ArticlePLoS genetics2018
The long-range interaction map of ribosomal DNA arrays.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Highly Aggressive and Metastatic MDA-MB-231 and Mel Z Cancer Cells Have Common Sets of Down- and Upregulated Genes During Formation of the Vasculogenic Mimicry Phenotype.International journal of molecular sciences · 2026Article
- During the Formation of Vasculogenic Mimicry by Melanoma Cells, the Silencing of Two Sets of Developmental Genes Is Coupled Either with an Increase or a Decrease in Contacts with the Nucleoli.International journal of molecular sciences · 2025Article
- Formation of the Vasculogenic Mimicry Phenotype in Melanoma Mel Z Cells Is Coupled with Changes in Inter-Chromosomal Contacts of Developmental Genes with rDNA Clusters.International journal of molecular sciences · 2025Article
- Emerging roles for the nucleolus in development and stem cells.Development (Cambridge, England) · 2025Review
- The Nucleolus: A Central Hub for Ribosome Biogenesis and Cellular Regulatory Signals.International journal of molecular sciences · 2025Review
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Hypermethylation at 45S rDNA promoter in cancers.PloS one · 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
- HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells.BMC genomics · 2024Article
- New Functional Motifs for the Targeted Localization of Proteins to the Nucleolus inInternational journal of molecular sciences · 2024Article
- Potential roles of inter-chromosomal interactions in cell fate determination.Frontiers in cell and developmental biology · 2024Review
- Induction of the Erythroid Differentiation of K562 Cells Is Coupled with Changes in the Inter-Chromosomal Contacts of rDNA Clusters.International journal of molecular sciences · 2023Article
- Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes.Nature reviews. Molecular cell biology · 2023Review
- Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer.Molecular biology of the cell · 2023Article
- Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions.Nature communications · 2023Article
- Article
- Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains.Nature communications · 2022Article
- Environmentally induced ribosomal DNA (rDNA) instability in human cells and populations exposed to hexavalent chromium [Cr (VI)].Environment international · 2021Article
- Review
- Prevalence and Phenotypic Impact of Robertsonian Translocations.Molecular syndromology · 2021Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The repeated rDNA array gives rise to the nucleolus, an organelle that is central to cellular processes as varied as stress response, cell cycle regulation, RNA modification, cell metabolism, and genome stability. The rDNA array is also responsible for the production of more than 70% of all cellular RNAs (the ribosomal RNAs). The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1 while the 45S rDNA arrays reside on the short arm of five human acrocentric chromosomes. These critical genome elements have remained unassembled and have been excluded from all Hi-C analyses to date. Here we built the first high resolution map of 5S and 45S rDNA array contacts with the rest of the genome combining over 15 billion Hi-C reads from several experiments. The data enabled sufficiently high coverage to map rDNA-genome interactions with 1MB resolution and identify rDNA-gene contacts. The map showed that the 5S and 45S arrays display preferential contact at common sites along the genome but are not themselves sufficiently close to yield 5S-45S Hi-C contacts. Ribosomal DNA contacts are enriched in segments of closed, repressed, and late replicating chromatin, as well as CTCF binding sites. Finally, we identified functional categories whose dispersed genes coalesced in proximity to the rDNA arrays or instead avoided proximity with the rDNA arrays. The observations further our understanding of the spatial localization of rDNA arrays and their contribution to the architecture of the cell nucleus.
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