RNA Splicing Dysregulation in Ageing

Before a protein-coding gene can be translated, its precursor messenger RNA usually has introns removed and exons joined by the spliceosome. Alternative choices of exons or splice sites can generate distinct mature transcripts from the same gene. In ageing research, dysregulation refers not to all alternative splicing, which is a normal regulatory process, but to age-associated changes in isoform balance, splice-site choice, intron removal, or accuracy that may disturb cellular function. [1] [9]

Who This Is Useful For

This page is for readers who want to understand how RNA processing fits between gene expression and protein production, why splicing patterns change with age, and where observational evidence ends and causal evidence begins. It is also useful when interpreting transcriptomic studies that report altered exons, retained introns, or RNA isoforms in older tissues.

What Changes with Age

Human studies have identified age-associated shifts in both the abundance of splicing factors and the relative use of RNA isoforms. A blood study spanning adults aged 30 to 104 found altered isoform balance in selected genes, while analysis of GTEx data identified tens of thousands of age-associated splicing events across 48 tissues. Most events in the latter analysis were tissue-specific, so there is no single splicing pattern that defines every ageing tissue. [2] [3]

A larger analysis of more than 14,000 human samples reported a general age-related decline in splicing fidelity across multiple tissues. The rate of inaccurate junction use varied by intron and tissue and was associated with the abundance of spliceosomal proteins and RNA-binding regulators. This distinguishes changes in normal alternative splicing from rare use of unannotated splice sites, although both can occur in the same ageing transcriptome. [5]

Intron Retention and Transcript Consequences

Intron retention occurs when an intron remains within an RNA transcript instead of being removed. Depending on its position and cellular handling, a retained intron can alter a protein-coding sequence, keep RNA in the nucleus, or make a transcript susceptible to degradation. It can also be a controlled mechanism of gene regulation, so its presence alone does not prove molecular damage. [4] [8]

Increased intron retention has been observed during ageing in fruit-fly head cells and in older mouse and human brain datasets. The affected genes were enriched for RNA processing and proteostasis functions, raising the possibility of feedback in which altered splicing affects systems that maintain RNA and protein quality. These cross-species associations are informative, but the study did not show that every retained intron causes functional decline. [4]

Why Splicing Regulation May Become Less Stable

Splice-site selection depends on core spliceosomal components, regulatory RNA-binding proteins, the sequence and chromatin context of a transcript, and the timing of transcription. Age-associated changes in any of these inputs can shift which RNA product is made. Human tissue analyses link lower abundance of some sequence-recognition proteins with reduced accuracy, while experiments across worms, flies, rodents, and human cells associate faster RNA polymerase II elongation with altered splicing and poorer transcript quality. [5] [7]

Different Forms of Age-Associated Splicing Change

Links with Cellular Senescence

Splicing changes are also found in cellular senescence, a durable stress-associated state that can accumulate in ageing tissues. In human fibroblast models, reduced expression of the splicing factor U2AF1 increased intron retention and produced senescence-associated features. A separate study found a coordinated shift in dozens of spliceosomal genes before conventional senescence markers appeared, and genetic or pharmacological spliceosome perturbation promoted entry into senescence. [8] [10]

These experiments provide evidence that disruption of splicing machinery can contribute to a senescent phenotype in cultured cells. They do not show that the same change initiates senescence in every cell type in an intact organism, nor that age-associated splicing changes are always upstream rather than a response to other cellular stresses. [8] [10]

Cause, Consequence, or Adaptive Response?

