Date Approved

9-16-2019

Embargo Period

9-17-2019

Document Type

Thesis

Degree Name

M.S. Bioinformatics

Department

Molecular and Cellular Biosciences

College

College of Science & Mathematics

First Advisor

Carone, Benjamin R.

Second Advisor

Alpaugh, Mary

Third Advisor

Spielman, Stephanie

Subject(s)

Epigenetics; Chemotherapy

Disciplines

Bioinformatics | Genetics and Genomics

Abstract

Bleomycin (BLM), a glycopeptide antibiotic commonly used in chemotherapeutic treatments, has been shown to produce single and double stranded DNA breaks. Subsequent analysis of DNA fragmentation patterns has demonstrated preferential digestion of chromatin in the TSS of active genes and the ability to produce nucleosome-sized fragments within intact chromatin. Nucleosome positioning plays a critical role in the regulation of gene activation. Currently, micrococcal nuclease (MNase) is used as the standard for mapping the position of nucleosomes in the genome. In order to identify whether BLM can be used as an effective nucleosome-mapping agent, BLM was used to digest chromatin in S. cerevisiae, followed by Next Generation Sequencing of paired-end DNA fragments. Our results demonstrate comparable DNA fragmentation patterns for both nucleosomes as well as other DNA-protein interactions and furthermore explain the propensity for BLM to digest within the promoters of active genes. Finally, we show that BLM can be used to identify genome-wide nucleosome and Transcription factor footprints as an effective alternative for MNase and additionally lacks the strong sequence biases of MNase digestion.

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