Definition Of The Landscape Of Chromatin Structure At The Frataxin Gene In Friedreich’S Ataxia

Author

Eunah Kim, The University of Texas Graduate School of Biomedical Sciences at HoustonFollow

Date of Graduation

12-2011

Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Sharon Y. R. Dent, Ph.D.

Committee Member

Michelle C. Barton, Ph.D.

Committee Member

Pierre McCrea, Ph.D.

Committee Member

Xiaobing Shi, Ph.D.

Committee Member

Min Gyu Lee, Ph.D.

Abstract

Friedreich’s ataxia (FRDA) is caused by the transcriptional silencing of the frataxin (FXN) gene. FRDA patients have expansion of GAA repeats in intron 1 of the FXN gene in both alleles. A number of studies demonstrated that specific histone deacetylase inhibitors (HDACi) affect either histone modifications at the FXN gene or FXN expression in FRDA cells, indicating that the hyperexpanded GAA repeat may facilitate heterochromatin formation. However, the correlation between chromatin structure and transcription at the FXN gene is currently limited due to a lack of more detailed analysis. Therefore, I analyzed the effects of the hyperexpanded GAA repeats on transcription status and chromatin structure using lymphoid cell lines derived from FRDA patients. Using chromatin immunoprecipitation and quantitative PCR, I observed significant changes in the landscape of histone modifications in the vicinity of the GAA tract in FRDA cells relative to control cells. Similar epigenetic changes were observed in GFP reporter construct containing 560 GAA repeats. Further, I detected similar levels of FXN

pre-mRNA at a region upstream of hyperexpanded GAA repeats in FRDA and control cells, indicating similar efficiency of transcription initiation in FRDA cells. I also showed that histone modifications associated with hyperexpanded GAA repeats are independent of transcription progression using the GFP reporter system. My data strongly support evidence that FXN deficiency in FRDA patients is consequence of defective transition from initiation to elongation of FXN transcription due to heterochromatin-like structures formed in the proximity of the hyperexpanded GAAs.

Keywords

Epigenetics, Chromatin Structure, Histone Modification, Frataxin, FRDA, Neurodegenerative Disease, Repetitive DNA, Triplet repeat, Repeat Diseases