ArticleGenome research2021
The human ribosomal DNA array is composed of highly homogenized tandem clusters.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 73 citations in OpenAlex.
- Dynamic evolution and hierarchical regulation of rDNA in polyploid oat.The Plant journal : for cell and molecular biology · 2026Article
- Elucidating structure-function relationships in the mammalian nucleolus.Nature reviews. Molecular cell biology · 2026Review
- A complete genome for the common marmoset.Cell · 2026Article
- AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.Bioinformatics (Oxford, England) · 2026Article
- Lineage-specific evolution, structural diversity, and activity of R2 retrotransposons in animals.Genome biology · 2026Article
- A Complete Genome for the Common Marmoset.bioRxiv : the preprint server for biology · 2026Article
- sic1 mutation leads to rDNA instability by partial duplication with SIR4.Nucleic acids research · 2026Article
- Nucleolar expansion: A biomolecular condensate mortality timer.Geromedicine · 2026Article
- Noncoding RNAs: The Not So "Junk" DNA Is the Blueprint of the Transcriptional Landscape of the RNA World.Experientia supplementum (2012) · 2026Review
- Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.Cell genomics · 2025Article
- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape.bioRxiv : the preprint server for biology · 2025Article
- Genetic variation in recalcitrant repetitive regions of theGenome research · 2025Article
- Interpreting the Origins and Functions of Noncoding RNAs From the Ribosomal Genes.Journal of cellular physiology · 2025Review
- Nucleolar FRG2 lncRNAs inhibit rRNA transcription and cytoplasmic translation, linking FSHD to dysregulation of muscle-specific protein synthesis.Nucleic acids research · 2025Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Impacts of ribosomal RNA sequence variation on gene expression and phenotype.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- It Takes a Village of Chromatin Remodelers to Regulate rDNA Expression.International journal of molecular sciences · 2025Review
- Combining DNA and protein alignments to improve genome annotation with LiftOn.Genome research · 2025Article
- Variation in the Content of Three Tandem Repeats of the Human Genome (Ribosomal, Satellite III, and Telomere) in Peripheral Blood Leukocyte DNA of People of Different Ages (5-101 Years).Journal of aging research · 2025Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of the human ribosomal DNA (rDNA) cluster has traditionally been hard to analyze owing to its highly repetitive nature. However, the recent development of long-read sequencing technology, such as Oxford Nanopore sequencing, has enabled us to study the large-scale structure of the genome. Using this technology, we found that human cells have a quite regular rDNA structure. Although each human rDNA copy has some variations in its noncoding region, contiguous copies of rDNA are similar, suggesting that homogenization through gene conversion frequently occurs between copies. Analysis of rDNA methylation by Nanopore sequencing further showed that all the noncoding regions are heavily methylated, whereas about half of the coding regions are clearly unmethylated. The ratio of unmethylated copies, which are speculated to be transcriptionally active, was lower in individuals with a higher rDNA copy number, suggesting that there is a mechanism that keeps the active copy number stable. In addition, the rDNA in progeroid syndrome patient cells with reduced DNA repair activity had more unstable copies compared with control normal cells, although the rate was much lower than previously reported using a fiber-FISH method. Collectively, our results clarify the view of rDNA stability and transcription regulation in human cells, indicating the presence of mechanisms for both homogenizations to ensure sequence quality and maintenance of active copies for cellular functions.
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