Axolotl epigenetic clocks offer insights into the nature of negligible senescence

Renowned for their regenerative abilities, axolotls also exhibit exceptional longevity, resistance to age-related diseases and apparent lack of physiological declines through lifespan, and have thus been considered organisms of negligible senescence. Whether axolotls display epigenetic hallmarks of ageing remains unknown. Here, we probe the axolotl DNA methylome throughout lifespan and present its first epigenetic clocks. Both at tissue-specific or pan-tissue levels, the clocks are biphasic, capable of predicting age during early life but not for the rest of its lifespan. We show that axolotls exhibit evolutionarily conserved features of epigenetic ageing during early life, yet their methylome is remarkably stable across lifespan, including at Polycomb Repressive Complex 2 (PRC2) target sites, suggesting that this species deviates from known patterns of epigenetic ageing. This study provides molecular insights into negligible senescence and furthers our understanding of ageing dynamics in animals capable of extreme regeneration.

[1]  D. Nachun,et al.  PRC2-AgeIndex as a universal biomarker of aging and rejuvenation , 2024, Nature communications.

[2]  B. Treutlein,et al.  Somite-independent regeneration of the axolotl primary body axis , 2024, bioRxiv.

[3]  A. Paradowska-Gorycka,et al.  Aging and the impact of global DNA methylation, telomere shortening, and total oxidative status on sarcopenia and frailty syndrome , 2023, Immunity & Ageing.

[4]  A. Haghani,et al.  Fundamental equations linking methylation dynamics to maximum lifespan in mammals , 2023, bioRxiv.

[5]  V. Busskamp,et al.  Cellular senescence promotes progenitor cell expansion during axolotl limb regeneration , 2023, bioRxiv.

[6]  A. Lu,et al.  Pan-primate studies of age and sex , 2023, GeroScience.

[7]  Sunwha Cho,et al.  Parallel shift of DNA methylation and gene expression toward the mean in mouse spleen with aging , 2023, Aging.

[8]  Maximina H. Yun,et al.  Senescent cells enhance newt limb regeneration by promoting muscle dedifferentiation , 2022, bioRxiv.

[9]  S. Horvath,et al.  Epigenetic profiling and incidence of disrupted development point to gastrulation as aging ground zero in Xenopus laevis , 2022, bioRxiv.

[10]  C. Niehrs,et al.  DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic aging , 2022, bioRxiv.

[11]  L. Peshkin,et al.  Age-associated DNA methylation changes in Xenopus frogs , 2022, bioRxiv.

[12]  David A. W. Miller,et al.  Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity , 2022, Science.

[13]  Charlotte A. Seid,et al.  Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species , 2022, bioRxiv.

[14]  Maximina H. Yun,et al.  Telomerase-independent maintenance of telomere length in a vertebrate , 2022, bioRxiv.

[15]  Margarita V. Meer,et al.  Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock , 2022, Aging cell.

[16]  S. Emmrich,et al.  DNA methylation clocks tick in naked mole rats but queens age more slowly than nonbreeders , 2021, Nature Aging.

[17]  D. Korbie,et al.  Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod , 2021, Molecular ecology resources.

[18]  Maximina H. Yun Salamander Insights Into Ageing and Rejuvenation , 2021, Frontiers in Cell and Developmental Biology.

[19]  B. Treutlein,et al.  Fibroblast dedifferentiation as a determinant of successful regeneration , 2021, Developmental cell.

[20]  S. Voss,et al.  The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci , 2021, Proceedings of the National Academy of Sciences.

[21]  S. Horvath,et al.  DNA Methylation Networks Underlying Mammalian Traits , 2021, bioRxiv.

[22]  Josephine A. Reinhardt,et al.  DNA methylation predicts age and provides insight into exceptional longevity of bats , 2021, Nature Communications.

[23]  M. Rauner,et al.  Post-embryonic development and aging of the appendicular skeleton in Ambystoma mexicanum , 2021, bioRxiv.

[24]  Robert W. Williams,et al.  Universal DNA Methylation Age Across Mammalian Tissues , 2021, bioRxiv.

[25]  F. Lyko,et al.  A chicken DNA methylation clock for the prediction of broiler health , 2021, Communications biology.

[26]  Soo Bin Kwon,et al.  A mammalian methylation array for profiling methylation levels at conserved sequences , 2021, Nature Communications.

[27]  D. Korbie,et al.  A DNA methylation age predictor for zebrafish , 2020, Aging.

[28]  Margarita V. Meer,et al.  Reprogramming to recover youthful epigenetic information and restore vision , 2020, Nature.

[29]  Jason Ernst,et al.  Universal annotation of the human genome through integration of over a thousand epigenomic datasets , 2020, Genome Biology.

[30]  Maximina H. Yun,et al.  Salamander‐Eci: An optical clearing protocol for the three‐dimensional exploration of regeneration , 2020, Developmental dynamics : an official publication of the American Association of Anatomists.

[31]  R. Verhaak,et al.  CASCADES, a novel SOX2 super-enhancer associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma multiforme , 2020, bioRxiv.

[32]  R. Breyer,et al.  DP1 Activation Reverses Age-Related Hypertension Via NEDD4L-Mediated T-Bet Degradation in T Cells , 2020, Circulation.

