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...et et al. 1998;sMartin et al. 2004). In starvation conditions, TOR regulates the utilization of alternativesenergy resources, allows autophagy and generally drives the cell towards survival pathwayss(=-=Beck and Hall 1999-=-; Kamada et al. 2004). The antibiotic rapamycin was found to mimicsstarvation responses in yeast through TOR inactivation and cell cycle arrest (Barbet et al.s1996). Rapamycin leads to the formation o...

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...essions andssubspecies, preventing the analysis of a "potential 5S dominance" (Tutois et al. 2002).sIn nonhybrid Arabidopsis thaliana, the RdDM silencing pathway (Herr et al. 2005; Kanno etsal. 2005; =-=Onodera et al. 2005-=-; Pontier et al. 2005; Zhang et al. 2007) which mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)sparticipates to 5S and 45S genes repression inv...

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...Of Rapamycin) pathway controls translation, growth and the cellscycle in response to environmental signals such as nutrients or growth stimulating factorss(Hay and Sonenberg 2004; Menand et al. 2002; =-=Schmelzle and Hall 2000-=-). Studies in yeastsand animal cells have shown that TOR acts positively on the activity of the eIF4F translationsinitiation complex and on the transcription of ribosomal protein and RNA genes therefo...

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...units is highly conserved between accessions andssubspecies, preventing the analysis of a "potential 5S dominance" (Tutois et al. 2002).sIn nonhybrid Arabidopsis thaliana, the RdDM silencing pathway (=-=Herr et al. 2005-=-; Kanno etsal. 2005; Onodera et al. 2005; Pontier et al. 2005; Zhang et al. 2007) which mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)spartici...

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...eIF4F translationsinitiation complex and on the transcription of ribosomal protein and RNA genes thereforespromoting growth in nutrient sufficient conditions (Beretta et al. 1996; Berset et al. 1998;s=-=Martin et al. 2004-=-). In starvation conditions, TOR regulates the utilization of alternativesenergy resources, allows autophagy and generally drives the cell towards survival pathwayss(Beck and Hall 1999; Kamada et al. ...

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...R acts positively on the activity of the eIF4F translationsinitiation complex and on the transcription of ribosomal protein and RNA genes thereforespromoting growth in nutrient sufficient conditions (=-=Beretta et al. 1996-=-; Berset et al. 1998;sMartin et al. 2004). In starvation conditions, TOR regulates the utilization of alternativesenergy resources, allows autophagy and generally drives the cell towards survival path...

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...s, preventing the analysis of a "potential 5S dominance" (Tutois et al. 2002).sIn nonhybrid Arabidopsis thaliana, the RdDM silencing pathway (Herr et al. 2005; Kanno etsal. 2005; Onodera et al. 2005; =-=Pontier et al. 2005-=-; Zhang et al. 2007) which mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)sparticipates to 5S and 45S genes repression involved in dosage contr...

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...sponses in yeast through TOR inactivation and cell cycle arrest (Barbet et al.s1996). Rapamycin leads to the formation of a ternary complex by binding simultaneously tosTOR and to the FKBP12 protein (=-=Choi et al. 1996-=-).sHowever, Arabidopsis thaliana, and more generally land plants were found to be resistant tosrapamycin due to mutations in the FKBP12 protein, suggesting TOR specificities in plants insat Pennsylvan...

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...the activity of the eIF4F translationsinitiation complex and on the transcription of ribosomal protein and RNA genes thereforespromoting growth in nutrient sufficient conditions (Beretta et al. 1996; =-=Berset et al. 1998-=-;sMartin et al. 2004). In starvation conditions, TOR regulates the utilization of alternativesenergy resources, allows autophagy and generally drives the cell towards survival pathwayss(Beck and Hall ...

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...ncing pathway (Herr et al. 2005; Kanno etsal. 2005; Onodera et al. 2005; Pontier et al. 2005; Zhang et al. 2007) which mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; =-=Wassenegger 2000-=-, 2005)sparticipates to 5S and 45S genes repression involved in dosage control (Blevins et al. 2009;sDouet et al. 2008; Douet et al. 2009; Earley et al. 2006; Preuss et al. 2008). The followingssectio...

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...bears considerable similarity in its secondary structure to plant 5S rRNA (Fu et al.s2009; Hammond et al. 2009), is alternatively skipped or included to produce either of the twostranscript isoforms (=-=Yoine et al. 2006-=-). The ES (Exon-skipped) isoform encodes the fullysfunctional TFIIIA protein. Instead, the EI (Exon-inclusion) isoform is eliminated by the NMDs(nonsense mediated decay) pathway. Two groups (Fu et al....

