Analysis of the 5S RNA Pool in <i>Arabidopsis thaliana</i>: RNAs Are Heterogeneous and Only Two of the Genomic 5S Loci Produce Mature 5S RNA

Cloix, Catherine; Tutois, Sylvie; Yukawa, Yasushi; Mathieu, Olivier; Cuvillier, C.; Espagnol, M.C.; Picard, Georges; Tourmente, Sylvette

doi:10.1101/gr.181301

Cited by 59 publications

(86 citation statements)

References 72 publications

(81 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Reciprocally, a higher proportion of 5S rDNA sequences from chromosome 3 were recovered by H3mK4 ChIP in the wild-type versus the ddm1 background. Because 5S rDNA loci from chromosome 3 are not transcribed in vivo because of the presence of numerous mutations (Cloix et al, 2002), the ChIP results for this locus cannot be correlated with 5S rDNA expression. …”

Section: Transcribed 5s Rdna Loci Are Less Associated With H3mk9 In Dmentioning

confidence: 99%

“…We then investigated whether changes in histone H3 methylation were distributed equally through the 5S rDNA regions, with the potential to be transcribed on chromosome 4 and the large locus of chromosome 5 versus nontranscribed regions on chromosome 3. For this purpose, ChIP PCR products from three independent ChIP experiments were sequenced and assigned to the corresponding 5S rDNA loci through the T-stretch signature present downstream of the transcribed region (Table 3) (Cloix et al, 2002). This analysis revealed that 5S rRNA genes from transcribed loci were significantly (Z test, P ϭ 0.05) more associated with H3mK9 in the wild type (89.7%) than in ddm1 (70.8%).…”

Section: Transcribed 5s Rdna Loci Are Less Associated With H3mk9 In Dmentioning

confidence: 99%

“…Arabidopsis expresses a major 5S rRNA transcript and some minor species that differ from the major transcript by one or two base substitutions. The 5S rDNA units homologous with major and minor 5S rRNA transcripts have been identified and belong to chromosome 4 as well as to the large block of chromosome 5 (Cloix et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Changes in 5S rDNA Chromatin Organization and Transcription during Heterochromatin Establishment in Arabidopsis

et al. 2003

Self Cite

View full text Add to dashboard Cite

In the Arabidopsis accession Columbia, 5S rDNA is located in the pericentromeric heterochromatin of chromosomes 3, 4, and 5. Both a major and some minor 5S rRNA species are expressed from chromosomes 4 and 5, whereas the genes on chromosome 3 are not transcribed. Here, we show that 5S rDNA methylation is reduced in 2-day-old seedlings versus 4-day-old or older aerial plant tissues, and the minor 5S rRNA species are expressed most abundantly at this stage. Similarly, when 5S rDNA is demethylated by 5-azacytidine treatment or via the decrease in DNA methylation1 ( ddm1 ) mutation, the expression of minor 5S rRNA species is increased. We also show that in leaf nuclei of mature wild-type plants, the transcribed fraction of 5S rDNA forms loops that emanate from chromocenters. These loops, which are enlarged in nuclei of mature ddm1 plants, are enriched for histone H3 acetylated at Lys-9 and methylated at Lys-4 compared with the heterochromatic chromocenters. Up to 4 days after germination, heterochromatin is not fully developed: the 5S rDNA resides in prechromocenters, does not form conspicuous loops, and shows the lowest transcription level. Our results indicate that the expression and chromatin organization of 5S rRNA genes change during heterochromatin establishment.

show abstract

Section: Transcribed 5s Rdna Loci Are Less Associated With H3mk9 In Dmentioning

confidence: 99%

Section: Transcribed 5s Rdna Loci Are Less Associated With H3mk9 In Dmentioning

confidence: 99%

See 1 more Smart Citation

Changes in 5S rDNA Chromatin Organization and Transcription during Heterochromatin Establishment in Arabidopsis

et al. 2003

Self Cite

View full text Add to dashboard Cite

show abstract

“…The 5S rRNA gene is repeated within large head-to-tail arrays on three chromosomes (III, IV, and V), the typical repeat unit ( ‫ف‬ 500 nucleotides) being composed of transcribed sequence (120 nucleotides) and flanking spacer sequence (Cloix et al, 2002). The small RNA 123 sequence was identified in the sense orientation within the 5S transcribed region in 116 of the chromosome III repeats and 21 of the chromosome V repeats.…”

