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DNA Secondary Structure in Human Disease and Gene Regulation

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abstract
DNA secondary structures have critical roles in normal cellular processes and human diseases, but the extent of their formation and regulation on a genome-wide level is still not fully understood. The goal of this work is to further explore the role of DNA secondary structure formation in human disease, and to characterize sites of predicted highly stable DNA secondary structure on a genome-wide level. We find that environmental chemical- and chemotherapeutic drug-induced DNA breakpoints at the leukemia-associated gene MLL in human hematopoietic stem cells coincide with sites of predicted DNA stem-loop structure and predicted topoisomerase II cleavage. This suggests a role for DNA secondary structure formation in mediating topoisomerase II-dependent DNA breakage at sites with a propensity to form leukemia-causing gene rearrangements. We also examine quadruplex-forming GGGGCC repeats known to cause ALS-FTD, and determine that DNA replication through the repeats leads to a length- and orientation-dependent increase in instability, including repeat expansions. Further, overall replication efficiency is decreased and replication fork stall is increased in a length- and orientation-dependent manner, suggesting that quadruplex formation by the expanded GGGGCC repeats is able to disrupt DNA replication, potentially leading to further expansion and disease. Finally, using the Mfold and ViennaRNA programs with thermodynamic paramaters for single-stranded DNA we analyze the ability of the complete human genomic DNA sequence to form stable DNA secondary structures. We find that predicted highly stable DNA secondary structure sites associate with sites of active transcription and open chromatin. Predicted Mfold and ViennaRNA sites are associated with RNA polymerase II binding sites in five cell lines, and are with bivalent chromatin in human embryonic stem cells, suggesting a role in regulation of gene expression at developmental loci. Our data suggests diverse roles for DNA secondary structure formation in human disease and gene regulation at loci throughout the genome. Overall, these results demonstrate the importance in understanding the mechanism of DNA secondary structure formation and regulation in human disease and normal cellular processes.
subject
Amyotrophic Lateral Sclerosis
DNA Secondary Structure
Fragile Sites
Genomic Instability
Leukemia
contributor
Thys, Ryan (author)
Wang, Yuh-Hwa (committee chair)
Hollis, Thomas (committee member)
Ornelles, David A (committee member)
Pardee, Timothy S (committee member)
Seals, Darren F (committee member)
date
2015-06-23T08:35:43Z (accessioned)
2015 (issued)
degree
Cancer Biology (discipline)
10000-01-01 (liftdate)
embargo
forever (terms)
identifier
http://hdl.handle.net/10339/57122 (uri)
language
en (iso)
publisher
Wake Forest University
title
DNA Secondary Structure in Human Disease and Gene Regulation
type
Dissertation

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