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...ammals and plants (reviewedsin McStay 2006; Tucker et al. 2010). Therefore, nucleolus forms around rRNA genessinherited from only one progenitor, whereas the other progenitor's rRNA genes are silents(=-=Chen and Pikaard 1997-=-). Nucleolar dominance has been well described in Arabidopsissat Pennsylvania State U niversity on M ay 8, 2016 http://pcp.oxfordjournals.org/ D ow nloaded from suecica, the allotetraploid hybrid of A...

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...00).sThe 45S genes are tandemly repeated at nucleolar organizer regions (NORs), termed as suchsbecause the nucleolus, the site of ribosome synthesis, is organized around rRNA genes duringsinterphase (=-=Lam et al. 2005-=-; Shaw and Doonan 2005). Around 570-750 copies of 45S genessper haploid genome are arranged in head to tail tandem arrays located at the tips of the shortsarms of chromosomes 2 and 4 (NOR 2 and 4) in ...

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...chsribosomal RNA is integrated in a ribosome, stoechiometric amounts of rRNA need to besproduced which requires a tight coordination between synthesis of the RNA and proteinsmoieties of the ribosome (=-=Laferte et al. 2006-=-).sThis review aims to compare 5S and 45S ribosomal RNA genes (named 5S and 45S genes insthis review) in the plant model Arabidopsis thaliana in terms of organization, transcriptionsand regulation, an...

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...te that phosphorylation of AtNUC-L1 by TORsmight be required for 5'ETS binding and activation of rRNA gene expression in Arabidopsis.sBinding of TOR to 5S rDNA has been reported in yeast and animals (=-=Li et al. 2006-=-; Wei et al.s2009) but not yet in Arabidopsis, even though the conservation of TOR suggests that TORsregulates also Pol III transcription in plants, to coordinate the transcription of the differentsrR...

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...been well described in Arabidopsissat Pennsylvania State U niversity on M ay 8, 2016 http://pcp.oxfordjournals.org/ D ow nloaded from suecica, the allotetraploid hybrid of A. thaliana and A. arenosa (=-=Chen et al. 1998-=-). In thisshybrid, the entire A. thaliana-derived NORs are selectively silenced, enriched for thesheterochromatic mark H3K9me2 and depleted for the euchromatic mark H3K4me3. However,sonly a subset of ...

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...nd 45S rDNA loci. It also suggests that the Pol Vscomplex might recruit other repressive epigenetic marks in addition to DNA methylation andsH3K9me2 which is dependent on DNA methylation at CG sites (=-=Mathieu et al. 2005-=-).sSince there is a need in the plant kingdom for rapid, reversible changes in gene expression tosrespond to growth demands or environmental changes, some of the rDNA repeats may besspecifically targe...

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...ar dominance describes thestranscription of 45S genes inherited from only one parent in genetic hybrids. Thesphenomenon is widespread, occuring in insects, amphibians, mammals and plants (reviewedsin =-=McStay 2006-=-; Tucker et al. 2010). Therefore, nucleolus forms around rRNA genessinherited from only one progenitor, whereas the other progenitor's rRNA genes are silents(Chen and Pikaard 1997). Nucleolar dominanc...

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...ome. Its transcription requires the 5S rDNAspecific transcription factor IIIA (TFIIIA) which binds to the internal promoter composed ofsthree conserved elements Box A, Intermediate Element and Box C (=-=Bogenhagen et al. 1980-=-;sat Pennsylvania State U niversity on M ay 8, 2016 http://pcp.oxfordjournals.org/ D ow nloaded from Cloix et al. 2000). The Arabidopsis internal promoter shows high sequence similarity with thesone i...

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...aryotic TOR (Target Of Rapamycin) pathway controls translation, growth and the cellscycle in response to environmental signals such as nutrients or growth stimulating factorss(Hay and Sonenberg 2004; =-=Menand et al. 2002-=-; Schmelzle and Hall 2000). Studies in yeastsand animal cells have shown that TOR acts positively on the activity of the eIF4F translationsinitiation complex and on the transcription of ribosomal prot...

