PRC2-AgeIndex as a universal biomarker of aging and rejuvenation – Nature.com

Posted: July 21, 2024 at 2:38 am

Moqri, M. et al. Biomarkers of aging for the identification and evaluation of longevity interventions. Cell. 186, 37583775 (2023).

Moqri, M. et al. Validation of biomarkers of aging. Nat. Med. 30, 360372 (2024).

Jylhava, J., Pedersen, N. L. & Hagg, S. Biological age predictors. EBioMedicine 21, 2936 (2017).

Article PubMed PubMed Central Google Scholar

Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371384 (2018).

Article PubMed CAS Google Scholar

Dabrowski, J. K. et al. Probabilistic inference of epigenetic age acceleration from cellular dynamics. Preprint at bioRxiv https://doi.org/10.1101/2023.03.01.530570 (2023).

Bell, C. G. et al. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 20, 249 (2019).

Article PubMed PubMed Central Google Scholar

Hannum, G. et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell 49, 359367 (2013).

Article PubMed CAS Google Scholar

Sziraki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018).

Article PubMed PubMed Central Google Scholar

Johansson, A., Enroth, S. & Gyllensten, U. Continuous aging of the human DNA methylome throughout the human lifespan. PLoS ONE 8, e67378 (2013).

Article ADS PubMed PubMed Central CAS Google Scholar

Zhou, W. et al. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat. Genet. 50, 591602 (2018).

Article PubMed PubMed Central CAS Google Scholar

Long, H. K. et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. eLife 2, e00348 (2013).

Article ADS PubMed PubMed Central Google Scholar

Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490495 (2011).

Article ADS PubMed CAS Google Scholar

Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 11341148 (2013).

Article PubMed PubMed Central CAS Google Scholar

Jeong, M. et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat. Genet. 46, 1723 (2014).

Article PubMed CAS Google Scholar

Zhang, X. et al. Large DNA methylation nadirs anchor chromatin loops maintaining hematopoietic stem cell identity. Mol. Cell 78, 506521.e506 (2020).

Article PubMed PubMed Central CAS Google Scholar

Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chedin, F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell 45, 814825 (2012).

Article PubMed PubMed Central CAS Google Scholar

Williams, K., Christensen, J. & Helin, K. DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep. 13, 2835 (2011).

Article PubMed PubMed Central Google Scholar

Bartke, T. et al. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470484 (2010).

Article PubMed PubMed Central CAS Google Scholar

Hagarman, J. A., Motley, M. P., Kristjansdottir, K. & Soloway, P. D. Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells. PLoS ONE 8, e53880 (2013).

Article ADS PubMed PubMed Central CAS Google Scholar

Lindroth, A. M. et al. Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 4, e1000145 (2008).

Article PubMed PubMed Central Google Scholar

Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444448 (2010).

Article ADS PubMed PubMed Central CAS Google Scholar

Lu, A. T. et al. Universal DNA methylation age across mammalian tissues. Nat. Aging 3, 11441166 (2023).

Article ADS PubMed PubMed Central CAS Google Scholar

Ohm, J. E. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet. 39, 237242 (2007).

Article PubMed PubMed Central CAS Google Scholar

Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39, 232236 (2007).

Article PubMed CAS Google Scholar

Slieker, R. C., Relton, C. L., Gaunt, T. R., Slagboom, P. E. & Heijmans, B. T. Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception. Epigenet. Chromatin 11, 25 (2018).

Article Google Scholar

Teschendorff, A. E. et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 20, 440446 (2010).

Article PubMed PubMed Central CAS Google Scholar

Widschwendter, M. et al. Epigenetic stem cell signature in cancer. Nat. Genet. 39, 157158 (2007).

Article PubMed CAS Google Scholar

Zheng, S. C., Widschwendter, M. & Teschendorff, A. E. Epigenetic drift, epigenetic clocks and cancer risk. Epigenomics 8, 705719 (2016).

Article PubMed CAS Google Scholar

Zhou, W. et al. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom. https://doi.org/10.1016/j.xgen.2022.100144 (2022).

Beerman, I. et al. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell 12, 413425 (2013).

Article PubMed CAS Google Scholar

Dozmorov, M. G. Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes. Epigenetics 10, 484495 (2015).

Article PubMed PubMed Central Google Scholar

Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).

