Decoding Lifespan: New DNA Research Unveils Secrets of Aging

Purple Glowing Mysterious DNA

Researchers at UCLA discovered a strong correlation between DNA methylation patterns and mammalian lifespan. Through extensive analysis, they found that DNA methylation, an epigenetic modification, plays a pivotal role in aging, with its effects visible across species and intimately tied to evolutionary and developmental processes.

UCLA scientists lead groundbreaking studies on mammalian aging and life span.

Researchers from the UCLA David Geffen School of Medicine and UCLA Health led an international research team that published two articles detailing changes in DNA – changes that researchers found are shared by humans and other mammals throughout history and are associated with life span and numerous other traits.

“We’ve discovered that the life spans of mammals are closely associated with chemical modifications of the DNA molecule, specifically known as epigenetics, or more accurately, methylation. In essence, mammals with longer life spans exhibit more pronounced DNA methylation landscapes, whereas those of shorter-lived species have more subdued, flatter methylation patterns,” said the senior author of both articles, Steve Horvath, Ph.D., ScD, an expert on the aging process and a professor in human genetics and biostatistics at UCLA at the time the studies were conducted.

Jason Ernst, a professor of biological chemistry, computer science, and computational medicine at UCLA, said, “The technology we designed to measure DNA methylation levels across mammals along with the tissue sample contributions from a large consortium of researchers led to the production of a highly unique data set, which, when analyzed with advanced computational and statistical tools, unveiled a deeper understanding of the relationship between DNA methylation, life span, aging, and other biological processes across mammals.”

The studies, one published in Science and the other in Nature Aging, focus on DNA methylation, or cytosine methylation, a chemical modification of cytosine, one of the four building blocks of the DNA molecule.

DNA methylation is a mechanism by which cells can control gene expression – turning genes on or off. In these studies, the researchers focused on DNA methylation differences across species at locations where the DNA sequence is generally the same.

Circle Plot Shows the Correlation Between Age and DNA Methylation Age

This circle plot shows the correlation between age and DNA methylation age for various species estimated by the two universal clocks developed. Credit: Ake Lu and Steve Horvath

To study the effects of DNA methylation, the nearly 200 researchers – collectively known as the Mammalian Methylation Consortium – collected and analyzed methylation data from more than 15,000 animal tissue samples covering 348 mammalian species. They found that changes in methylation profiles closely parallel changes in genetics through evolution, demonstrating that there is an intertwined evolution of the genome and the epigenome that influences the biological characteristics and traits of different mammalian species.

Among the Science study’s findings:

  • Methylation, as evidenced by the epigenetic “marks” it leaves, bears a substantial correlation with maximum life span across mammalian species. Looking at methylation profiles on the DNA molecule as terrain with peaks and troughs, Horvath commented that species with long lives have prominent peaks and valleys, developed during extended gestation and development periods. In contrast, short-lived species have short gestation periods and rapid development, resulting in cells with a flatter, less-defined methylation landscape.
  • The maximum life span of a species is associated with specific developmental processes, as suggested by the involvement of certain genes and genetic transcription factors.
  • Cytosines whose methylation levels correlate with maximum life span differ from those that change with chronological age, suggesting that molecular pathways pertaining to average life span within a species are distinct from those determining the species’ maximum life span.
  • Evolution acts not only at the genetic level, but also at the epigenetic level. “Our results demonstrate that DNA methylation is subjected to evolutionary pressures and selection,” said the authors, whose database has been made public for other researchers.

Horvath and the consortium researchers used a subset of the database to study the methylation profiles of 185 species of mammals. Identifying changes in methylation levels that occur with age across all mammals, they developed a “universal pan-mammalian clock,” a mathematical formula that can accurately estimate age in all mammalian species. The results of this study are published in Nature Aging.

Horvath and a UCLA team introduced the concept of an epigenetic clock for age measurement, using human saliva samples, in 2011. Two years later, Horvath demonstrated that cytosine methylation enables the creation of a mathematical model for estimating age across all human tissues. The new work, which describes universal clocks, demonstrates that a single formula can accurately estimate age across mammalian tissues and species.

Among the Nature Aging study’s findings:

  • The pan-mammalian clocks maintain their high accuracy across species with varying life spans, from short-lived mice and rats to long-lived humans, bats, and whales.
  • The universal pan-mammalian clocks are predictors of mortality risk in humans and mice, which suggests they could prove valuable for preclinical studies. Therefore, an intervention that reverses epigenetic age in a mouse, according to the clock, might be applicable to humans as well.
  • The study identified specific regions in the genetic material of cells that either gain or lose methylation with chronological age.
  • The research revealed that developmental genes play a role in the functioning of epigenetic clocks.
  • The research connects developmental pathways with chronological aging effects and tissue degradation. This refutes the long-standing belief that aging is driven solely by random cellular damage that accumulates over time. Instead, the epigenetic aspects of aging follow a predetermined “program.”
  • The discovery of the pan-mammalian clocks provides compelling evidence that aging processes are evolutionarily conserved – remaining consistent through time – and are closely linked with developmental processes across all mammalian species.