Section: Small Rnas From Arabidopsis Structural Rnamentioning

confidence: 99%

Endogenous and Silencing-Associated Small RNAs in Plants[W]

et al. 2002

View full text Add to dashboard Cite

A large set of endogenous small RNAs of predominantly 21 to 24 nucleotides was identified in Arabidopsis. These small RNAs resembled micro-RNAs from animals and were similar in size to small interfering RNAs that accumulated during RNA silencing triggered by multiple types of inducers. Among the 125 sequences identified, the vast majority (90%) arose from intergenic regions, although small RNAs corresponding to predicted protein-coding genes, transposon-like sequences, and a structural RNA gene also were identified. Evidence consistent with the derivation of small RNAs of both polarities, and from highly base-paired precursors, was obtained through the identification and analysis of clusters of small RNA loci. The accumulation of specific small RNAs was regulated developmentally. We propose that Arabidopsis small RNAs participate in a wide range of post-transcriptional and epigenetic events.

show abstract

“…In the Arabidopsis Col-0 accession, the 5S rRNA genes occur within the pericentromeric heterochromatin of chromosomes 3, 4, and 5 (Campbell, 1992), and the 45S rRNA genes occur in the nucleolar organizer regions (NORs) at the tips of the short arms of the acrocentric chromosomes 2 and 4 (NOR2 and NOR4) Layat et al, 2012). Transcription of the 5S rRNA gene by RNA polymerase III (Pol III) produces a 5S rRNA transcript (Cloix et al, 2002), and transcription of the 45S rRNA gene by RNA polymerase I (Pol I) produces a long polycistronic 45S pre-rRNA that is processed into the 5.8S, 18S, and 25S rRNA mature forms (Gruendler et al, , 1991Unfried et al, 1989).…”

Section: Mas2 Colocalizes With the 45s Rdnamentioning

confidence: 99%

Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing

et al. 2015

View full text Add to dashboard Cite

Ribosome biogenesis requires stoichiometric amounts of ribosomal proteins and rRNAs. Synthesis of rRNAs consumes most of the transcriptional activity of eukaryotic cells, but its regulation remains largely unclear in plants. We conducted a screen for ethyl methanesulfonate-induced suppressors of Arabidopsis thaliana ago1-52, a hypomorphic allele of AGO1 (ARGONAUTE1), a key gene in microRNA pathways. We identified nine extragenic suppressors as alleles of MAS2 (MORPHOLOGY OF AGO1-52 SUPPRESSED2). Positional cloning showed that MAS2 encodes the putative ortholog of NKAP (NF-k B activating protein), a conserved eukaryotic protein involved in transcriptional repression and splicing in animals. The mas2 point mutations behave as informational suppressors of ago1 alleles that cause missplicing. MAS2 is a single-copy gene whose insertional alleles are embryonic lethal. In yeast two-hybrid assays, MAS2 interacted with splicing and ribosome biogenesis proteins, and fluorescence in situ hybridization showed that MAS2 colocalizes with the 45S rDNA at the nucleolar organizer regions (NORs). The artificial microRNA amiR-MAS2 partially repressed MAS2 and caused hypomethylation of 45S rDNA promoters as well as partial NOR decondensation, indicating that MAS2 negatively regulates 45S rDNA expression. Our results thus reveal a key player in the regulation of rRNA synthesis in plants.

show abstract

Analysis of the 5S RNA Pool in Arabidopsis thaliana: RNAs Are Heterogeneous and Only Two of the Genomic 5S Loci Produce Mature 5S RNA

Cited by 59 publications

References 72 publications

Changes in 5S rDNA Chromatin Organization and Transcription during Heterochromatin Establishment in Arabidopsis

Changes in 5S rDNA Chromatin Organization and Transcription during Heterochromatin Establishment in Arabidopsis

Endogenous and Silencing-Associated Small RNAs in Plants[W]

Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing

Contact Info

Product

Resources

About