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...ion initiation insA. thaliana (Doelling et al. 1993; Doelling and Pikaard 1995). Nucleolin, a nucleolar protein,splays a role in Pol I transcription and processing of 45S pre-rRNA (Gaume et al. 2011;s=-=Mongelard and Bouvet 2007-=-).sIn Arabidopsis, 5S and 45S arrays are physically separated. Wicke et al. (2011) recentlysreported that the physical linkage of all rRNA genes observed in streptophyte algae, mossessand lycophytes m...

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...nd inssome extent at CHG) decreases specifically in the 5'ETS sequences (Pontvianne et al. 2010).sConsidering the nucleosome remodeling activity of nucleolin proteins in mammals (Angelovset al. 2006; =-=Erard et al. 1988-=-; Kharrat et al. 1991), it is rational to propose that binding ofsAtNUC-L1 to rRNA genes may be required to position nucleosomes in specificstranscriptional frames that determine the "on" or "off" sta...

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...0 copies of 5S genes pershaploid genome, which are arranged in tandem arrays located within the pericentromericsheterochromatin of chromosomes 3, 4 and 5 in the Columbia accession (Figures 1B and 2)s(=-=Campell et al. 1992-=-). A typical 5S rDNA unit is 500 bp-long and consists of a 120 bpstranscribed sequence, with an internal promoter and an approximately 380 bp intergenicsspacer. Transcription by Pol III gives rise to ...

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...ase Is(Pol I), while 5S ribosomal RNAs are transcribed by RNA polymerase III (Pol III).sRibosomal RNAs (rRNA) associate with around 80 proteins to form the 40S and 60Ssribosomal subunits (Figure 1A) (=-=Korostelev and Noller 2007-=-). Since one molecule of eachsribosomal RNA is integrated in a ribosome, stoechiometric amounts of rRNA need to besproduced which requires a tight coordination between synthesis of the RNA and protein...

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...erg et al. 1984). The protein binds specifically within the internal control region (ICR)sof the 5S RNA gene and to the 5S RNA product. Zinc fingers 4 to 7 are responsible for thesbinding to 5S rRNA (=-=Clemens et al. 1993-=-) whereas fingers 1 to 3 are critical for the binding tosthe 3'-portion of the internal promoter (C-box element) of the Xenopus 5S gene (Clemens etsal. 1992). In yeast, a second species where TFIIIA h...

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...NA genes by TFIIIAsTranscription factor IIIA (TFIIIA) which was first isolated from Xenopus oocytes, containssnine zinc finger domains and is required for transcription of the 5S RNA gene by Pol IIIs(=-=Ginsberg et al. 1984-=-). The protein binds specifically within the internal control region (ICR)sof the 5S RNA gene and to the 5S RNA product. Zinc fingers 4 to 7 are responsible for thesbinding to 5S rRNA (Clemens et al. ...

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...,sonly a subset of the dominant A. arenosa 45S genes is active, decondensed and associatedswith H3K4me3 whereas the remaining excess, inactive fraction is heterochromatic andsassociated with H3K9me2 (=-=Lawrence et al. 2004-=-). HDT1 and HDA6, two histonesdeacetylases and DRM2 (DOMAINS REARRANGED METHYLTRANSFERASE 2) a desnovo methyltransferase, are required to maintain DNA hypermethylation at the promoters ofssilenced gen...

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...s of 5S siRNA andsconsequently 5S siRNA which match to the IGS overaccumulate (Blevins et al. 2009),sleading to enhanced RdDM and increased de novo methylation (Blevins et al. 2009) mediatedsby DRM2 (=-=Mathieu et al. 2007-=-) in these mutants. However, despite the 5S rDNAsasymmetrical hypermethylation in these mutants, 5S rDNA is hypomethylated at symmetricalscytosines leading to derepression of minor 5S genes. In absenc...

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...d Bouvet 2007). InsArabidopsis, AtNUC-L1 (a nucleolin-like protein) localizes in the nucleolus and plays a rolesin 45S rDNA chromatin condensation and in controlling homeostatic rRNA gene expressions(=-=Pontvianne et al. 2007-=-). For that, AtNUC-L1 specifically binds rRNA gene promoterssequences and directs rRNA transcription from the transcription initiation site (Pontvianne etsal. 2007). To demonstrate that AtNUC-L1 inter...

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... rRNA expressionsThe eukaryotic TOR (Target Of Rapamycin) pathway controls translation, growth and the cellscycle in response to environmental signals such as nutrients or growth stimulating factorss(=-=Hay and Sonenberg 2004-=-; Menand et al. 2002; Schmelzle and Hall 2000). Studies in yeastsand animal cells have shown that TOR acts positively on the activity of the eIF4F translationsinitiation complex and on the transcripti...

