Abstract
The epigenome orchestrates many biological processes in higher eukaryotes by providing unique gene expression instruction in each cell type. However, we are still far from the complete understanding of the particular epigenetic dynamics required for proper cellular differentiation and lineage specification during development. This dissertation explores the dynamic epigenetic changes in early development and in tissue regeneration using zebrafish as a model organism. First, I identify genomic targets that exhibit programmed DNA methylation change during zebrafish early development. These developmental stage-specific differentially methylated regions (DMRs) have multiple signatures of distal developmental enhancers. Their methylation dynamic patterns correlate with their target gene expression much stronger than promoter methylation dynamics. I use transgenic zebrafish reporter assays to show the functional enhancer activities of these developmental stage-specific DMRs in live zebrafish embryos. I exploit these methylation dynamics to reconstruct putative gene regulatory networks important for organogenesis in developing zebrafish embryos. Second, I explore epigenomic dynamics of the osteoblast lineage cells in regenerating zebrafish fin. I investigate how different epigenetic marks contribute to initiating regeneration machinery along with keeping cell identity during tissue regeneration. In summary, this dissertation improves our understanding of how the epigenome regulates cell type specific transcription in development and regeneration by integrating functional epigenomics with developmental biology.
Committee Chair
Ting Wang
Committee Members
Douglas Chalker, Barak Cohen, Stephen Johnson, Kelly Monk,
Degree
Doctor of Philosophy (PhD)
Author's Department
Biology & Biomedical Sciences (Molecular Genetics & Genomics)
Document Type
Dissertation
Date of Award
Summer 8-15-2017
Language
English (en)
DOI
https://doi.org/10.7936/K7736QBW
Recommended Citation
Lee, Hyung Joo, "Epigenome Dynamics in Vertebrate Development and Regeneration" (2017). Arts & Sciences Theses and Dissertations. 1226.
The definitive version is available at https://doi.org/10.7936/K7736QBW
Comments
Permanent URL: https://doi.org/10.7936/K7736QBW