BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans

We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC–mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network

Brachypodium distachyon - a model plant to study grass genome structure, dynamics and evolution

Plenary Session: Present status of cell, tissue and organ in vitro cultur

In situ

Epigenetic modifications of the chromatin structure are crucial for many biological processes and act on genes during the development and germination of seeds. The spatial distribution of 3 epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 was investigated in ‘matured,’ ‘dry,’ ‘imbibed” and ‘germinating’ embryos of a model grass, Brachypodium. Our results indicate that the patterns of epigenetic modification differ in the various types of tissues of embryos that were analyzed. Such a tissue-specific manner of these modifications may be linked to the switch of the gene expression profiles in various organs of the developing embryo

Schematic representation of a longitudinal cross section through a Brachypodium embryo with specific organ tissues marked.

<p>Schematic representation of a longitudinal cross section through a Brachypodium embryo with specific organ tissues marked.</p

Spatial Distribution of Epigenetic Modifications in <i>Brachypodium distachyon</i> Embryos during Seed Maturation and Germination

<div><p>Seed development involves a plethora of spatially and temporally synchronised genetic and epigenetic processes. Although it has been shown that epigenetic mechanisms, such as DNA methylation and chromatin remodelling, act on a large number of genes during seed development and germination, to date the global levels of histone modifications have not been studied in a tissue-specific manner in plant embryos. In this study we analysed the distribution of three epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 in ‘matured’, ‘dry’ and ‘germinating’ embryos of a model grass, <i>Brachypodium distachyon</i> (Brachypodium). Our results indicate that the abundance of these modifications differs considerably in various organs and tissues of the three types of Brachypodium embryos. Embryos from matured seeds were characterised by the highest level of H4K5ac in RAM and epithelial cells of the scutellum, whereas this modification was not observed in the coleorhiza. In this type of embryos H3K4me2 was most evident in epithelial cells of the scutellum. In ‘dry’ embryos H4K5ac was highest in the coleorhiza but was not present in the nuclei of the scutellum. H3K4me1 was the most elevated in the coleoptile but absent from the coleorhiza, whereas H3K4me2 was the most prominent in leaf primordia and RAM. In embryos from germinating seeds H4K5ac was the most evident in the scutellum but not present in the coleoptile, similarly H3K4me1 was the highest in the scutellum and very low in the coleoptile, while the highest level of H3K4me2 was observed in the coleoptile and the lowest in the coleorhiza. The distinct patterns of epigenetic modifications that were observed may be involved in the switch of the gene expression profiles in specific organs of the developing embryo and may be linked with the physiological changes that accompany seed desiccation, imbibition and germination.</p></div

The immunodetection of H4K5ac in ‘matured’ (A–D), ‘dry’ (E–H) and ‘germinating’ (I–L) Brachypodium embryos.

<p>Cross sections through the scutellum (<b>A, I</b>), the scutellum, coleoptile and leaf primordia (<b>E</b>), the SAM with leaf primordia (<b>B, F, J</b>), the RAM (<b>C, G, K</b>), the distal part of RAM, the root cap and coleorhiza (<b>D, H</b>) and the coleorhiza (<b>L</b>). Bar: 50 µm. Enlargements of selected cross sections are provided (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101246#pone.0101246.s001" target="_blank">Figure S1</a>).</p

The immunodetection of H3K4me1 in ‘matured’ (A–C), ‘dry’ (D–G) and ‘germinating’ (H–K) Brachypodium embryos.

<p>Cross sections through the scutellum (<b>A, D, H</b>), the coleoptile and SAM with leaf primordia (<b>B</b>), the coleoptile and leaf primordia (<b>E, I</b>), the SAM (<b>J</b>), the RAM, the root cap and coleorhiza (<b>C, K</b>), RAM (<b>F</b>), the distal part of RAM and the coleorhiza (<b>G</b>). Bar: 50 µm.</p

Starch accumulation in ‘matured’ (A–D), ‘dry’ (E–H) and ‘germinating’ (I–L) Brachypodium embryos detected by PAS reaction.

<p>Cross sections through the scutellum (A, E, I), coleoptile and SAM with leaf primordia (B, F, J), RAM (C, G, K), the root cap and coleorhiza (D, H, L). Bar: 50 µm.</p

Longitudinal cross sections through the whole ‘matured’ (A), ‘dry’ (B) and ‘germinating’ (C) Brachypodium embryo. Bar: 0.5 mm.

<p>Longitudinal cross sections through the whole ‘matured’ (A), ‘dry’ (B) and ‘germinating’ (C) Brachypodium embryo. Bar: 0.5 mm.</p