Arabidopsis thaliana Transcriptome and Chromatin Dynamics during a Phosphate Starvation Response Reveal New Insights Into H3K27me3 and H2A.Z mediated gene regulation Open Access
Holder, Dylan (Summer 2024)
Abstract
Modifications to and variants of canonical nucleosome components give each nucleosome a unique identity thought to create a chromatin state that alters the propensity for a given locus to be subject to activation or silencing. In order for plants to mount an effective transcriptional response to nutrient stress, transcription machinery must overcome the established chromatin state at responsive genes. How transcription machinery rapidly overcomes the supposed repressive chromatin landscape at quiescent genes in response to activating signals and then effectively re-silence these genes once those signals are removed is not understood. We performed time-resolved and cell type specific profiling to understand how plants alter their transcriptome and chromatin landscape to achieve effective gene activation during phosphate starvation and then rapid silencing upon phosphate resupply. To our surprise, we found that activation of phosphate starvation response genes can occur without removal of gene body H2A.Z or H3K27me3, two features of chromatin thought to contribute to gene silencing. This finding coupled with recent observations from our lab suggesting that H2A.Z lost from induced genes is continuously replenished, highlighting the need to decouple the established roles these nucleosome modifications play in developmental gene regulation from their role in responsive gene regulation. The results presented here not only provide a cell-type and time-resolved resource for studying the chromatin dynamics of a systemic nutrient stress and recovery, but also suggest that our understanding of the dynamic chromatin landscape in responsive gene activation and repression is incomplete.
Table of Contents
Chapter 1:
Histone Variants in the Specialization of Plant Chromatin 1
Chapter 2:
Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z 55
Chapter 3:
Conclusion 108
Figures and Tables
Chapter 1:
Figure 1. The nature of histone variants and their distribution in chromatin. 31
Figure 2. Chromatin landscape changes in response to histone variant depletion. 32
Table 1. Histone variant genes, proteins, and functions in Arabidopsis thaliana 34
Chapter 2:
Figure 1. Root-hair RNA-seq during a phosphate starvation reveals several classes of phosphate starvation responses. 85
Figure 2. Root-hair INTACT-CUT&Tag compared to seedling ChIP-seq. 86
Figure 3. Chromatin dynamics during a phosphate starvation and recovery. 87
Figure 4. Phosphate starvation-induced (PSi) genes are enriched for H3K27me3 and gbH2A.Z but do not show significant changes in chromatin profile enrichment after P starvation. 88
Figure 5. H3K27me3 enriched PSi genes do not rely on PRC2 for proper regulation 90
Figure 6. Genes induced after 30m of P resupply lose H2A.Z and H3K4me3 while genes induced after 96h of P starvation do not. 91
Supplemental Figure 1. Overview of RNA-seq and chromatin profiling data. 92
Supplemental Figure 2. Chromatin features across the time course. 93
Supplemental Figure 3. Confirmation of transcript, H3K27me3, and H2A.Z levels at PSi genes in whole root. 94
Supplemental Figure 4. Phenotypes of PRC2 knockdown plants. 95
Supplemental Figure 5. Expression changes at genes with differential chromatin enrichment, chromatin dynamics of PSi genes across the starvation time course and 0h chromatin profiles at genes of interest. 95
About this Dissertation
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Primary PDF
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Arabidopsis thaliana Transcriptome and Chromatin Dynamics during a Phosphate Starvation Response Reveal New Insights Into H3K27me3 and H2A.Z mediated gene regulation () | 2024-07-24 14:23:14 -0400 |
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Supplemental Files
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Supplemental Dataset 2 (supplemental dataset for Chapter 2) | 2024-07-24 14:23:25 -0400 |
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Supplemental Dataset 1 (supplemental dataset for Chapter 2) | 2024-07-24 14:23:45 -0400 |
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Supplemental Table 1 (supplemental table for Chapter 2) | 2024-07-24 14:24:03 -0400 |
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Supplemental Dataset 3 (supplemental dataset for Chapter 2) | 2024-07-24 14:24:22 -0400 |
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