[33]  Warren A. Vieira,et al.  Advancements to the Axolotl Model for Regeneration and Aging , 2019, Gerontology.

[34]  S. Horvath,et al.  DNA methylation aging clocks: challenges and recommendations , 2019, Genome Biology.

[35]  C. Schmitt,et al.  Cellular Senescence: Defining a Path Forward , 2019, Cell.

[36]  C. Miaud,et al.  Slow life-history strategies are associated with negligible actuarial senescence in western Palearctic salamanders , 2019, bioRxiv.

[37]  M. Hindell,et al.  Age estimation in a long‐lived seabird (Ardenna tenuirostris) using DNA methylation‐based biomarkers , 2019, Molecular ecology resources.

[38]  S. Voss,et al.  A chromosome-scale assembly of the axolotl genome , 2019, Genome research.

[39]  Tobias Gerber,et al.  Application and optimization of CRISPR–Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum) , 2018, Nature Protocols.

[40]  B. Treutlein,et al.  Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration , 2018, Science.

[41]  Trey Ideker,et al.  DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. , 2018, Molecular cell.

[42]  P. Laird,et al.  SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions , 2018, Nucleic acids research.

[43]  S. Horvath,et al.  DNA methylation-based biomarkers and the epigenetic clock theory of ageing , 2018, Nature Reviews Genetics.

[44]  W. Freeman,et al.  Revisiting the genomic hypomethylation hypothesis of aging , 2018, Annals of the New York Academy of Sciences.

[45]  D. Odom,et al.  Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species , 2018, Genome Biology.

[46]  Michael Hiller,et al.  The axolotl genome and the evolution of key tissue formation regulators , 2018, Nature.

[47]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[48]  M. Bulyk,et al.  Polycomb-like proteins link the PRC2 complex to CpG islands , 2017, Nature.

[49]  John J. Cole,et al.  Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions , 2017, Genome Biology.

[50]  A. Brunet,et al.  The Aging Epigenome. , 2016, Molecular cell.

[51]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[52]  Maximina H. Yun Changes in Regenerative Capacity through Lifespan , 2015, International journal of molecular sciences.

[53]  D. Gardiner,et al.  DNA Methylation Dynamics Regulate the Formation of a Regenerative Wound Epithelium during Axolotl Limb Regeneration , 2015, PloS one.

[54]  Maximina H. Yun,et al.  Recurrent turnover of senescent cells during regeneration of a complex structure , 2015, eLife.

[55]  Mikhail G Dozmorov,et al.  Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes , 2015, Epigenetics.

[56]  S. Bryant,et al.  The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods. , 2015, Regeneration.

[57]  D. Reinberg,et al.  An AUTS2–Polycomb complex activates gene expression in the CNS , 2014, Nature.

[58]  D. Beach,et al.  Ageing as developmental decay: insights from p16(INK4a.). , 2014, Trends in molecular medicine.

[59]  Mukul S. Bansal,et al.  A comparative encyclopedia of DNA elements in the mouse genome , 2014, Nature.

[60]  João Pedro de Magalhães,et al.  The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource , 2014, Nucleic Acids Res..

[61]  D. Odom,et al.  Evolution of transcription factor binding in metazoans — mechanisms and functional implications , 2014, Nature Reviews Genetics.

[62]  P. Murawala,et al.  Optimized axolotl (Ambystoma mexicanum) husbandry, breeding, metamorphosis, transgenesis and tamoxifen-mediated recombination , 2014, Nature Protocols.

[63]  Maximina H. Yun,et al.  Regulation of p53 is critical for vertebrate limb regeneration , 2013, Proceedings of the National Academy of Sciences.

[64]  S. Horvath DNA methylation age of human tissues and cell types , 2013, Genome Biology.

[65]  K. Kurimoto,et al.  Replication‐coupled passive DNA demethylation for the erasure of genome imprints in mice , 2012, The EMBO journal.

[66]  P. Reddien,et al.  The cellular basis for animal regeneration. , 2011, Developmental cell.

[67]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[68]  Trevor Hastie,et al.  Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent. , 2011, Journal of statistical software.

[69]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[70]  Wenjun Guo,et al.  Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2 , 2008, Nature Biotechnology.

[71]  J. Brockes,et al.  Comparative aspects of animal regeneration. , 2008, Annual review of cell and developmental biology.

[72]  A. Regev,et al.  An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors , 2008, Nature Genetics.

[73]  Acknowledgements , 2003, Psychoneuroendocrinology.

[74]  S. Bryant,et al.  Vaccinia as a tool for functional analysis in regenerating limbs: ectopic expression of Shh. , 2000, Developmental biology.

[75]  T. Kara Ageing in amphibians. , 1994, Gerontology.

[76]  A. Ingram The reactions to carcinogens in the axolotl (Ambystoma mexicanum) in relation to the "regeneration field control" hypothesis. , 1971, Journal of embryology and experimental morphology.

[77]  Maximina H. Yun,et al.  Baculovirus Production and Infection in Axolotls. , 2023, Methods in molecular biology.

[78]  Xin Liu A Structural Perspective on Gene Repression by Polycomb Repressive Complex 2. , 2021, Sub-cellular biochemistry.

[79]  Trinity Catholic Welcome to the , 2015 .

[80]  Konstantinos Sousounis,et al.  Aging and regeneration in vertebrates. , 2014, Current topics in developmental biology.