title: Expanded GAA repeats impede transcription elongation through the FXN gene and induce transcriptional silencing that is restricted to the FXN locus.
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.
authors.affiliation: Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA.
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
authors.forename: Yue
authors.initials: Y
authors.lastname: Lu
authors.affiliation: 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.
authors.forename: Urszula
authors.initials: U
authors.lastname: Polak
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Lin
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Shen
authors.affiliation: Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Abramson Research Center Room 502, Philadelphia, PA 19104, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Farmer
authors.affiliation: Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Abramson Research Center Room 502, Philadelphia, PA 19104, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Seyer
authors.affiliation: Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA.
authors.forename: Angela D
authors.initials: AD
authors.lastname: Bhalla
authors.affiliation: 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.
authors.forename: Natalia
authors.initials: N
authors.lastname: Rozwadowska
authors.affiliation: Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Abramson Research Center Room 502, Philadelphia, PA 19104, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Lynch
authors.affiliation: 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.
authors.forename: Jill Sergesketter
authors.initials: JS
authors.lastname: Butler
authors.affiliation: 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.
authors.forename: Marek
authors.initials: M
authors.lastname: Napierala
mesh_terms: D000225:Adenine; D005621:Friedreich Ataxia / Q000235:genetics*; D020868:Gene Silencing; D056426:Genetic Loci; D006147:Guanine; D006657:Histones / Q000378:metabolism; D033862:Iron-Binding Proteins; D017423:Sequence Analysis, RNA; D061805:Transcription Elongation, Genetic; D019680:Trinucleotide Repeat Expansion; D000096923:Frataxin
chemical_list: D000225:Adenine; D006147:Guanine; D006657:Histones; D033862:Iron-Binding Proteins; D000096923:Frataxin