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...in et al. 2004). In starvation conditions, TOR regulates the utilization of alternativesenergy resources, allows autophagy and generally drives the cell towards survival pathwayss(Beck and Hall 1999; =-=Kamada et al. 2004-=-). The antibiotic rapamycin was found to mimicsstarvation responses in yeast through TOR inactivation and cell cycle arrest (Barbet et al.s1996). Rapamycin leads to the formation of a ternary complex ...

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...roundsthe NORs during transcription by Pol I (Figure 2) (Saez-Vasquez and Medina 2008). Indeed,sa loop of decondensed 45S rDNA repeats that originates from the NOR has been observed insthe nucleolus (=-=Probst et al. 2004-=-). Excess, inactive 45S genes are highly condensed andssequestered in heterochromatin at the external periphery of the nucleolus (Raska et al. 2004;sSaez-Vasquez and Medina 2008; Shaw and Jordan 1995)...

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...NA loci are activesEukaryotes contain thousands of rRNA genes, and it has been believed that the number ofsthese genes far exceeds the number expected to be required to supply ample cytoplasmicsrRNA (=-=Rogers and Bendich 1987-=-) and excess copies are transcriptionally repressed. Indeed,sheterochromatic chromocenters (CC), that can easily be observed as bright DAPI-positivesdomains with fluorescence microscopy (Figure 2), an...

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...the promoters ofssilenced genes, whereas acetylated histones H3K9, H3K14 and tetra-acetylated histone H4s(K5, K8, K12 and K16) are associated with active promoters whose cytosines areshypomethylated (=-=Earley et al. 2006-=-; Lawrence et al. 2004). RNAi-mediated knockdown ofsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2), DCL3 (DICER like protein) orsDRM2, components of the RdDM (RNA-directed DNA methylation) pathway (Matzke et a...

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...g AtNUC-L2 (a second nucleolin-like protein) andsother small RNA (Pontvianne et al. 2007). The Atnuc-L1 mutant also showed a significantlysreduced sugar-induced expression of ribosomal protein genes (=-=Kojima et al. 2007-=-). Thereforeswe can expect that nucleolin protein from plants might also control expression of Pol IIIsgenes. However to date whether or not Pol III transcription of 5S rRNA is affected in AtnucL1 has...

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...es from the NOR has been observed insthe nucleolus (Probst et al. 2004). Excess, inactive 45S genes are highly condensed andssequestered in heterochromatin at the external periphery of the nucleolus (=-=Raska et al. 2004-=-;sSaez-Vasquez and Medina 2008; Shaw and Jordan 1995).sThese results provide evidence that for both rDNA families, a fraction of the genes "escapes"sfrom heterochromatin to be transcribed.sTranscripti...

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... 45S genessper haploid genome are arranged in head to tail tandem arrays located at the tips of the shortsarms of chromosomes 2 and 4 (NOR 2 and 4) in Arabidopsis (Figure 1B) (Copenhaver et al.s1995; =-=Copenhaver and Pikaard 1996-=-). Each rRNA gene transcription unit is ~10 kb-long andsconsists of sequences encoding a precursor transcript that includes the structural rRNAs (18S,s5.8S, 25S), the Internal Transcribed Spacers (ITS...

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...hesIGS. The sequences extending from –55 upstream to +6 downstream from the transcriptionsstart site (+1) are sufficient to program minimal and accurate Pol I transcription initiation insA. thaliana (=-=Doelling et al. 1993-=-; Doelling and Pikaard 1995). Nucleolin, a nucleolar protein,splays a role in Pol I transcription and processing of 45S pre-rRNA (Gaume et al. 2011;sMongelard and Bouvet 2007).sIn Arabidopsis, 5S and ...

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... composed ofsthree conserved elements Box A, Intermediate Element and Box C (Bogenhagen et al. 1980;sat Pennsylvania State U niversity on M ay 8, 2016 http://pcp.oxfordjournals.org/ D ow nloaded from =-=Cloix et al. 2000-=-). The Arabidopsis internal promoter shows high sequence similarity with thesone in Xenopus 5S RNA genes (Bogenhagen et al. 1980; Cloix et al. 2000).sThe 45S genes are tandemly repeated at nucleolar o...

