Epigenetic regulation of the defense gene induction in Arabidopsis thaliana in response to Pseudomonas syringae

Bordiya, Yogendra
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Plants and animals respond to an ever changing environment by making changes in the physiological level of various proteins and metabolites. This rapid physiological change in response to the environment is achieved by massive transcriptional reprogramming. Therefore, switching the large number of genes on and off at the right time in the right place requires highly sophisticated transcriptional regulation and is very important in mounting responses appropriate for the environmental change/stress. Recent studies suggest that epigenetics is one of the critical components in the regulation of transcription to help responding and adapting to environmental changes/stresses. The epigenetic regulation is achieved through the modification of chromatin structure, which is generally mediated by DNA/histone modifications, small RNAs (sRNAs), long non-coding RNA, and nucleosome positioning. In my dissertation, I have studied the role of epigenetic components which regulate defense responses in Arabidopsis thaliana in response to Pseudomonas syringae. To this end, I assessed biotic-stress-triggered changes in chromatin accessibility and characterized several epigenetic mutants in gene silencing in Arabidopsis. From these assessments, I particularly focused on testing the hypothesis that these epigenetic changes are important in the induction dynamics of defense genes triggered by infection. Intriguingly, I found that biotic-stress-triggered chromatin changes were frequently associated with transposable elements (TEs) proximal to defense genes, some of which functioned as transcriptional enhancers. This observation suggested that a TE controlling mechanism(s) might be important in defense responses. Indeed, I found that more than a hundred TEs become transcriptionally induced under biotic stress, which merited further characterization of mutants involved in RNA-dependent DNA methylation (RdDM), the best characterized regulatory mechanism for TEs. I chose to characterize four DCL (dicer-like) genes that are important in the biogenesis of sRNAs, critical modulators for TEs and chromatin remodeling. Among these dcl mutants, dcl1 displayed the most compromised resistance and induction of defense genes against avirulent P. syringae, suggesting that some sRNAs may be necessary for the rapid defense responses. In contrast, dcl2 and dcl3 showed marginally enhanced resistance and elevated expression of defense genes to the avirulent pathogen. In particular, dcl2 and dcl3 showed substantially increased expression of defense genes without pathogen challenges, suggesting that DCL2/3-generated sRNAs are important in suppressing defense genes. Note that the expression analysis of defense genes was performed using a novel targeted RNA-seq analysis known as RASL-seq (RNA-mediated oligonucleotide Annealing, Selection, and Ligation with next-generation sequencing). Selection of the defense genes used for the RASL-seq was chosen on the basis of my RNA-seq analysis, which identified rapidly induced genes at different time points in response to avirulent P. syringae relative to the virulent counterpart. In addition to altered defense gene induction in the mutants, I found that many RdDM genes including MORC1 were transcriptionally suppressed as early as 6 hr post infection, suggesting that RdDM components may play a role regulating the dynamics of defense responses.
Plant immune system, Epigenetics
Bordiya, Y. (2017). <i>Epigenetic regulation of the defense gene induction in Arabidopsis thaliana in response to Pseudomonas syringae</i> (Unpublished dissertation). Texas State University, San Marcos, Texas.