Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Histone variants contribute to chromatin complexity by creating specialized nucleosomes. Here, to investigate the pattern of H2A.Z histone variant distribution and its role in modulating gene expression in rice (Oryza sativa L.), we performed genome-wide profiling of ARP6-dependent H2A.Z deposition in rice seedlings. We demonstrated that under controlled conditions, the majority of H2A.Z deposition is within protein-coding genes (PCG), and the most highly expressed genes are enriched with H2A.Z at their 5’ ends near the transcription start site (TSS), whereas the medium- to low-expressed genes contain H2A.Z across the entire gene. Based on H2A.Z deposition, we categorized genes into “housekeeping” and “stress-responsive” genes, which reflects their functions. Analysis of 24-hour Pi deficiency showed a significant reduction of H2A.Z at the TSS of housekeeping genes and gene body of stress-responsive genes, with the latter significantly overlapping with Pi deficiency-induced up-regulation of the affected genes. Reciprocally, genes containing an increase in H2A.Z demonstrated a significant correlation with down-regulated genes. These results revealed the negative role of H2A.Z deposition inside the gene body of stress-responsive genes. Also, we found that RNA interference (RNAi)-mediated Knock-down of ACTIN-RELATED PROTEIN 6 (ARP6), which encodes a key component of the SWR1 complex that catalyzes H2A.Z deposition, resulted in a H2A.Z genic pattern that was remarkably similar to that of Pi-deficient wild type (WT). However, the analysis of responses at the H2A.Z level unique to either ARP6 Knock-down or Pi deficiency demonstrated that Knock-down of ARP6 has a larger impact on loss of H2A.Z at the TSS of housekeeping genes associated with plastid functions and translation, whereas Pi deficiency leads to a greater impact on loss of H2A.Z in the gene bodies of stress-related genes, including many transcription factor genes. Moreover, the analysis of the combined effect of Pi deficiency and ARP6-RNAi Knock-down showed no apparent synergistic effect on changes in H2A.Z deposition or transcript abundance, but resulted in the identification of several categories of genes exhibiting diverse responses to Pi-deficiency, ARP6 Knock-down, or in response to the combined perturbations. Together the results show that a short-term Pi deficiency treatment mimics knock-down of a key determinant of H2A.Z deposition (i.e. ARP6) in terms of differential H2A.Z deposition and changes in gene expression. Because short-term Pi deficiency induces stress components shared among a number of environmental stressors, the results suggest that H2A.Z deposition in the gene body acts as a repressor of many genes that are responsive to diverse stimuli. In addition, deposition of H2A.Z at the TSS may play an important role for the expression of housekeeping genes, particularly those linked to translation and plastid functions.



Committee Chair

Smith, Aaron