Epigenetic mechanisms governing plant growth, development, and responses to nematode parasitism

Epigenetic mechanisms, including histone and DNA methylation and microRNAs, play key roles in mediating transcriptional changes during plant development and stress responses. However, how these interconnected epigenetic components regulate gene expression in a spatiotemporal fashion remains partially known. Here, I generated 15 transgenic Arabidopsis GUS reporter lines for genes involved in DNA methylation and demethylation pathways. The spatiotemporal expression patterns of these genes were profiled in various plant organs during development, exogenous phytohormone response, and plant-parasitic nematode pathogenesis. The analyses revealed unique and overlapping expression patterns in roots, shoots, and reproductive organs, emphasizing the importance of a DNA methylation—demethylation equilibrium. Additionally, promoter activities suggest hormone-linked methylome regulatory mechanisms facilitate tissue differentiation.

In the syncytia and galls formed by the cyst (Heterodera schachtii) and the root-knot (Meloidogyne incognita) nematodes, respectively, CG and non-CG methyltransferases exhibited similar and distinct expression patterns at various stage of infection. DNA demethylases were more active in response to M. incognita than to H. schachtii. Furthermore, hypermethylated mutants defective in active DNA demethylation exhibited opposite responses to infection, which can be partially explained by the opposite regulation of pathogenesis-related genes by H. schachtii and M. incognita. These results suggest methylation-dependent mechanisms similarly and differentially regulate plant responses to infection by two distinct nematode species.

Finally, the regulatory mechanism through which miR778 induces histone modifications, DNA methylation, and transcriptome reprogramming during H. schachtii parasitism of Arabidopsis was investigated. miR778 post-transcriptionally silences the histone 3 lysine 9 (H3K9) dimethyltransferases SUVH5 and SUVH6 in roots following nematode infection. Genetic manipulation of the expression of miR778 and its target genes via overexpression, target mimicry, and T-DNA insertional mutation altered plant susceptibility to H. schachtii. Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis and RNA-seq analysis of suvh5 and suvh6 single mutants revealed novel functions for SUVH5 and SUVH6 in affecting many genes with development- and defense-related functions under nematode-infected conditions. Additionally, SUVH5/6-mediated H3K9 dimethylation associates with CG methylation in response to H. schachtii. Taken together, the data presented in this study highlight the importance of epigenetic mechanisms in establishing plant-nematode interactions and open new avenues for developing epigenetic signatures for nematode resistance.