Browsing by Subject "Epigenetics"

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Interplay between nutrition, senescence and cytosine methylation in Arabidopsis thaliana
(2023) Vatov, Emil; Ludewig, Uwe
In monocarpic plants, senescence is the last stage of leaf development and usually leads to the death of the organism. Systematic degradation of leaf components provides nutrients for the newly developing flowers and seeds. The physiology and transcriptional changes that occur in A. thaliana during this process are very well documented. However, the involvement of epigenic mechanisms remains to be established. In this study, the role of cytosine methylation in the regulation of monocarpic leaf senescence was examined in A. thaliana. Hypomethylated ddc (drm1/2 cmt3) and hypermethylated ros1 mutants showed consistent senescence-specific phenotypes. Disrupted de-novo methylation resulted in delayed, while disrupted demethylation resulted in earlier flowering and appearance of first symptoms of senescence. Both genotypes executed the senescence program faster than Col-0, with lower leaf:seed and higher C:N ratios. During nitrogen, or phosphorus withdrawal and resupply, nutrient remobilization was not inhibited in the two mutants. However, the plant’s response in terms of changes in shoot and root growth was delayed, or non existent. Furthermore, the impact of N withdrawal on delay of the flowering time was inhibited in the two mutants. These results support involvement of cytosine methylation in stress response signaling and downstream effects on organ development and flowering times. The stress response and senescence specific phenotypes of ddc could be partially due to disrupted WRKY signaling, as loss of methylation in W-box binding sites was prevalent, specifically near the transcription start sites of ORFs, and WRKY18, 25 and 53 appeared to be sensitive towards cytosine methylation. Overall decrease in cytosine methylation levels was observed, as early as the opening of the first flowers, together with a decrease in chlorophyll concentrations and an increase in H2O2 and glucose levels in the wild type Col-0. Inhibition in maintenance methylation in the early stages of reproductive growth is consistent with these observations. A complex interaction between four cytokinins was present as early as flower induction, followed by a mass turnover of bound auxin (IAA) at flower opening, that resulted in near doubling of free IAA at seed development. Plant defense responses were induced thereafter, as an increase in salicylic acid (SA) and camalexin occurred, followed by an increase in jasmonic acid (JA) and abscisic acid (ABA). Active RNA-dependent DNA methylation (RdDM) was indicated by a moderate overrepresentation of hypermethylated CHG and CHH loci, together with partial recovery of total methylation levels at the latest stages during seed maturation. Considering the delayed senescence phenotype of ddc, de-novo methylation via RdDM appears to be involved in initiation and execution of the senescence program. Furthermore, hypomethylation at ROS1 gene regulatory region was related to down regulation of gene expression. As an antagonist of RdDM, together with the early senescence phenotype of ros1, these results strengthen the importance of de-novo methylation for senescence, while active demethylation gets down regulated. Overall, methylation changes were little related to known gene expression changes that are associated with senescence. Limited targeting of WRKY and bZIP binding sites hinders conclusions about senescence specific effects of cytosine methylation in signal transduction networks. Altogether, the present work shines light on the importance of proper maintenance of cytosine methylation for flowering time, nutrient remobilization and senescence, and identifies defined cytosine methylation changes during senescence in a comprehensive physiological framework.
Site-dependent differences in DNA methylation and their impact on plant establishment in Populus trichocarpa
(2016) Schönberger, Brigitte; Ludewig, Uwe
Phosphate (Pi) limits total biomass production in natural tree ecosystems. Due to the low mobility of Pi in soil, higher plants, like trees, require special adaptations for phosphorus (P) acquisition. The genetic and physiological basis of this adaptation has been studied extensively. In addition, phosphorus starvation was recently suggested to affect epigenetic modifications in varying annual plant species. However, the impact of differential DNA methylation and microRNAs (miRNAs) on gene expression as well as site-dependent P-related physiology is largely unknown in perennials. In this study Populus trichocarpa clones, established from stem cuttings from two different locations, were grown in hydroponic culture with different P levels. Morphological and physiological parameters as well as, using bisulfite sequencing, site-specific genome-wide methylomes were determined. Gene and miRNA expression of differentially methylated regions was quantified via qPCR. Site-dependent differences in plant establishment were encountered, together with site-specific differentially methylated chromosomal regions. Methylation differences were nucleotide context-specific and extensively regulated miRNAs and their target genes in an organ-specific way. Though no direct relation between differential methylation in coding regions and their corresponding gene expression was observed, a general site-dependent transcriptional repression by DNA methylation was detected. Nevertheless, differential DNA methylation and gene expression was not affected by P nutrition, although recent studies described P-starvation induced DNA methylation changes, suggesting species-specific epigenetic mechanisms. However, differentially methylated miRNAs, together with their target genes, showed P-dependent expression profiles, indicating miRNA expression changes as a P-related epigenetic modification in poplar. Hence, it was shown that differences in DNA methylation or differentially methylated miRNAs might influence plant establishment and partially correlate with P acquisition, and thus be responsible for a site-dependent adaptation and growth performance, interesting for plant breeding, conservation biology and biodiversity studies of vegetatively propagated perennials.