205: Ancient RNA Expression Profiles from the Woolly Mammoth

️ Episode 205: Ancient RNA Expression Profiles from the Woolly Mammoth In this episode of PaperCast Base by Base, we explore how ancient RNA preserved in permafrost can reveal tissue-specific gene expression and regulatory dynamics in the extinct woolly mammoth. Study Highlights:Researchers analyzed skeletal muscle and skin from ten Late Pleistocene woolly mammoths preserved in Siberian permafrost, extracting both ancient DNA and RNA to assess the authenticity and quality of the recovered molecules. Using alignment strategies optimized for short, damaged transcripts and mapping primarily to the Asian elephant genome, they identified characteristic damage patterns, exonic enrichment, and expression hotspots that distinguish genuine ancient RNA from residual DNA contamination. One exceptionally well-preserved specimen, known as Yuka, yielded a detailed skeletal muscle transcriptome, including abundant sarcomeric and mitochondrial genes that indicate a predominance of slow-twitch muscle fibers and reveal preserved tissue identity after tens of thousands of years. The team also detected mammoth-specific sequence variants, muscle-enriched microRNAs, and candidate novel microRNA loci, showing that ancient RNA can capture both coding and regulatory layers of the transcriptome. Together, these results establish robust quality-control and analytical frameworks for decoding ancient transcriptomes, demonstrating that RNA can persist long enough to recover biologically meaningful expression profiles from extinct megafauna. Conclusion:Ancient RNA sequencing from permafrost-preserved mammoths opens the door to integrative paleogenomic studies that combine genomes, proteomes, and transcriptomes to reconstruct tissue biology and gene regulation in long-extinct species. Music:Enjoy the music based on this article at the end of the episode. Reference:Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Dehasque M, Aslanzadeh M, Bozlak E, Brown K, van der Valk T, Kalogeropoulos P, Chacón-Duque JC, Biryukova I, Heintzman PD, Furugård C, Plotnikov V, Protopopov A, Andersson B, Ersmark E, Peterson KJ, Friedländer MR, Dalén L. Ancient RNA expression profiles from the extinct woolly mammoth. Cell. 2026;189(1):1–18. https://doi.org/10.1016/j.cell.2025.10.025 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

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