ArticleGenome biology and evolution2016
A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 51 citations in OpenAlex.
- T2T genomes ofGenome research · 2026Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- 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
- The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type.BMC biology · 2024Article
- HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells.BMC genomics · 2024Article
- MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs).Nucleic acids research · 2024Article
- Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer.Molecular biology of the cell · 2023Article
- First discovered, long out of sight, finally visible: ribosomal DNA.Trends in genetics : TIG · 2022Review
- Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method.BMC musculoskeletal disorders · 2021Article
- Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries.Biochimica et biophysica acta. Gene regulatory mechanisms · 2021Review
- Article
- Efficient Nuclease-Directed Integration of Lentivirus Vectors into the Human Ribosomal DNA Locus.Molecular therapy : the journal of the American Society of Gene Therapy · 2020Article
- Ribosome heterogeneity in stem cells and development.The Journal of cell biology · 2020Review
- Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner.BMC biology · 2020Article
- Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays.Nucleus (Austin, Tex.) · 2019Article
- Ribosomal DNA and the Nucleolus as Keystones of Nuclear Architecture, Organization, and Function.Trends in genetics : TIG · 2019Review
- Integrative rDNAomics-Importance of the Oldest Repetitive Fraction of the Eukaryote Genome.Genes · 2019Review
- Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation.Communications biology · 2019Article
- Nucleolus and chromatin.Histochemistry and cell biology · 2018Review
- Evolutionary Dynamics of Copy Number and Meiotic Recombination in Murine 5S rDNA: Possible Involvement of Natural Selection.Journal of molecular evolution · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosomal RNAs (rRNAs) account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.
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