ArticleNucleic acids research2018
Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 77 citations in OpenAlex.
- Systematic Review of Plant Ribosome Heterogeneity and Specialization.Frontiers in plant science · 2020Pooled it
- Genome sequence assembly of the 5S rDNA loci informs haplotype specificity and evolution in the greater duckweed Spirodela polyrhiza.Communications biology · 2026Article
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
- T2T Genomes Unveil Centromere Architecture and Adaptive Divergence in Large Yellow Croaker (Larimichthys crocea).Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Pruning the Tree: Comparing OTUs and ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in Phylogenetic Studies.Ecology and evolution · 2025Article
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution.The New phytologist · 2025Article
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Ribosome-associated proteins: unwRAPping ribosome heterogeneity in the twenty-first century.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae).The Plant journal : for cell and molecular biology · 2024Article
- Contrasting patterns of 5S rDNA repeats in European and Asian ecotypes of greater duckweed,Frontiers in plant science · 2024Article
- Telomere-to-telomere genome assembly of melon (Horticulture research · 2023Article
- Discrimination of Green Coffee (Antioxidants (Basel, Switzerland) · 2023Article
- Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis.BMC plant biology · 2023Article
- Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes.Nucleic acids research · 2022Article
- Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants ofPlants (Basel, Switzerland) · 2022Article
- Optimization of Genome Knock-In Method: Search for the Most Efficient Genome Regions for Transgene Expression in Plants.International journal of molecular sciences · 2022Review
- Genomic architecture of 5S rDNA cluster and its variations within and between species.BMC genomics · 2022Article
- Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato.International journal of molecular sciences · 2022Article
- High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads.Genomics, proteomics & bioinformatics · 2022Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.
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