References: “DNA methylation networks underlying mammalian traits” by Amin Haghani, Caesar Z. Li, Todd R. Robeck, Joshua Zhang, Ake T. Lu, Julia Ablaeva, Victoria A. Acosta-Rodríguez, Danielle M. Adams, Abdulaziz N. Alagaili, Javier Almunia, Ajoy Aloysius, Nabil M.S. Amor, Reza Ardehali, Adriana Arneson, C. Scott Baker, Gareth Banks, Katherine Belov, Nigel C. Bennett, Peter Black, Daniel T. Blumstein, Eleanor K. Bors, Charles E. Breeze, Robert T. Brooke, Janine L. Brown, Gerald Carter, Alex Caulton, Julie M. Cavin, Lisa Chakrabarti, Ioulia Chatzistamou, Andreas S. Chavez, Hao Chen, Kaiyang Cheng, Priscila Chiavellini, Oi-Wa Choi, Shannon Clarke, Joseph A. Cook, Lisa N. Cooper, Marie-Laurence Cossette, Joanna Day, Joseph DeYoung, Stacy Dirocco, Christopher Dold, Jonathan L. Dunnum, Erin E. Ehmke, Candice K. Emmons, Stephan Emmrich, Ebru Erbay, Claire Erlacher-Reid, Chris G. Faulkes, Zhe Fei, Steven H. Ferguson, Carrie J. Finno, Jennifer E. Flower, Jean-Michel Gaillard, Eva Garde, Livia Gerber, Vadim N. Gladyshev, Rodolfo G. Goya, Matthew J Grant, Carla B. Green, M. Bradley Hanson, Daniel W. Hart, Martin Haulena, Kelsey Herrick, Andrew N. Hogan, Carolyn J. Hogg, Timothy A. Hore, Taosheng Huang, Juan Carlos Izpisua Belmonte, Anna J. Jasinska, Gareth Jones, Eve Jourdain, Olga Kashpur, Harold Katcher, Etsuko Katsumata, Vimala Kaza, Hippokratis Kiaris, Michael S. Kobor, Pawel Kordowitzki, William R. Koski, Michael Krützen, Soo Bin Kwon, Brenda Larison, Sang-Goo Lee, Marianne Lehmann, Jean-François Lemaître, Andrew J. Levine, Xinmin Li, Cun Li, Andrea R. Lim, David T. S. Lin, Dana M. Lindemann, Schuyler W. Liphardt, Thomas J. Little, Nicholas Macoretta, Dewey Maddox, Craig O. Matkin, Julie A. Mattison, Matthew McClure, June Mergl, Jennifer J. Meudt, Gisele A. Montano, Khyobeni Mozhui, Jason Munshi-South, William J. Murphy, Asieh Naderi, Martina Nagy, Pritika Narayan, Peter W. Nathanielsz, Ngoc B. Nguyen, Christof Niehrs, Batsaikhan Nyamsuren, Justine K. O’Brien, Perrie O’Tierney Ginn, Duncan T Odom, Alexander G. Ophir, Steve Osborn, Elaine A. Ostrander, Kim M. Parsons, Kimberly C. Paul, Amy B. Pedersen, Matteo Pellegrini, Katharina J. Peters, Jessica L. Petersen, Darren W. Pietersen, Gabriela M. Pinho, Jocelyn Plassais, Jesse R. Poganik, Natalia A. Prado, Pradeep Reddy, Benjamin Rey, Beate R. Ritz, Jooke Robbins, Magdalena Rodriguez, Jennifer Russell, Elena Rydkina, Lindsay L. Sailer, Adam B. Salmon, Akshay Sanghavi, Kyle M. Schachtschneider, Dennis Schmitt, Todd Schmitt, Lars Schomacher, Lawrence B. Schook, Karen E. Sears, Ashley W. Seifert, Aaron B.A. Shafer, Anastasia V. Shindyapina, Melanie Simmons, Kavita Singh, Ishani Sinha, Jesse Slone, Russel G. Snell, Elham Soltanmohammadi, Matthew L. Spangler, Maria Spriggs, Lydia Staggs, Nancy Stedman, Karen J. Steinman, Donald T Stewart, Victoria J. Sugrue, Balazs Szladovits, Joseph S. Takahashi, Masaki Takasugi, Emma C. Teeling, Michael J. Thompson, Bill Van Bonn, Sonja C. Vernes, Diego Villar, Harry V. Vinters, Ha Vu, Mary C. Wallingford, Nan Wang, Gerald S. Wilkinson, Robert W. Williams, Qi Yan, Mingjia Yao, Brent G. Young, Bohan Zhang, Zhihui Zhang, Yang Zhao, Peng Zhao, Wanding Zhou, Joseph A. Zoller, Jason Ernst, Andrei Seluanov, Vera Gorbunova, X. William Yang, Ken Raj and Steve Horvath, 11 August 2023, Science.
DOI: 10.1126/science.abq5693

