Traits that influence the climatic adaptation of trees are affected by the climatic conditions during seed development. This is due to epigenetic memory influencing growth patterns and gene activities without altering the DNA sequence itself. The EpiMemo project aims to improve our understanding of the mechanisms behind this epigenetic memory. In the project, genetically identical Norway spruce trees are studied along with corresponding embryos (equivalent to the embryonic plant of the seed). These trees and embryos were generated through a tissue culture technique called somatic embryogenesis. Trees originating from embryos developed under warmer conditions show later dehardening and bud burst in the spring, and later formation of winter buds, compared to trees from embryos developed under cooler conditions.
We have shown that these differences are associated with significant variations in DNA methylation in genes related to epigenetic regulation, biological clocks and control of the growth-dormancy cycle and frost tolerance. Some of these genes display different DNA methylation patterns throughout the year depending on the temperature during embryo development, while others show differences only at specific times of the year.
Consistent with the idea that DNA methylation patterns can influence gene activity, these plant groups also show distinct differences in gene expression (mRNA levels) for protein-coding genes. The most pronounced differences in gene activities occur in the spring prior to bud burst and during the autumn and winter, aligning with the differences in the timing of dehardening, bud burst and winter bud formation between the plant groups.
We also compared the annual DNA methylation patterns through the annual cycle in plants from warmer and cooler embryogenesis climate with binding sites for transcription factors – proteins that control gene expression. These results and the overlap between differences in gene activities and DNA methylation patterns suggest that certain genes involved in stress and defence responses and the regulation of the growth-dormancy cycle and biological clocks may play a role in the epigenetic memory.
Clear differences between the plant groups were also found in the activities of genes encoding small regulatory RNA molecules (sRNA). Different levels of sRNAs in plants from warmer and cooler embryo development climate corresponded to differences in levels of specific mRNAs. As expected, high levels of certain sRNAs matched low levels of specific mRNAs, indicating that some sRNAs may contribute to the epigenetic memory affecting the regulation of the growth-dormancy cycle.
Similar differences in gene activities and DNA methylation were also observed in corresponding somatic embryos developed under cooler and warmer conditions.
So far, the results suggest that DNA methylation in specific genes and small regulatory RNA molecules play a role in the epigenetic memory of temperature during seed (embryo) development. These epigenetic mechanisms may therefore enable faster climatic adaptation in long-lived plants than the slower adaptation that occurs through natural selection.
Epigenetic memory may be induced by environmental conditions experienced during embryogenesis. How such a memory affects an organism’s ability to survive and adapt is a topic of great interest. Questions of intense debate are which life stages that are the most sensitive, how altered epigenetic marks are maintained mitotically through a long life and how they alter the phenotype. In EpiMemo we will probe these questions using the long-lived tree species Norway spruce as our experimental system. We will use a unique set of clonal epitype trees with a stable epigenetic memory of the climatic conditions (cold/warm) during embryogenesis and corresponding epitype embryos. To elucidate if the epigenetic memory is associated with differential DNA methylation between epitypes, we will look for stable DNA methylation differences in stem cells of the apical meristems of shoot tips/buds in epitype trees through the annual cycle and in mature embryos. A machine learning pattern recognition approach will be used to distinguish stable DNA methylation differences between epitypes from dynamic changes through the annual cycle. In addition, we will examine mRNA and sRNA gene expression differences (DEG) between epitypes to establish if changes in DNA methylation marks are associated with the observed DEG. We will also study how and when during embryogenesis the epigenetic memory is laid down, by analysing the DNA methylation, mRNA and sRNA expression during different stages of embryogenesis. To verify that DNA methylation differences are causing the phenotypic differences between epitypes we will use targeted editing of DNA methylation of identified target genes by means of transcriptional gene silencing (TGS). Understanding the evolutionary significance of epigenetic memory in climatic adaptation will reveal how perennial plants may epigenetically adjust their annual cycle to local climate changes more rapidly than classical natural selection can cope with.
