Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans
Open accessAbstract
Ribosomes are essential intracellular machines composed of proteins and RNA molecules. The DNA sequences (rDNA) encoding ribosomal RNAs (rRNAs) are tandemly repeated and give origin to the nucleolus. Here we develop a computational method for estimating rDNA dosage (copy number) and mitochondrial DNA abundance using whole-genome short-read DNA sequencing. We estimate these attributes across hundreds of human genomes and their association with global gene expression. The analyses uncover abundant variation in rDNA dosage that is coupled with the expression of hundreds of functionally coherent gene sets. These include associations with genes coding for chromatin components that target the nucleolus, including CTCF and HP1β. Finally, the data show an inverse association between rDNA dosage and mitochondrial DNA abundance that is manifested across genotypes. Our findings uncover a novel and cryptic source of hypervariable genomic diversity with global regulatory consequences (ribosomal eQTL) in humans. The variation provides a mechanism for cellular homeostasis and for rapid and reversible adaptation.
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In human blood cells, ribosomal DNA and mitochondrial DNA copy number vary between individuals and are inversely correlated with one another.
“sequencing data from human blood cells show ribosomal DNA (rDNA) and mitochondrial copy number (or “dose”), both of which can vary between individuals, are inversely correlated between one another (Gibbons et al., 2014).”
From Skeletal Muscle Ribosome and Mitochondrial Biogenesis in Response to Different Exercise Training Modalities (2021) · cites this paper as Gibbons et al., 2014
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References 67 · Cited by 165
- Authors
- Gibbons, J. G., Branco, A. T., Yu, S., & Lemos, B.
- Affiliations
- Harvard University (US)
- Corresponding author
- Lemos, Bernardo
- Venue
- Nature Communications
- Published
- 2014-09-11
- Volume
- 5
- Issue
- 1
- Pages
- 4850-4850
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W1978040768
- Cited by
- 165
- References
- 67
- Citations by year
- 2026: 9 · 2025: 13 · 2024: 11 · 2023: 14 · 2022: 15 · 2021: 20 · 2020: 17 · 2019: 15 · 2018: 24 · 2017: 12 · 2016: 7 · 2015: 8
- FWCI
- 10.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (T32HL007118)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- ribosomal DNA copy number, gene expression variation, nucleolus, chromatin, CTCF, HP1β, cellular homeostasis, genomic diversity, human genome
- MeSH terms
- Chromobox Protein Homolog 5, Cell Nucleolus, DNA, Mitochondrial, DNA, Ribosomal, Dosage Compensation, Genetic, Humans, Mitochondria, Gene Expression, Genome, Human, Quantitative Trait Loci, DNA Copy Number Variations
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