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... regions are eliminated in DCL3-RNAi lines and are depleted insRDR2-RNAi plants, suggesting a role for the siRNAs in the selective silencing of A. thalianaderived rRNA genes (Costa-Nunes et al. 2010; =-=Preuss et al. 2008-=-; Tucker et al. 2010).sInterestingly, when silent A. thaliana-derived rRNA genes subjected to nucleolar dominancesare derepressed with aza-dC (an inhibitor of DNA methylation) or TSA (histone deacetyl...

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...and Echeverria 2006). Transcription by Pol Isgives rise to a precursor or pre-rRNA, which is then processed into the 18S, 5.8S and 25SsrRNA mature forms (Gruendler et al. 1991; Gruendler et al. 1989; =-=Unfried et al. 1989-=-),sintegrated in the ribosome (Figure 1A). Transcription starts from the promoter localized in thesIGS. The sequences extending from –55 upstream to +6 downstream from the transcriptionsstart site (+1...

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.... 1992). In yeast, a second species where TFIIIA has been extensively studied, the ICR is assurprisingly short control region relative to the ICRs of Xenopus and Arabidopsis which areshighly similar (=-=Challice and Segall 1989-=-; Cloix et al. 2000). Later, the TFIIIA protein, presentsin every organism, has been characterized in several other species including Arabidopsissthaliana where it binds both 5S rDNA and 5S rRNA. It s...

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...ional repression between 5S and 45SsrDNA.sEarley et al. (2010) analysed the molecular basis for 45S rDNA repression in A. thaliana. Inshda6 mutants, symmetric methylation at CG/CNG motifs is reduced (=-=Earley et al. 2010-=-).sSurprisingly, spurious Pol II transcription occurs throughout the intergenic spacers. Thesresulting sense and antisense spacer transcripts facilitate a massive overproduction of siRNAsdiced by two ...

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...a;sVaillant et al. 2007). In addition, a particular set of transcripts, termed 5S-210, that extendsinto the intergenic spacer (IGS) downstream of 5S RNA genes overaccumulate in met1 andsddm1 mutants (=-=Vaillant et al. 2006-=-). These transcripts are the precursors of 5S siRNA andsconsequently 5S siRNA which match to the IGS overaccumulate (Blevins et al. 2009),sleading to enhanced RdDM and increased de novo methylation (B...

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...extending from –55 upstream to +6 downstream from the transcriptionsstart site (+1) are sufficient to program minimal and accurate Pol I transcription initiation insA. thaliana (Doelling et al. 1993; =-=Doelling and Pikaard 1995-=-). Nucleolin, a nucleolar protein,splays a role in Pol I transcription and processing of 45S pre-rRNA (Gaume et al. 2011;sMongelard and Bouvet 2007).sIn Arabidopsis, 5S and 45S arrays are physically s...

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... bysan Inter Genic Spacer (IGS) (Sáez-Vásquez and Echeverria 2006). Transcription by Pol Isgives rise to a precursor or pre-rRNA, which is then processed into the 18S, 5.8S and 25SsrRNA mature forms (=-=Gruendler et al. 1991-=-; Gruendler et al. 1989; Unfried et al. 1989),sintegrated in the ribosome (Figure 1A). Transcription starts from the promoter localized in thesIGS. The sequences extending from –55 upstream to +6 down...

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...ormed in thesnucleolus. There is now extensive evidence of 5S gene clusters at chromosomal locationssdistant from the 45S rDNA that preferentially associate with the nucleolus or nucleolarsperiphery (=-=Haeusler and Engelke 2006-=-; Montijn et al. 1999). Whether this is the case insArabidopsis merits investigation.sNucleolar dominance and repression of ribosomal RNA genes are mediated bysepigenetic mechanismssAs reported above,...

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...t CHG) decreases specifically in the 5'ETS sequences (Pontvianne et al. 2010).sConsidering the nucleosome remodeling activity of nucleolin proteins in mammals (Angelovset al. 2006; Erard et al. 1988; =-=Kharrat et al. 1991-=-), it is rational to propose that binding ofsAtNUC-L1 to rRNA genes may be required to position nucleosomes in specificstranscriptional frames that determine the "on" or "off" state ofsrRNA genes. Man...

