The Trouble with Triples:Elucidating the Behavior of Trinucleotide Repeats in Chromatin

Volle, Catherine B.

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Year:: 2014
Contributor:: Volle, Catherine B (creator); Delaney, Sarah (Director); Gerbi, Susan (Reader); Freiman, Richard (Reader); Zhitkovich, Anatoly (Reader); Freudenreich, Catherine (Reader); Brown University. BIOMED: Molecular Biology, Cell Biology, and Biochemistry (sponsor)
Genre:: theses
Subject:: Nucleosome; DNA Hairpin; Trinucleotide repeats; Chromatin
Extent:: xviii, 224 p.
DOI: https://doi.org/10.7301/Z0K935W9

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Abstract:: Trinucleotide repeats (TNRs) occur throughout the genome and their expansion can affect varied cellular processes such as gene expression, mRNA processing, and protein folding. TNR expansion, facilitated by formation of stable non-canonical secondary structures (e.g. hairpins), has been linked to several neurodegenerative diseases, such as Huntington’s Disease (caused by expansion of CAG/CTG repeats) and Fragile X Syndrome (caused by expansion of CGG/CCG repeats). TNR structure and expansion has been studied in vitro using both oligonucleotides and TNRs incorporated into plasmids; however, genomic DNA is packaged into chromatin, and little is know about the effect of packaging on the ability of repetitive DNA to expand. Previous studies have shown that disease-length, expanded CAG/CTG repeats readily incorporate into the basic unit of chromatin packing, the nucleosome core particle (NCP), composed of 146 base pairs of DNA wrapped around a core of eight histone proteins. However, long CGG/CCG repeats exclude NCP formation. Here, we seek to investigate not only the properties associated with healthy-length repeats incorporated into NCPs, but also the effect of the flanking gene sequence. Additionally we investigate the behavior of a hairpin formed by CAG repeats when flanked by well-matched duplex, forming a three- way junction, and how hairpin formation can affect chromatin packaging. To assess the global forces regulating interaction between the TNRs and the histone core, we performed competitive nucleosome exchanges to determine the efficiency with which various TNR sequences incorporate into NCPs. We then used enzymatic and chemical probing to determine the effect of histone occupancy on the TNRs, including the formation of possible non-canonical structures. Understanding the intricacies underlying the interaction between unexpanded TNRs and the histone core is important to understanding how TNRs expand in the genome.
Notes:: Thesis (Ph.D. -- Brown University (2014)

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Rights: In Copyright
Restrictions on Use: Collection is open for research.

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Volle, Catherine B., "The Trouble with Triples:Elucidating the Behavior of Trinucleotide Repeats in Chromatin" (2014). Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations. Brown Digital Repository. Brown University Library. https://doi.org/10.7301/Z0K935W9

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Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations

Theses and Dissertations for the Molecular Biology, Cell Biology, and Biochemistry department.
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