“Universal DNA methylation age across mammalian tissues” by A. T. Lu, Z. Fei, A. Haghani, T. R. Robeck, J. A. Zoller, C. Z. Li, R. Lowe, Q. Yan, J. Zhang, H. Vu, J. Ablaeva, V. A. Acosta-Rodriguez, D. M. Adams, J. Almunia, A. Aloysius, R. Ardehali, A. Arneson, C. S. Baker, G. Banks, K. Belov, N. C. Bennett, P. Black, D. T. Blumstein, E. K. Bors, C. E. Breeze, R. T. Brooke, J. L. Brown, G. G. Carter, A. Caulton, J. M. Cavin, L. Chakrabarti, I. Chatzistamou, H. Chen, K. Cheng, P. Chiavellini, O. W. Choi, S. M. Clarke, L. N. Cooper, M. L. Cossette, J. Day, J. DeYoung, S. DiRocco, C. Dold, E. E. Ehmke, C. K. Emmons, S. Emmrich, E. Erbay, C. Erlacher-Reid, C. G. Faulkes, S. H. Ferguson, C. J. Finno, J. E. Flower, J. M. Gaillard, E. Garde, L. Gerber, V. N. Gladyshev, V. Gorbunova, R. G. Goya, M. J. Grant, C. B. Green, E. N. Hales, M. B. Hanson, D. W. Hart, M. Haulena, K. Herrick, A. N. Hogan, C. J. Hogg, T. A. Hore, T. Huang, J. C. Izpisua Belmonte, A. J. Jasinska, G. Jones, E. Jourdain, O. Kashpur, H. Katcher, E. Katsumata, V. Kaza, H. Kiaris, M. S. Kobor, P. Kordowitzki, W. R. Koski, M. Krützen, S. B. Kwon, B. Larison, S. G. Lee, M. Lehmann, J. F. Lemaitre, A. J. Levine, C. Li, X. Li, A. R. Lim, D. T. S. Lin, D. M. Lindemann, T. J. Little, N. Macoretta, D. Maddox, C. O. Matkin, J. A. Mattison, M. McClure, J. Mergl, J. J. Meudt, G. A. Montano, K. Mozhui, J. Munshi-South, A. Naderi, M. Nagy, P. Narayan, P. W. Nathanielsz, N. B. Nguyen, C. Niehrs, J. K. O’Brien, P. O’Tierney Ginn, D. T. Odom, A. G. Ophir, S. Osborn, E. A. Ostrander, K. M. Parsons, K. C. Paul, M. Pellegrini, K. J. Peters, A. B. Pedersen, J. L. Petersen, D. W. Pietersen, G. M. Pinho, J. Plassais, J. R. Poganik, N. A. Prado, P. Reddy, B. Rey, B. R. Ritz, J. Robbins, M. Rodriguez, J. Russell, E. Rydkina, L. L. Sailer, A. B. Salmon, A. Sanghavi, K. M. Schachtschneider, D. Schmitt, T. Schmitt, L. Schomacher, L. B. Schook, K. E. Sears, A. W. Seifert, A. Seluanov, A. B. A. Shafer, D. Shanmuganayagam, A. V. Shindyapina, M. Simmons, K. Singh, I. Sinha, J. Slone, R. G. Snell, E. Soltanmaohammadi, M. L. Spangler, M. C. Spriggs, L. Staggs, N. Stedman, K. J. Steinman, D. T. Stewart, V. J. Sugrue, B. Szladovits, J. S. Takahashi, M. Takasugi, E. C. Teeling, M. J. Thompson, B. Van Bonn, S. C. Vernes, D. Villar, H. V. Vinters, M. C. Wallingford, N. Wang, R. K. Wayne, G. S. Wilkinson, C. K. Williams, R. W. Williams, X. W. Yang, M. Yao, B. G. Young, B. Zhang, Z. Zhang, P. Zhao, Y. Zhao, W. Zhou, J. Zimmermann, J. Ernst, K. Raj and S. Horvath, 10 August 2023, Nature Aging.
DOI: 10.1038/s43587-023-00462-6

Competing interests Science paper: S.H., A.A., and J.E. are inventors on patent/patent application number WO2020150705 held/submitted by the University of California, Los Angeles that covers the mammalian methylation array technology. S.H. and R.T.B. are founders of the nonprofit Epigenetic Clock Development Foundation, which has licensed several patents from UC Regents and distributes the mammalian methylation array.

Competing interests Nature Aging paper: The Regents of the University of California filed a patent application (publication number WO2020150705) related to this work on which S.H., A. Arneson and J.E. are named inventors. S.H. and R.T.B. are founders of the non-profit Epigenetic Clock Development Foundation, which has licensed several patents from UC Regents, and distributes the mammalian methylation array. The remaining authors declare no competing interests.

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