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Dissertation
INSIGHTS INTO THE ROLE OF CHROMATIN STRUCTURE ON TRANSCRIPTIONAL VARIATION ACROSS GENOTYPE, ENVIRONMENT, AND DEVELOPMENTAL STAGE IN ORYZA SATIVA
Washington State University
Doctor of Philosophy (PhD), Washington State University
01/2022
DOI:
https://doi.org/10.7273/000004373
Handle:
https://hdl.handle.net/2376/118900
Abstract
Gene expression is an important biological process that transmits the effects of genetic variations toward important plant phenotypes through complex biological networks. In the last decade, studies utilizing new technologies for investigating nuclear chromatin in plants have discovered that nuclear DNA interacts through multi-layered hierarchical epigenomic structures including DNA methylation, chromosome A/B compartments, and topologically associated domains (TADs). The research contained in this dissertation spans two distinct studies with an overall objective of determining the extent that these epigenomic features contribute to variations in gene expression across different genotypes, environments, and developmental stages. Chapter 1 is a descriptive literature review of current knowledge regarding the different layers of epigenomic structures. The first research study, contained in chapter 2, explores the stability of transcriptional heritability across optimal and stress conditions in a diverse population of rice. This research discovered that genome-wide distributions of stress-specific heritable expression were enriched within specific genomic hotspots. Highly and lowly expressed genes were found to be distributed differently along chromosomes in patterns that closely match chromatin structure. For the second study, contained in chapter 3, variation in gene transcription along developing rice internodes were characterized and tested for potential transcriptomic regulatory relationships with epigenomic features including DNA methylation, A/B compartments, and TAD domains. This research discovered that CpG methylation greatly differed between transposable elements and non-transposable element genes particularly within promoter and 5’ untranslated regions but did not greatly differ within gene bodies. This study also found that for actively expressed genes, CpG methylation appeared to only be involved in transcriptional regulation of a small minority of genes. This small group of genes was significantly enriched for functional terms including the WD40 domain and protein kinase activity. While chromatin A/B compartments did not appear to have major roles in transcriptional regulation aside from TE repression, actively expressed genes were associated with TAD borders and gene repression was associated with TAD interiors. Chapter 4 reflects on how lessons learned in this research can guide future epigenomic research and identifies two potential applications for epigenomic research including expression engineering and genomic selection modeling (appendix 1).
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Details
- Title
- INSIGHTS INTO THE ROLE OF CHROMATIN STRUCTURE ON TRANSCRIPTIONAL VARIATION ACROSS GENOTYPE, ENVIRONMENT, AND DEVELOPMENTAL STAGE IN ORYZA SATIVA
- Creators
- Matthew Thomas McGowan
- Contributors
- Zhiwu Zhang (Advisor)Stephen P Ficklin (Advisor)Karen A Sanguinet (Committee Member)Laura E Bartley (Committee Member)Rebecca J McGee (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Program in Molecular Plant Sciences
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 209
- Identifiers
- 99900883134701842
- Language
- English
- Resource Type
- Dissertation