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... with 5-aza C or in thesmutant of the chromatin remodeling factor DDM1, symmetric methylation at CG/CNG motifssis reduced, and a silencing release of minor 5S genes is observed (Mathieu et al. 2003a;s=-=Vaillant et al. 2007-=-). In addition, a particular set of transcripts, termed 5S-210, that extendsinto the intergenic spacer (IGS) downstream of 5S RNA genes overaccumulate in met1 andsddm1 mutants (Vaillant et al. 2006). ...

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...er (IGS) (Sáez-Vásquez and Echeverria 2006). Transcription by Pol Isgives rise to a precursor or pre-rRNA, which is then processed into the 18S, 5.8S and 25SsrRNA mature forms (Gruendler et al. 1991; =-=Gruendler et al. 1989-=-; Unfried et al. 1989),sintegrated in the ribosome (Figure 1A). Transcription starts from the promoter localized in thesIGS. The sequences extending from –55 upstream to +6 downstream from the transcr...

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...s are tandemly repeated at nucleolar organizer regions (NORs), termed as suchsbecause the nucleolus, the site of ribosome synthesis, is organized around rRNA genes duringsinterphase (Lam et al. 2005; =-=Shaw and Doonan 2005-=-). Around 570-750 copies of 45S genessper haploid genome are arranged in head to tail tandem arrays located at the tips of the shortsarms of chromosomes 2 and 4 (NOR 2 and 4) in Arabidopsis (Figure 1B...

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...s in the FKBP12 protein, suggesting TOR specificities in plants insat Pennsylvania State U niversity on M ay 8, 2016 http://pcp.oxfordjournals.org/ D ow nloaded from addition to conserved activities (=-=Sormani et al. 2007-=-). Indeed, TOR controls embryogenesis,spost-embryonic development and 45S rRNA production by phosphorylation of varioussdownstream targets in Arabidopsis. ChIP experiments have shown that TOR activate...

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...NA unit is 500 bp-long and consists of a 120 bpstranscribed sequence, with an internal promoter and an approximately 380 bp intergenicsspacer. Transcription by Pol III gives rise to a 120 nt 5S rRNA (=-=Cloix et al. 2002-=-) which issintegrated into the large subunit of the ribosome. Its transcription requires the 5S rDNAspecific transcription factor IIIA (TFIIIA) which binds to the internal promoter composed ofsthree c...

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... the pericentromeric 5Sslocus on chromosome 5 are not randomly positioned along the 5S array. This analysissrevealed an increasing number of mutations along the 5S locus (AGI 2000; Cloix et al. 2002;s=-=Vaillant et al. 2008-=-). This suggests that 5S major genes, constitutively transcribed, reside atsthe euchromatic side of the 5S array. The most mutated 5S genes (containing 3 to 10smutations in their coding sequence) at t...

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...ang et al. 2007) which mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)sparticipates to 5S and 45S genes repression involved in dosage control (=-=Blevins et al. 2009-=-;sDouet et al. 2008; Douet et al. 2009; Earley et al. 2006; Preuss et al. 2008). The followingssection presents the common principles in transcriptional repression between 5S and 45SsrDNA.sEarley et a...

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...re is now extensive evidence of 5S gene clusters at chromosomal locationssdistant from the 45S rDNA that preferentially associate with the nucleolus or nucleolarsperiphery (Haeusler and Engelke 2006; =-=Montijn et al. 1999-=-). Whether this is the case insArabidopsis merits investigation.sNucleolar dominance and repression of ribosomal RNA genes are mediated bysepigenetic mechanismssAs reported above, the repression of rR...

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...describes thestranscription of 45S genes inherited from only one parent in genetic hybrids. Thesphenomenon is widespread, occuring in insects, amphibians, mammals and plants (reviewedsin McStay 2006; =-=Tucker et al. 2010-=-). Therefore, nucleolus forms around rRNA genessinherited from only one progenitor, whereas the other progenitor's rRNA genes are silents(Chen and Pikaard 1997). Nucleolar dominance has been well desc...

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...DNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)sparticipates to 5S and 45S genes repression involved in dosage control (Blevins et al. 2009;sDouet et al. 2008; =-=Douet et al. 2009-=-; Earley et al. 2006; Preuss et al. 2008). The followingssection presents the common principles in transcriptional repression between 5S and 45SsrDNA.sEarley et al. (2010) analysed the molecular basis...