The evidence supports all three possibilities in different contexts. In C. elegans, splicing homeostasis predicted remaining lifespan, and the splicing factor SFA-1 was required for lifespan extension under dietary restriction and reduced TORC1 signalling; its overexpression also extended lifespan. Experiments slowing RNA polymerase II increased lifespan in worms and flies while reversing several age-associated transcriptional changes. [6] [7]

Those findings make a purely passive interpretation unlikely in model organisms. For humans, however, much of the evidence remains observational, tissue-specific, or derived from cultured cells. Some splicing shifts may be maladaptive errors, some may compensate for stress, and others may reflect changes in cell composition within older tissue samples. Current evidence does not justify treating RNA splicing dysregulation as a single master mechanism of human ageing. [3] [5] [9]

Evidence Quality and Interpretation

Confidence is high that RNA splicing patterns change with chronological age and that the changes vary across tissues. Confidence is also substantial that particular disruptions can alter senescence and lifespan-related phenotypes under experimental conditions. Confidence is lower about which individual events matter in normal human ageing, their direction of causality, and whether a blood or bulk-tissue signature represents intrinsic changes within cells rather than a shift in the mixture of cell types. [2] [3] [5] [6] [9]

What This Does Not Mean

• It does not mean alternative splicing is inherently defective; regulated isoform choice is a normal part of gene control. [1]
• It does not mean every retained intron produces a harmful protein or is translated at all. [4] [8]
• It does not mean a splicing pattern measured in blood applies uniformly to brain, muscle, or other tissues. [3] [5]
• It does not mean lifespan effects in worms or flies establish a treatment strategy for human ageing. [6] [7]

Practical Interpretation Examples

• If an older tissue shows more splice variants: determine whether these are regulated annotated isoforms, retained introns, or rare inaccurate junctions before calling the change loss of fidelity. [3] [5]
• If one splicing factor declines with age: that is a plausible mechanism for downstream changes, but it does not show that the factor alone explains tissue ageing. [5] [8]
• If a model-organism manipulation preserves splicing and extends lifespan: it supports causality in that model and pathway, while human relevance still requires direct testing. [6] [7]

Summary

RNA splicing dysregulation in ageing includes altered isoform balance, intron retention, changes in spliceosomal regulators, and increasing use of inaccurate splice sites. The patterns are widespread but heterogeneous across tissues. Experimental studies show that splicing can influence senescence and lifespan-related pathways, while human studies more often establish association. The most defensible interpretation is therefore that splicing dysregulation is one interacting component of ageing biology, with effects that depend on the transcript, cell type, tissue, and biological context. [3] [5] [6] [9]

References

1. Wahl, M. C., Will, C. L., & Luhrmann, R. "The spliceosome: design principles of a dynamic RNP machine." Cell (2009). https://pubmed.ncbi.nlm.nih.gov/19239890/
2. Harries, L. W. et al. "Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing." Aging Cell (2011). https://pmc.ncbi.nlm.nih.gov/articles/PMC3173580/
3. Wang, K. et al. "Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases." Scientific Reports (2018). https://pmc.ncbi.nlm.nih.gov/articles/PMC6053367/
4. Adusumalli, S. et al. "Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer's disease." Aging Cell (2019). https://pubmed.ncbi.nlm.nih.gov/30868713/
5. Garcia-Ruiz, S. et al. "Splicing accuracy varies across human introns, tissues, age and disease." Nature Communications (2025). https://pmc.ncbi.nlm.nih.gov/articles/PMC11772838/
6. Heintz, C. et al. "Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elegans." Nature (2017). https://pmc.ncbi.nlm.nih.gov/articles/PMC5361225/
7. Debes, C. et al. "Ageing-associated changes in transcriptional elongation influence longevity." Nature (2023). https://www.nature.com/articles/s41586-023-05922-y
8. Yao, J. et al. "Prevalent intron retention fine-tunes gene expression and contributes to cellular senescence." Aging Cell (2020). https://pmc.ncbi.nlm.nih.gov/articles/PMC7744961/
9. Bhadra, M. et al. "Alternative splicing in aging and longevity." Human Genetics (2020). https://pmc.ncbi.nlm.nih.gov/articles/PMC8176884/
10. Kwon, S. M. et al. "Global spliceosome activity regulates entry into cellular senescence." FASEB Journal (2021). https://pubmed.ncbi.nlm.nih.gov/33337569/