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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Updated: May 31, 2025

Measuring Single-Cell Mitochondrial DNA Copy Number and Heteroplasmy Using Digital Droplet Polymerase Chain Reaction
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rDNA Copy Number Variation and Methylation During Normal and Premature Aging.

Alva B C Geisen1, Natalia Santana Acevedo1, Junko Oshima2

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PubMed
Summary

Human ribosomal DNA (rDNA) copy number (CN) varies widely but remains stable with age. Promoter methylation increases with age, potentially regulating rDNA activity and compensating for copy number variations.

Keywords:
Werner syndromeagingdroplet digital PCRrDNA copy number variationrDNA promoter methylationrDNA transcription unit

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Area of Science:

  • Genetics
  • Molecular Biology
  • Epigenetics

Background:

  • Ribosomal RNA (rRNA) is crucial for protein synthesis, forming the ribosome.
  • The human genome contains hundreds of ribosomal DNA (rDNA) transcription units (TU).
  • Understanding rDNA copy number and methylation is key to cellular function and aging.

Purpose of the Study:

  • To determine the absolute copy number (CN) and methylation status of individual rDNA TU in healthy individuals.
  • To investigate the relationship between rDNA CN, methylation, age, and sex.
  • To explore potential links between rDNA CN variation and disease risk.

Main Methods:

  • Droplet digital PCR (ddPCR) for absolute rDNA copy number quantification.
  • Deep bisulfite sequencing for assessing rDNA promoter methylation status.
  • Analysis of blood samples from healthy individuals across a range of ages.

Main Results:

  • Absolute rDNA CN ranged from 243 to 895 (median 469), with no significant differences between sexes or with age.
  • RDNA TU with unmethylated or lowly methylated promoters decreased with age, while hypermethylated copies increased.
  • The number of hypomethylated (active) rDNA TU was independent of absolute CN, but hypermethylated (inactive) copies increased with CN.

Conclusions:

  • RDNA copy number exhibits significant inter-individual variation but is stable throughout adulthood.
  • Age-related promoter hypermethylation of rDNA may compensate for copy number variations.
  • Altered rDNA CN may influence health and disease risk, though further research is needed.