Academy

Transcriptomics in Longevity Research

Introduction
The transcriptome is the complete set of RNA molecules produced by an organism’s genome under specific conditions. Unlike the genome, which is largely constant, the transcriptome changes dynamically based on developmental stage, environment, and health status. Profiling the transcriptome helps researchers understand which genes are active, how they are regulated, and how cells respond to stress or aging.

Key Technologies

• Illumina Short-Read Sequencing: Generates millions of high-accuracy reads of 50–300 base pairs, ideal for quantifying expression levels but limited in reconstructing full-length transcripts.
• Oxford Nanopore Long-Read Sequencing: Produces reads over tens of thousands of base pairs, capturing entire transcripts and complex splicing patterns, but with higher raw error rates.
• Hybrid Assembly: Combines short-read accuracy and long-read continuity. Error correction tools (e.g., Ratatosk) use short-reads to polish long-reads. Assemblers (e.g., Trinity) then reconstruct full-length transcripts.

Applications in Longevity Science

• Organ-Specific Expression: By sequencing RNA from various tissues (e.g., brain, liver, heart), researchers identify genes uniquely active in organs that influence aging and resilience.
• Evolutionary Selection: Comparative analyses across species reveal genes and pathways under positive or negative selection. Elevated dN/dS ratios indicate adaptive changes linked to lifespan extension.
• Pathway Discovery: Transcriptomics uncovers critical biological processes—such as mitochondrial function, stress responses, and detoxification—that correlate with longevity across species.

Case Study: The Olm
The olm (Proteus anguinus) is the longest-lived amphibian, with a predicted lifespan exceeding 100 years. Researchers used hybrid transcriptome assembly to:

1. Sequence RNA from six organs using both Illumina and Nanopore technologies.
2. Assemble and annotate 18,924 protein-coding genes.
3. Quantify organ-specific expression and perform gene ontology enrichment.
4. Conduct dN/dS selection analyses, identifying COL4A5 and mitochondrial translation pathways as adaptive targets.

Why It Matters
Transcriptome analysis provides a detailed snapshot of gene activity and evolutionary adaptations in long-lived species. Insights from organisms like the olm can guide the identification of molecular targets for aging interventions, enhancing our understanding of healthy lifespan extension.