Epigenetics: 330-year-old poplar tree tells about its life
Similar to genetic mutations, epigenetic changes, i.e. alterations of genes that do not occur on the primary DNA sequence, sometimes occur randomly in plants and can be transmitted over generations. Using trees as an example, a research team has now shown for the first time that such "epimutations" increase continuously over the lifetime of a plant and can be used as a molecular clock to determine the age of a tree.
Epigenetics studies heritable changes in the activity of genes that are not based on changes in the primary DNA sequence. "While in mammals epigenetic marks are usually reset with each generation, this is not always the case in plants. Epigenetic changes within a generation can be stably passed on to the next generation in plants and even inherited over many generations," says Frank Johannes, Professor of Population Epigenetics and Epigenomics at the Technical University of Munich (TUM)..
His research team is interested in how often epimutations occur in plant genomes, how stable they are across generations, and whether they can influence important plant traits.
Trees carry many epimutations
"Because of their longevity, trees can provide us with epigenetic insights over large periods of time," says Prof. Johannes. Together with Robert J. Schmitz, Professor at the University of Georgia (USA) and Hans Fisher Fellow at the Institute for Advanced Study at TUM (TUM-IAS), he has now published two studies on the subject.
The team focused on a 330-year-old poplar tree. They compared DNA methylation, a mechanism in plants that represents a chemical change in DNA, in leaves of different branches of the tree. They were able to show that epigenetic changes increase continuously as a function of tree age. The further apart two leaves were from each other in relation to the branch's developmental period, the less similar they were at the level of DNA methylation. From this, the researchers concluded that the rate of epimutations per year is approximately 10,000 times higher than the genetic mutation rate in the same tree.
Tree age datable with epigenetics
From this discovery came the insight that epimutations can also serve as a kind of molecular clock to determine the age of the tree. "Only some branches had been dated by counting growth rings, but unfortunately not the main trunk. But we needed this information for our analysis. So we treated the overall age of the tree as an unknown parameter and let the DNA methylation data of the leaves tell us how old the tree is. This gave an estimate of about 330 years," reports Prof. Johannes.
It later turned out that this estimate was consistent with the diameter-based dating of the main trunk and with other information about the life history of this particular tree. "This was the first indication that there is such a thing as an epigenetic clock in trees".
A window into the past
Prof. Johannes' team is now investigating whether environmental changes experienced by trees over their long lives leave epigenetic signatures that can be read to learn about their past.
"Our goal is to merge historical environmental data with our epigenetic work to understand whether trees epigenetically 'record' specific environmental challenges such as droughts or temperature fluctuations. This kind of information can be useful for looking into the future, especially in the face of global climate change."
Publications:
Brigitte Hofmeister; Johanna Denkena; Maria Colome-Tatche; Yadollah Shahryary; Rashmi Hazarika; Jane Grimwood; Sujan Mamidi; Jerry Jenkins; Paul Grabowski; Avinash Sreedasyam; Shengqiang Shu; Kathleen Lail; Anna Lipzen; Catherine Adam; Kerrie Barry; Rotem Sorek; David Kudrna; Rod Wing; Talag Jayson; David Hall; Daniel Jacobson; Gerald Tuskan; Jeremy Schmutz; Frank Johannes; Robert J Schmitz: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.. Genome Biology, 21, 259 (2020). DOI: 10.1186/s13059-020-02162-5
Yadollah Shahryary; Aikaterini Symeonidi; Rashmi R Hazarika; Johanna Denkena; Talha Mubeen; Brigitte Hofmeister; Thomas van Gurp; Maria Colomé-Tatché; Koen Verhoeven; Gerald Tuskan; Robert J Schmitz; Frank Johannes: AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.. Genome Biology, 21, 260 (2020). DOI: 10.1186/s13059-020-02161-6
More information:
In an ongoing follow-up project, Frank Johannes is working with Hans Pretzsch, Professor of Forest Growth Science at the TUM, together. His chair leads a European beech experiment in the Steigerwald/Central Germany, where individual trees have been closely monitored since their first planting in 1870. Detailed growth and climate data are available for these trees. Now they are investigating whether and how the developmental history of these trees can be reconstructed using epigenetic measurements.
