Spatial Distribution of Epigenetic Modifications in Brachypodium distachyon Embryos during Seed Maturation and Germination

Abstract

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, Brachypodium distachyon (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.

Seed response to strigolactone is controlled by abscisic acid-independent DNA methylation in the obligate root parasitic plant, Phelipanche ramosa L. Pomel

“…Indeed, tissues surrounding the embryo were shown to be more intensively demethylated than the embryo during seed imbibition in wheat and oilseed rape ( Lu et al , 2006 ; Meng et al , 2012 ). In addition, extensive DNA demethylation in the endosperms of Arabidopsis ( Hsieh et al , 2009 ), Oryza sativa (rice) ( Zemach et al , 2010 ), and Zea mays (maize) ( Lauria et al , 2004 ) and local histone modifications in Brachypodium distachyon embryos ( Wolny et al , 2014 ) have been reported. Interestingly, in P. ramosa seeds, PrCYP707A1 was shown to be expressed in the perisperm cells close to the micropyle a few hours after GR24 stimulation ( Lechat et al , 2012 ), suggesting a spatial distribution of epigenetic modifications during seed germination in P. ramosa , as already demonstrated in autotrophic plants.…”

The role of chromatin modifications in somatic embryogenesis in plants

“…The methods for the determination of methylation levels in DNA can be divided into at least into six general groups: global DNA methylation, regional DNA methylation, genome-wide analysis, DNA methylation analysis by sequencing, detection of specific methylation patterns, and individual CpG analysis ( Figure 5 ). Some of these have been applied to study the process of both SE and zygotic embryogenesis ( El-Tantawy et al, 2014 ; Nic-Can and De-la-Peña, 2014 ; Wolny et al, 2014 ; Pérez et al, 2015b ); however, it is necessary to expand current strategies in order to have a more precise understanding of these important processes. For a complete analysis of all of the techniques used to study chromatin modifications, see Tost (2009) , Kovalchuk and Zemp (2010) , Tollefsbo (2011) , and Spillane and McKeown (2014) .…”

In situanalysis of epigenetic modifications in the chromatin ofBrachypodium distachyonembryos

“…6 The global levels of the distribution of the histone modifications of 3 epigenetic markers, i.e., H4K5ac, H3K4me2 and H3K4me1 in 'matured,' 'dry,' 'imbibed' and 'germinating' embryos of a model grass, Brachypodium distachyon (Brachypodium), were studied in a tissue and organ-specific manner. 7 Our results indicate that the abundance of these modifications differs in various organs and tissues of the 4 types of Brachypodium embryos. Embryos from matured seeds were characterized by the highest level of H4K5ac in RAM and epithelial cells of the scutellum.…”