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Abstract
Transcription of nuclear genes in eukaryotic organisms occurs in a chromatin environment, where the template DNA is wrapped around histone octamers to form nucleosomes. The interplay between transcription and the local chromatin structure is studied in this dissertation both at stress and normal conditions. Exposure to heat triggers a conserved response of rapid alteration in gene expression. We studied the role of chromatin in the induction, maintenance and attenuation of temperature-dependent transcriptional changes. The results from genome-wide time course analyses of RNA abundance, RNA Polymerase II occupancy, histone variant distribution (H3.1 vs. H3.3) and a histone modification (H3K36me3) in Arabidopsis during heat stress indicated heat treatment led to the rapid and complete loss of both H3.1 and H3.3 as well as H3K36me3 signals, which was concomitant with the recruitment of Pol II to extraordinarily high levels. Attenuation of transcription (i.e. the loss of Pol II) was accompanied by the redeposition of new H3.3, but not H3.1. Histone modifications appeared to be re-established at a much later time. Our results also showed there was no evidence that heat-inducible genes were pre-deposited with any unusual chromatin state, or that H2A.Z may affect nucleosome theromostability in planta. Approximately 1/4 of the total Pol II signals relocalized from a specific set of genes to heat-inducible genes during transcriptional activation, and from early inducible genes to late inducible genes during transcriptional attenuation. Inevitably, all intra-nucleosomal DNA-histone interactions must be at least transiently disrupted during transcription. However, nucleosome organization on differentially expressed genes did not show any observable differences perhaps because the pattern of nucleosome positioning is determined by the combination of DNA sequence, nucleosome remodelers, DNA methylation, transcription factors including activators, components of the pre-initiation complex, elongating Pol II, histone modifications and histone variants. This dissertation, for the first time, showed H3K4 tri-methyltransferase SDG2 interacts with a group of SMC like coiled-coil domain proteins that may direct it to chromatin for establishing the H3K4me3 pattern. It also showed the first genome-wide profiling of a new histone double mark H3K27me3S28ph, and suggested it may be involved in H3K27me3 target gene de-repression.