. Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.

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AtNUC-L1 controls symmetrical DNA methylation and nucleosome positioning to determine the “on” or “off” state of transcriptionally active rRNA genes.In WT plants AtNUC-L1 (in green) binds chromatin and 5′ETS rRNA sequences. AtNUC-L1 binding to the 5′ETS might maintain a suitable gene methylation pattern (red bullets) to set nucleosome (in grey) positioning and transcription from the GP. In this model, AtNUC-L1 might be required for nucleolar localization, assembly and/or activity of DNA-MT, MC-BP or DME/ROS1 protein complexes that repress or active rRNA transcription of specific loci in WT plants.
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pgen-1001225-g008: AtNUC-L1 controls symmetrical DNA methylation and nucleosome positioning to determine the “on” or “off” state of transcriptionally active rRNA genes.In WT plants AtNUC-L1 (in green) binds chromatin and 5′ETS rRNA sequences. AtNUC-L1 binding to the 5′ETS might maintain a suitable gene methylation pattern (red bullets) to set nucleosome (in grey) positioning and transcription from the GP. In this model, AtNUC-L1 might be required for nucleolar localization, assembly and/or activity of DNA-MT, MC-BP or DME/ROS1 protein complexes that repress or active rRNA transcription of specific loci in WT plants.

Mentions: A few years ago we reported a plant nucleolin containing -U3snoRNP complex that specifically binds four conserved motifs in the 5′ETS (A123B, shown in Figure S8) and proposed a role for this complex in coupling transcription and processing of pre-rRNA [54], [55]. Here we demonstrate that AtNUC-L1 interacts directly with 5′ETS rRNA gene sequences but does not co-precipitate with RNA Pol I subunits (Figure S8). Thus, considering the nucleosome remodeling activity of nucleolin proteins [23], [56], it is rational to propose that binding of AtNUC-L1 to rRNA genes may be required to position nucleosomes in specific transcriptional frames that determine the ‘on’ or ‘off’ state of transcriptional active rRNA genes (Figure 8). Accordingly, demethylation of the 5′ETS rRNA gene sequences and activation of VAR1 suggest that AtNUC-L1 maintains gene methylation required for accurate nucleosome position for transcription (Figure 8). Indeed, several studies point to a major role of CpG methylation in nucleosome positioning and binding of multiples protein factors could be involve in repositioning of nucleosome [57], [58]. In this context, AtNUC-L1 activity might be required for rRNA gene methylation or demethylation to repress or activates RNA Pol I transcription. We do not know if AtNUC-L1 interacts with any DNA Methyl transferase (DNA-MT), demethylases (DME/ROS1) and/or Methyl cytocine –Binding protein (Mc-BP) (For references [59], [60]). However, nucleolin like proteins in plants interact in a large Ribo Nucleoprotein Complex (RNP) with the RNA methyltranferase fibrillarin (Figure S8) and other DNA/RNA modification activities, including RdRP and TSN proteins, which have been implicated in chromatin silencing [55].


Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana.

Pontvianne F, Abou-Ellail M, Douet J, Comella P, Matia I, Chandrasekhara C, Debures A, Blevins T, Cooke R, Medina FJ, Tourmente S, Pikaard CS, Sáez-Vásquez J - PLoS Genet. (2010)

AtNUC-L1 controls symmetrical DNA methylation and nucleosome positioning to determine the “on” or “off” state of transcriptionally active rRNA genes.In WT plants AtNUC-L1 (in green) binds chromatin and 5′ETS rRNA sequences. AtNUC-L1 binding to the 5′ETS might maintain a suitable gene methylation pattern (red bullets) to set nucleosome (in grey) positioning and transcription from the GP. In this model, AtNUC-L1 might be required for nucleolar localization, assembly and/or activity of DNA-MT, MC-BP or DME/ROS1 protein complexes that repress or active rRNA transcription of specific loci in WT plants.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2991258&req=5

pgen-1001225-g008: AtNUC-L1 controls symmetrical DNA methylation and nucleosome positioning to determine the “on” or “off” state of transcriptionally active rRNA genes.In WT plants AtNUC-L1 (in green) binds chromatin and 5′ETS rRNA sequences. AtNUC-L1 binding to the 5′ETS might maintain a suitable gene methylation pattern (red bullets) to set nucleosome (in grey) positioning and transcription from the GP. In this model, AtNUC-L1 might be required for nucleolar localization, assembly and/or activity of DNA-MT, MC-BP or DME/ROS1 protein complexes that repress or active rRNA transcription of specific loci in WT plants.
Mentions: A few years ago we reported a plant nucleolin containing -U3snoRNP complex that specifically binds four conserved motifs in the 5′ETS (A123B, shown in Figure S8) and proposed a role for this complex in coupling transcription and processing of pre-rRNA [54], [55]. Here we demonstrate that AtNUC-L1 interacts directly with 5′ETS rRNA gene sequences but does not co-precipitate with RNA Pol I subunits (Figure S8). Thus, considering the nucleosome remodeling activity of nucleolin proteins [23], [56], it is rational to propose that binding of AtNUC-L1 to rRNA genes may be required to position nucleosomes in specific transcriptional frames that determine the ‘on’ or ‘off’ state of transcriptional active rRNA genes (Figure 8). Accordingly, demethylation of the 5′ETS rRNA gene sequences and activation of VAR1 suggest that AtNUC-L1 maintains gene methylation required for accurate nucleosome position for transcription (Figure 8). Indeed, several studies point to a major role of CpG methylation in nucleosome positioning and binding of multiples protein factors could be involve in repositioning of nucleosome [57], [58]. In this context, AtNUC-L1 activity might be required for rRNA gene methylation or demethylation to repress or activates RNA Pol I transcription. We do not know if AtNUC-L1 interacts with any DNA Methyl transferase (DNA-MT), demethylases (DME/ROS1) and/or Methyl cytocine –Binding protein (Mc-BP) (For references [59], [60]). However, nucleolin like proteins in plants interact in a large Ribo Nucleoprotein Complex (RNP) with the RNA methyltranferase fibrillarin (Figure S8) and other DNA/RNA modification activities, including RdRP and TSN proteins, which have been implicated in chromatin silencing [55].

Bottom Line: We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately.Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes.Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.

View Article: PubMed Central - PubMed

Affiliation: UMR 5096 CNRS-IRD-University de Perpignan, Perpignan, France.

ABSTRACT
In eukaryotes, 45S rRNA genes are arranged in tandem arrays in copy numbers ranging from several hundred to several thousand in plants. Although it is clear that not all copies are transcribed under normal growth conditions, the molecular basis controlling the expression of specific sets of rRNA genes remains unclear. Here, we report four major rRNA gene variants in Arabidopsis thaliana. Interestingly, while transcription of one of these rRNA variants is induced, the others are either repressed or remain unaltered in A. thaliana plants with a disrupted nucleolin-like protein gene (Atnuc-L1). Remarkably, the most highly represented rRNA gene variant, which is inactive in WT plants, is reactivated in Atnuc-L1 mutants. We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately. Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes. Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.

Show MeSH