Doctor of Philosophy (PhD)


Biological Sciences

Document Type



In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and transcriptional changes in response to environmental perturbation remain unclear.

We report a high-resolution map of nucleosome patterns in the rice (Oryza sativa) genome by deep sequencing of micrococcal nuclease digested chromatin. The results reveal that nucleosome patterns at rice genes were affected by both cis- and trans- determinants, including GC content and transcription. A negative correlation between nucleosome occupancy across the transcription start site (TSS) and transcription was observed, and the nucleosome patterns across the TSS were correlated with distinct functional categories of genes. A parallel experiment was done monitoring nucleosome dynamics and transcription changes in response to phosphate starvation for 24 hours. Phosphate starvation resulted in numerous instances of nucleosome dynamics across the genome which were enhanced at differentially expressed genes.

This work demonstrates that rice nucleosome patterns are suggestive of gene functions, and reveal a link between chromatin remodeling and transcriptional changes in response to deficiency of a major macronutrient. The findings help to enhance the understanding towards eukaryotic gene regulation at the chromatin level.



Committee Chair

Larkin, John C