Doctoral Dissertations
Date of Award
5-2021
Degree Type
Dissertation
Degree Name
Doctor of Philosophy
Major
Plant, Soil and Environmental Sciences
Major Professor
Tarek Hewezi
Committee Members
Feng Chen, Reza Hajimorad, Labrador-San Jose, Mariano, Neal Stewart,
Abstract
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.
Recommended Citation
Bennett, Meredith M., "Epigenetic mechanisms governing plant growth, development, and responses to nematode parasitism. " PhD diss., University of Tennessee, 2021.
https://trace.tennessee.edu/utk_graddiss/6677
Summary description of changes in promoter activity of DNA methylation and demethylation-related genes in two-week-old roots in response to phytohormone treatments.
Table 2.3.xlsx (10 kB)
Summary description of changes in promoter activity of DNA methylation and demethylation-related genes in two-week-old shoots in response to phytohormone treatments.
Table 4.1.xlsx (165 kB)
List of DEGs identified in suvh5 compared to Col-0 under noninfected conditions.
Table 4.2.xlsx (475 kB)
List of DEGs identified in suvh6 compared to Col-0 under noninfected conditions.
Table 4.3.xlsx (28 kB)
GO term analysis of DEGs common and unique to suvh5 and suvh6.
Table 4.4.xlsx (366 kB)
List of DEGs in H. schachtii-infected suvh5 compared to infected Col-0.
Table 4.5.xlsx (131 kB)
List of DEGs in H. schachtii-infected suvh6 compared to infected Col-0.
Table 4.6.xlsx (654 kB)
List of DEGs in H. schachtii-infected Col-0 compared to noninfected Col-0.
Table 4.7.xlsx (37 kB)
GO term enrichment analysis of DEGs identified in H. schachtii-infected Col-0, suvh5, and suvh6.
Table 4.8.xlsx (98 kB)
H3K9me2 peaks depleted in suvh5 compared to Col-0 overlapping with protein-coding genes, miRNAs and TEs.
Table 4.9.xlsx (56 kB)
H3K9me2 peaks depleted in suvh6 compared to Col-0 overlapping with protein-coding genes, miRNAs and TEs.
Table 4.10.xlsx (142 kB)
H3K9me2 peaks depleted in H. schachtii-infected suvh5 compared to infected Col-0 overlapping with protein-coding genes, miRNAs and TEs.
Table 4.11.xlsx (1580 kB)
H3K9me2 peaks depleted in H. schachtii-infected suvh6 compared to infected Col-0 overlapping with protein-coding genes, miRNAs and TEs.
Table 4.12.xlsx (491 kB)
H3K9me2 peaks enriched in H. schachtii-infected Col-0 compared to noninfected Col-0 overlapping with protein-coding genes, miRNAs and TEs.
Table 4.13.xlsx (63 kB)
H3K9me2 peaks depleted in H. schachtii-infected Col-0 compared to noninfected Col-0 overlapping with protein-coding genes, miRNAs and TEs.