Comparative transcriptomics of longevity: methods of interspecies RNA-seq analysis
Anton Kulaga1, Dmitri Toren2, Vadim Fraifeld2, Robi Tacutu1
Why do species differ in their lifespan? Why are the naked mole rat and bowhead whale resistant to cancer and hypoxia? Are there particular expression patterns that ensure long life and resistance to diseases and extreme conditions? These and similar questions require careful comparative genomics and transcriptomics analyses.
While for comparative genomics there are established methods based on multiple sequence alignments and phylogenetics, comparative transcriptomics is less developed and more challenging. Comparison of expression levels of different species involves many degrees of uncertainty and sources of potential errors including heterogeneity in samples, differences in sequencing equipment and sample preparation protocols, low quality of many de novo transcriptome and genome assemblies, potential errors in alignments and transcriptome assemblies, etc.
To address the above-mentioned challenges and gain some insight into the expression patterns of long-lived animals, we developed an approach for cross-species gene expression comparison analysis and used it to evaluate unique and similar expression patterns across 7 mammalian species with different lifespans (three whales and four terrestrial mammals: naked mole rat, mouse, cow, and humans). To increase the robustness of the alignments for protein-coding genes, we aligned known and predicted protein sequences for the species of interest to Uniref90 clusters. As RNA-Seq is only accurate for relative quantitation of expression, we focused on comparing the ranks of GO expression levels.
Our findings showed a high degree of similarity between closely-related species and similar expression patterns between long-lived species ( regulation of apoptosis, DNA repair, hypoxia resistance processes, etc.). The results obtained advance our understanding of the evolution of longevity and adaptation to stressful environment.
- Institute of Biochemistry of the Romanian Academy
- 2. Ben-Gurion University of the Negev
Why do species differ in their lifespan? Why are the naked mole rat and bowhead whale resistant to cancer and hypoxia? Are there particular expression patterns that ensure long life and resistance to diseases and extreme conditions? These and similar questions require careful comparative genomics and transcriptomics analyses.
While for comparative genomics there are established methods based on multiple sequence alignments and phylogenetics, comparative transcriptomics is less developed and more challenging. Comparison of expression levels of different species involves many degrees of uncertainty and sources of potential errors including heterogeneity in samples, differences in sequencing equipment and sample preparation protocols, low quality of many de novo transcriptome and genome assemblies, potential errors in alignments and transcriptome assemblies, etc.
To address the above-mentioned challenges and gain some insight into the expression patterns of long-lived animals, we developed an approach for cross-species gene expression comparison analysis and used it to evaluate unique and similar expression patterns across 7 mammalian species with different lifespans (three whales and four terrestrial mammals: naked mole rat, mouse, cow, and humans). To increase the robustness of the alignments for protein-coding genes, we aligned known and predicted protein sequences for the species of interest to Uniref90 clusters. As RNA-Seq is only accurate for relative quantitation of expression, we focused on comparing the ranks of GO expression levels.
Our findings showed a high degree of similarity between closely-related species and similar expression patterns between long-lived species ( regulation of apoptosis, DNA repair, hypoxia resistance processes, etc.). The results obtained advance our understanding of the evolution of longevity and adaptation to stressful environment.