Article PubMed PubMed Central Google Scholar

Lu, R. J. et al. Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation. Nat. Aging 1, 715733 (2021).

Article PubMed PubMed Central Google Scholar

Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: In the right place at the right time. Science 361, 13361340 (2018).

Article ADS PubMed PubMed Central CAS Google Scholar

Minteer, C. et al. Tick tock, tick tock: mouse culture and tissue aging captured by an epigenetic clock. Aging Cell 21, e13553 (2022).

Article PubMed PubMed Central CAS Google Scholar

Mozhui, K. & Pandey, A. K. Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans. Mech. Ageing Dev. 162, 2737 (2017).

Article PubMed PubMed Central CAS Google Scholar

Rozenblit, M. et al. Evidence of accelerated epigenetic aging of breast tissues in patients with breast cancer is driven by CpGs associated with polycomb-related genes. Clin. Epigenet. 14, 30 (2022).

Article CAS Google Scholar

Ying, K. et al. Biolearn, an open-source library for biomarkers of aging. Preprint at bioRxiv https://doi.org/10.1101/2023.12.02.569722 (2023).

Ying, K. et al. ClockBase: a comprehensive platform for biological age profiling in human and mouse. Preprint at bioRxiv https://doi.org/10.1101/2023.02.28.530532 (2023).

Chen, C. C., Lim, C. Y., Lee, P. J., Hsu, A. L. & Ching, T. T. S-adenosyl methionine synthetase SAMS-5 mediates dietary restriction-induced longevity in Caenorhabditis elegans. PLoS ONE 15, e0241455 (2020).

Article PubMed PubMed Central CAS Google Scholar

Hahn, O. et al. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biol. 18, 56 (2017).

Article PubMed PubMed Central Google Scholar

Petkovich, D. A. et al. Using DNA methylation profiling to evaluate biological age and longevity interventions. Cell Metab. 25, 954960.e956 (2017).

Article PubMed PubMed Central CAS Google Scholar

Browder, K. C. et al. In vivo partial reprogramming alters age-associated molecular changes during physiological aging in mice. Nat. Aging 2, 243253 (2022).

Article PubMed CAS Google Scholar

Chondronasiou, D. et al. Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. Aging Cell 21, e13578 (2022).

Article PubMed PubMed Central CAS Google Scholar

Cipriano, A. et al. Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming. Nat. Aging https://doi.org/10.1038/s43587-023-00539-2 (2023).

Ocampo, A. et al. In vivo amelioration of age-associated hallmarks by partial reprogramming. Cell 167, 17191733.e1712 (2016).

Article PubMed PubMed Central CAS Google Scholar

Sarkar, T. J. et al. Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells. Nat. Commun. 11, 1545 (2020).

Article ADS PubMed PubMed Central CAS Google Scholar

Arneson, A. et al. A mammalian methylation array for profiling methylation levels at conserved sequences. Nat. Commun. 13, 783 (2022).

Article ADS PubMed PubMed Central CAS Google Scholar

Ludwin, S. K. Proliferation of mature oligodendrocytes after trauma to the central nervous system. Nature 308, 274275 (1984).

Article ADS PubMed CAS Google Scholar

Horvath, S. et al. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol. 13, R97 (2012).

Article PubMed PubMed Central CAS Google Scholar

Seale, K., Horvath, S., Teschendorff, A., Eynon, N. & Voisin, S. Making sense of the ageing methylome. Nat. Rev. Genet. 23, 585605 (2022).

Article PubMed CAS Google Scholar

Simpson, D. J. et al. Region-based epigenetic clock design improves RRBS-based age prediction. Aging Cell 22, e13866 (2023).

Article PubMed PubMed Central CAS Google Scholar

Youn, A. & Wang, S. The MiAge calculator: a DNA methylation-based mitotic age calculator of human tissue types. Epigenetics 13, 192206 (2018).

Article PubMed PubMed Central Google Scholar

Koldobskiy, M. A., Camacho, O., Reddy, P., Belmonte, J. C. I. & Feinberg, A. P. Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets. Preprint at bioRxiv https://doi.org/10.1101/2023.06.08.544045 (2023).

Read more:
PRC2-AgeIndex as a universal biomarker of aging and rejuvenation - Nature.com

Related Posts