ArticlePLoS genetics2011
Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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94 citing papers in PubMed, 1 synthesis or guideline pooled it, 173 citations in OpenAlex.
- Meta-analysis reveals that genes regulated by the Y chromosome in Drosophila melanogaster are preferentially localized to repressive chromatin.Genome biology and evolution · 2013Pooled it
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- Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans.PLoS genetics · 2025Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Effect of copper and nickel exposure on ribosomal DNA variation in Daphnia pulex mutation accumulation lines.G3 (Bethesda, Md.) · 2025Article
- Diversity of ribosomes at the level of rRNA variation associated with human health and disease.Cell genomics · 2024Article
- Transcriptional Silencing of 35S rDNA inInternational journal of molecular sciences · 2024Article
- Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.G3 (Bethesda, Md.) · 2024Article
- Ribosomal DNA copy number variation associates with hematological profiles and renal function in the UK Biobank.Cell genomics · 2024Article
- Ribosomal DNA copy number is associated with body mass in humans and other mammals.Nature communications · 2024Article
- Directional selection, not the direction of selection, affects telomere length and copy number at ribosomal RNA loci.Scientific reports · 2024Article
- Description of the complete rDNA repeat unit structure ofComparative cytogenetics · 2024Article
- Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages.Communications biology · 2023Article
- Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast.Genome biology and evolution · 2023Article
- Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq.BMC genomics · 2023Article
- Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans.Genetics · 2023Article
- Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli.Cellular and molecular life sciences : CMLS · 2023Article
- Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast.Cell reports · 2023Article
34 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The ribosomal rDNA gene array is an epigenetically-regulated repeated gene locus. While rDNA copy number varies widely between and within species, the functional consequences of subtle copy number polymorphisms have been largely unknown. Deletions in the Drosophila Y-linked rDNA modifies heterochromatin-induced position effect variegation (PEV), but it has been unknown if the euchromatic component of the genome is affected by rDNA copy number. Polymorphisms of naturally occurring Y chromosomes affect both euchromatin and heterochromatin, although the elements responsible for these effects are unknown. Here we show that copy number of the Y-linked rDNA array is a source of genome-wide variation in gene expression. Induced deletions in the rDNA affect the expression of hundreds to thousands of euchromatic genes throughout the genome of males and females. Although the affected genes are not physically clustered, we observed functional enrichments for genes whose protein products are located in the mitochondria and are involved in electron transport. The affected genes significantly overlap with genes affected by natural polymorphisms on Y chromosomes, suggesting that polymorphic rDNA copy number is an important determinant of gene expression diversity in natural populations. Altogether, our results indicate that subtle changes to rDNA copy number between individuals may contribute to biologically relevant phenotypic variation.
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