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... al. 2006). The ES (Exon-skipped) isoform encodes the fullysfunctional TFIIIA protein. Instead, the EI (Exon-inclusion) isoform is eliminated by the NMDs(nonsense mediated decay) pathway. Two groups (=-=Fu et al. 2009-=-; Hammond et al. 2009)sproposed a post-transcriptional negative feedback auto-regulation model specific to plantsTFIIIA genes. The model stipulates that when TFIIIA protein levels are low, the alterna...

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...ences (Figure 2) indicates that A. thaliana contains three major 45S gene variants,sVAR1, VAR2 and VAR3 representing respectively 48, 30 and 22% of total 45S genes, and thesvery low copy number VAR4 (=-=Pontvianne et al. 2010-=-). Remarkably, VAR2, 3 and 4 aresexpressed in WT plants, however we do not know whether all copies are transcribed, whereassthe most highly represented VAR1 is inactive. However, VAR1 is transcribed i...

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...o apply to 5S rDNA loci. However, the sequence ofsthe transcribed region of 5S rDNA units is highly conserved between accessions andssubspecies, preventing the analysis of a "potential 5S dominance" (=-=Tutois et al. 2002-=-).sIn nonhybrid Arabidopsis thaliana, the RdDM silencing pathway (Herr et al. 2005; Kanno etsal. 2005; Onodera et al. 2005; Pontier et al. 2005; Zhang et al. 2007) which mediates de novosDNA methylati...

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...ns with fluorescence microscopy (Figure 2), and which are sites where heterochromatinscoalesces (Fransz et al. 2002), include centromeric repeats, other heterochromatic repeats andssilent rRNA genes (=-=Costa-Nunes et al. 2010-=-). From these observations, the followingsquestions arose: what distinguishes active and silent rRNA genes, do they differ in primaryssequence and how is their differential regulation achieved?sIn the...

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...on. Hammond et al. (2009) demonstrated that ribosomalsprotein L5 directly binds the 5S rRNA-like structure of the alternative exon, which parallels asknown binding interaction between L5 and 5S rRNA (=-=Szymanski et al. 2002-=-). This bindingspromotes exon skipping and is expected to promote production of the TFIIIA protein.sThis model stipulates a quantitative regulation of the 5S rRNA transcription by TFIIIA andsillustrat...

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...h mediates de novosDNA methylation at asymmetrical CHH sites (Huettel et al. 2007; Wassenegger 2000, 2005)sparticipates to 5S and 45S genes repression involved in dosage control (Blevins et al. 2009;s=-=Douet et al. 2008-=-; Douet et al. 2009; Earley et al. 2006; Preuss et al. 2008). The followingssection presents the common principles in transcriptional repression between 5S and 45SsrDNA.sEarley et al. (2010) analysed ...

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...S), the Internal Transcribed Spacers (ITS) and the External Transcribed Spacerss(ETS) (Figure 2). The rRNA gene units are separated from the adjacent gene in the array bysan Inter Genic Spacer (IGS) (=-=Sáez-Vásquez and Echeverria 2006-=-). Transcription by Pol Isgives rise to a precursor or pre-rRNA, which is then processed into the 18S, 5.8S and 25SsrRNA mature forms (Gruendler et al. 1991; Gruendler et al. 1989; Unfried et al. 1989...

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...2016 http://pcp.oxfordjournals.org/ D ow nloaded from The nucleolus is a substructure that results from expression of 45S genes. It is formed aroundsthe NORs during transcription by Pol I (Figure 2) (=-=Saez-Vasquez and Medina 2008-=-). Indeed,sa loop of decondensed 45S rDNA repeats that originates from the NOR has been observed insthe nucleolus (Probst et al. 2004). Excess, inactive 45S genes are highly condensed andssequestered ...

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...s (Probst et al. 2004). Excess, inactive 45S genes are highly condensed andssequestered in heterochromatin at the external periphery of the nucleolus (Raska et al. 2004;sSaez-Vasquez and Medina 2008; =-=Shaw and Jordan 1995-=-).sThese results provide evidence that for both rDNA families, a fraction of the genes "escapes"sfrom heterochromatin to be transcribed.sTranscription by Pol I but also maturation steps of the precurs...

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...sults from a 5SsRNA exonization in the gene that occured early in evolution of angiosperms. This exon,swhich bears considerable similarity in its secondary structure to plant 5S rRNA (Fu et al.s2009; =-=Hammond et al. 2009-=-), is alternatively skipped or included to produce either of the twostranscript isoforms (Yoine et al. 2006). The ES (Exon-skipped) isoform encodes the fullysfunctional TFIIIA protein. Instead, the EI...