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The DNA in the eukaryotic genome is wrapped in 147--bp segments around an octamer of histone proteins to form the fundamental subunit of chromatin, the nucleosome. Nucleosomes regulate the access of proteins to DNA, thus regulating important DNA-templated events such as transcription, translation, recombination, and repair. In order to characterize the chromatin landscape in maize, we mapped nucleosome positions using micrococcal nuclease (MNase) to enrich for nucleosomal DNA. We mapped nucleosomes under a variety of experimental conditions and in different tissues. We identified an unexpected, nonuniform source of variation which we traced to the degree to which chromatin is digested with MNase. We exploited this property to identify nucleosomes in the maize genome that possessed unique biochemical traits as being hypersensitive or hyper-resistant to MNase digestion. These regions were associated with important biological processes, including gene expression levels, transcription-factor binding, and highly-conserved noncoding sequences. In addition, we found that these nucleosomes displayed tissue specificity, implicating this special type of chromatin feature in regulating gene expression under different cell physiologies. We extended this work to the human genome and made similar discoveries: hypersensitive nucleosomes were associated with gene expression levels and were enriched in important regulatory elements. We also found hyper-resistant nucleosomes to be highly-associated with paused RNA polymerase II, implicating these nucleosomes in regulating transcriptional elongation. Thus, our approach to chromatin profiling uncovers novel biochemical states of multicellular organisms that are likely important for transcription, differentiation, and cellular responses.
A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Includes bibliographical references.
Hank Bass, Professor Co-Directing Dissertation; Jonathan Dennis, Professor Co-Directing Dissertation; Jinfeng Zhang, University Representative; Brian Chadwick, Committee Member; Dave Gilbert, Committee Member.
Florida State University
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