Nucleosome positioning in Arabidopsis
Usher, Sarah Louise (2009) Nucleosome positioning in Arabidopsis. PhD thesis, University of Warwick.
WRAP_THESIS_Usher_2009.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Official URL: http://webcat.warwick.ac.uk/record=b2285154~S15
The aim of this project was to test hypotheses relating to nucleosome positioning in Arabidopsis to provide a basis for better understanding of epigenetic transcriptional regulation in plants. Prior to this study, virtually no information existed regarding nucleosome positioning in plants. Eukaryote chromosomes consist of chromatin, composed of nucleosomes separated by linker DNA of variable lengths. Nucleosomes consist of 147 bp of DNA wrapped 1.7 times around a histone octamer. Whilst no consensus nucleosome positioning DNA sequence exists, sequence preferences influence positioning, and contribute to the complex epigenetic processes which act to control transcriptional activity. These details of the underlying mechanisms are known to differ between the plant and animal kingdoms.
High-throughput sequencing technologies were utilised to generate large datasets of mono- and di-nucleosome sequences from wild-type Arabidopsis. These enabled genome-wide analysis and inference of plant-specific patterns of nucleosome positioning and sequence properties. Further data were generated from a methyltransferase antisense (MET1) which is depleted in methylated CG epigenetic marks.
The internal distributions of dinucleotides within Arabidopsis nucleosomes were similar to those observed in non-plant eukaryotes. A unique periodicity in the distribution of linker lengths was detected in Arabidopsis wild type chromatin. In contrast, the MET1 antisense line displayed the expected periodicity, indicating systematic differences in chromatin organisation. There was a significant increase in nucleosome occupancy within exons compared with introns. However, this difference was less marked in the MET1 antisense. Specific patterns of nucleosome phasing were observed around transcription start sites. Linker lengths within rRNA gene clusters associated with nucleolar organiser regions (NORs) differed depending on chromosome of origin, suggesting differences in higher order chromatin structure between the NORs. Comparison of the nucleosome position and DNA methylation within the rRNA gene cluster revealed interesting differences between the two regions, which may reflect interactions affecting chromatin structure and transcriptional regulation.
|Item Type:||Thesis or Dissertation (PhD)|
|Subjects:||Q Science > QK Botany
Q Science > QH Natural history > QH426 Genetics
|Library of Congress Subject Headings (LCSH):||Arabidopsis thaliana -- Research, Arabidopsis thaliana -- Genetics, Genetic transcription -- Research, Eukaryotic cells -- Genetics|
|Official Date:||September 2009|
|Institution:||University of Warwick|
|Theses Department:||Warwick HRI|
|Supervisor(s)/Advisor:||King, Graham J. ; Kurup, Smita ; Baker, Guy, Dr.|
|Sponsors:||Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)|
|Format of File:|
|Extent:||206 leaves : ill., charts|
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