Ribosome Diversity Encoded in RNA: From Sequence Variation to Human Physiology and Disease

Hidden Genetic Diversity in the Ribosome

The human genome contains hundreds of copies of rRNA genes (rDNA), arranged in highly repetitive arrays across acrocentric chromosomes. Because of their repetitive nature, these regions have historically been excluded from genomic analyses, leaving a major gap in our understanding of human genetic variation.

Using long-read sequencing, computational innovation, and biochemical validation, we generated the first comprehensive atlas of rRNA sequence variation present in actively translating ribosomes . This revealed several unexpected principles:

• Human cells harbor hundreds of rRNA sequence variants

• These variants are not random—they are incorporated into translating ribosomes

• A subset of variants are highly abundant and form distinct ribosome subtypes

• Many variants localize to expansion segments (ESs)—flexible regions extending from the ribosome surface

Critically, these findings demonstrate that ribosome composition is encoded at the level of RNA sequence variation, introducing a previously unrecognized source of ribosome heterogeneity.

Ribosome Subtypes: A New Layer of Biological Regulation

Not all rRNA variants are equivalent. We identified two major classes:

1. Ribosome Subtypes (Common, High-Abundance Variants)

These variants are present in many rDNA copies and give rise to stable ribosome populations with distinct sequence compositions. They are:

• Heritable across individuals

• Structurally distinct

• Differentially expressed across tissues

2. Rare rRNA Mutations (Low-Abundance Variants)

These occur in fewer rDNA copies and behave more like somatic or disease-associated mutations, with potential pathological consequences.

This distinction is central:

Some rRNA variants encode normal functional diversity, while others contribute to disease.

Expansion Segments: Hotspots of Functional Specialization

A striking finding from both studies is that many functionally relevant variants localize to expansion segments (ESs)—large, flexible regions of rRNA that extend from the ribosome surface.

Historically, ES regions were considered poorly conserved and of unclear function. Our work overturns this assumption.

We show that:

• ES regions harbor highly abundant and variable sequence variants

• These variants alter RNA structure, as revealed by DMS probing (see structural differences in ES regions on page 11 of the Cell Genomics paper)

• ES regions exhibit independent functional behavior, with different ESs associated with distinct biological outcomes

This suggests that ES regions act as regulatory hubs on the ribosome, potentially influencing interactions with mRNAs, RNA-binding proteins, or translational machinery.

Linking Ribosome Variation to Human Traits

To directly test whether ribosome diversity impacts human biology, we developed a new computational framework—RiboVAn—to quantify rRNA variants in nearly 500,000 individuals from the UK Biobank .

This enabled the first large-scale association between ribosome composition and human phenotypes.

Key findings:

• Specific ribosome subtypes are causally associated with human traits

• Different expansion segments regulate distinct physiological processes

For example:

• es15l variants → adiposity and metabolic traits

• es39l variants → body size and growth

• es27l variants → blood traits and disease susceptibility

As shown in the association maps (Figure 3, page 13), these relationships are highly specific—different regions of the ribosome influence different aspects of physiology.

This provides direct evidence that:

The ribosome itself encodes information that shapes organismal traits.

Ribosome Variation and Disease

Beyond normal physiology, we find that rRNA mutations are associated with disease risk.

By analyzing mutation burden across rRNA regions, we show that rare variants are linked to:

• Cancer

• Cardiovascular disease

• Type 2 diabetes

• Congenital disorders

Importantly, these disease associations arise from mutations within the ribosome itself, rather than traditional protein-coding genes.

This reveals a fundamentally new disease mechanism:

Genetic variation in the translational machinery can directly drive disease.

Chromosome-Specific Ribosome Encoding

Another unexpected discovery is that ribosome subtypes exhibit chromosome-specific origins.

rRNA genes reside on five acrocentric chromosomes (13, 14, 15, 21, 22), and we find that:

• Certain ribosome variants are preferentially encoded by specific chromosomes

• Different chromosomes contribute distinct ribosome subtypes

• This organization persists despite frequent chromosomal rearrangements

This suggests that the genome encodes parallel ribosome populations, each potentially tuned for specific regulatory functions.

A New View of Gene Expression

Together, these studies redefine the central dogma:

• Gene expression is not only controlled by DNA and mRNA

• It is also shaped by the composition of the ribosome itself

This leads to a new conceptual framework:

From:

Uniform ribosomes translating diverse mRNAs

To:

Diverse ribosomes selectively interpreting the transcriptome

In this model, the ribosome becomes an active regulatory layer, capable of influencing which proteins are produced, when, and in which cellular context.

Broader Implications

These findings have wide-reaching consequences across biology and medicine:

1. A New Source of Genetic Variation

rRNA genes represent one of the largest and most previously unexplored sources of genetic variation in the human genome.

2. Ribosome Specialization as a Regulatory Principle

Ribosome heterogeneity provides a mechanism for cell-type-specific and context-dependent translation.

3. Expansion Segments as Functional Platforms

ES regions emerge as key regulatory elements that may mediate interactions with mRNAs and regulatory factors.

4. New Disease Mechanisms

Mutations in rRNA introduce a new class of disease drivers—defects in the translational machinery itself.

5. Therapeutic Opportunities

Targeting ribosome composition or function could enable precision modulation of translation in disease.

A Paradigm Shift

These studies collectively establish a new paradigm:

The ribosome is not a passive machine—it is a genetically encoded, variable, and regulatory entity that shapes human physiology and disease.

By uncovering rRNA variation as a fundamental driver of ribosome diversity, this work opens an entirely new dimension of gene regulation—one that is embedded directly within the core machinery of life.

Rothschild D, Raj A, Brown J, Thayer N, Hotz M, Hendrickson D, Pritchard JK, Barna M. Ribosome heterogeneity arising from common and rare rRNA sequence variants affects diverse human phenotypes. medRxiv [Preprint]. 2025 Nov 19:2025.09.02.25334953. doi: 10.1101/2025.09.02.25334953. PMID: 40950416; PMCID: PMC12424869.

Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M. Diversity of ribosomes at the level of rRNA variation associated with human health and disease. Cell Genom. 2024 Sep 11;4(9):100629. doi: 10.1016/j.xgen.2024.100629. Epub 2024 Aug 6. PMID: 39111318; PMCID: PMC11480859.