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Hum Mol Genet. 2015 Dec 15;24(24):6932-43. doi: 10.1093/hmg/ddv397. Epub 2015 Sep 23.

Expanded GAA repeats impede transcription elongation through the FXN gene and induce transcriptional silencing that is restricted to the FXN locus.

Author information

1
Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA.
2
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
3
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA, Department of Cell Biology, Poznan University of Medical Sciences, Rokietnicka 5D, Poznan 60-806, Poland.
4
Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Abramson Research Center Room 502, Philadelphia, PA 19104, USA.
5
Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA, Institute of Human Genetics, Polish Academy of Science, Strzeszynska 32, Poznan 60-479, Poland.
6
Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA, mnapiera@uab.edu jsbutler@uab.edu.
7
Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA, Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland and mnapiera@uab.edu jsbutler@uab.edu.

Abstract

Friedreich's ataxia (FRDA) is a severe neurodegenerative disease caused by homozygous expansion of the guanine-adenine-adenine (GAA) repeats in intron 1 of the FXN gene leading to transcriptional repression of frataxin expression. Post-translational histone modifications that typify heterochromatin are enriched in the vicinity of the repeats, whereas active chromatin marks in this region are underrepresented in FRDA samples. Yet, the immediate effect of the expanded repeats on transcription progression through FXN and their long-range effect on the surrounding genomic context are two critical questions that remain unanswered in the molecular pathogenesis of FRDA. To address these questions, we conducted next-generation RNA sequencing of a large cohort of FRDA and control primary fibroblasts. This comprehensive analysis revealed that the GAA-induced silencing effect does not influence expression of neighboring genes upstream or downstream of FXN. Furthermore, no long-range silencing effects were detected across a large portion of chromosome 9. Additionally, results of chromatin immunoprecipitation studies confirmed that histone modifications associated with repressed transcription are confined to the FXN locus. Finally, deep sequencing of FXN pre-mRNA molecules revealed a pronounced defect in the transcription elongation rate in FRDA cells when compared with controls. These results indicate that approaches aimed to reactivate frataxin expression should simultaneously address deficits in transcription initiation and elongation at the FXN locus.

PMID:
26401053
PMCID:
PMC4654050
DOI:
10.1093/hmg/ddv397
[Indexed for MEDLINE]
Free PMC Article

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