microRNAs in the Formation of Epigenetic Memory in Plants: The Case of Norway Spruce Embryos

Abstract

MicroRNAs (miRNA, miR) are short non-protein coding RNA molecules that are involved in both the nuclear and the posttranscriptional regulation of gene expression. miRNAs are endogenous mediators of RNA-interference forming part of the epigenetic machinery and influence gene expression post-transcriptionally without affecting the DNA sequence. In Norway spruce, epigenetic memory is established in response to the temperature conditions during embryogenesis and it affects the timing of bud burst and bud set, vitally important adaptive traits for long-lived forest species. Somatic embryogenesis at different epitype inducing (EpI) temperatures closely mimics the natural processes of epigenetic memory formation in seeds, giving rise to epigenetically different clonal plants in a reproducible and predictable manner, with respect to altered bud phenology. Developing Norway spruce embryos possesses a more complex small non-coding RNA (sRNA) structure than that reported for other somatic tissues. A variety of the predicted miRNAs showed distinct EpI temperature-dependent expression patterns. These putative EpI miRNAs target spruce genes with a wide range of functions, including genes known to be involved in epigenetic regulation, which in turn could provide a feedback process leading to the placement of epigenetic marks. Major features of miRNAs are related to their pleiotropic and synergistic actions, whereby a single miRNA can have several potential mRNA targets, and a single mRNA usually also has multiple miRNA binding sites. Moreover, miRNAs binding to a single mRNA often acts in a synergistic fashion. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation. Further functional and expression studies are necessary in order to elucidate the common miRNA-mediated regulatory mechanisms that underlie memory formation in plants. The use of artificial miRNAs, as well as overexpression and knockout/down of both miRNAs and their targets, will be the best techniques for determining the specific roles of individual miRNAs in memorizing the response to environmental stresses. In the present minireview, we illustrate the current knowledge regarding the epigenetics–miRNA regulatory networks aiming to provide biological insights into epigenetic memory formation in plants with a particular emphasis in spruce.