Intraindividual rDNA copy number variation and methylation in humans

Area of Science:

• Genetics
• Molecular Biology
• Epigenetics

Background:

• Ribosomal DNA (rDNA) transcription units (TU) exhibit significant inter-individual variation.
• Limited data exists on intra-individual rDNA copy number (CN) variation in normal human tissues.
• Cancer is known for extensive rDNA CN instability.

Purpose of the Study:

• To quantify absolute rDNA CN and active rDNA CN in multiple normal tissues from the same individuals.
• To investigate the extent of intra-individual variation in rDNA CN and its epigenetic regulation.
• To determine the relationship between absolute and active rDNA CN across different tissues.

Main Methods:

• Droplet digital PCR (ddPCR) for absolute rDNA CN quantification.
• Deep bisulfite sequencing for promoter methylation analysis and active rDNA CN estimation.
• Analysis of up to six tissues from 13 autopsy probands.

Main Results:

• Absolute rDNA CN and a specific variant (A variant) were generally consistent across tissues within individuals.
• Some individuals showed significant absolute CN variations between tissues, indicating potential loss of CN control.
• Active rDNA CN, determined by hypomethylation, was largely independent of absolute CN due to promoter methylation.
• Cerebellum and cerebrum consistently displayed lower active rDNA CN compared to other analyzed tissues.
• An estimated >50 active rDNA TU are necessary for normal tissue/organ function.

Conclusions:

• Absolute and active rDNA CN are generally maintained across different tissues during development and differentiation within an individual, with notable exceptions.
• Active rDNA CN exhibits systematic variation between tissues, with brain tissues having lower levels.
• Epigenetic regulation, specifically promoter methylation, plays a crucial role in controlling active rDNA CN independently of total rDNA CN.