title: Altered nucleosome positioning at the transcription start site and deficient transcriptional initiation in Friedreich ataxia.
abstract: Most individuals with Friedreich ataxia (FRDA) are homozygous for an expanded GAA triplet repeat (GAA-TR) mutation in intron 1 of the FXN gene, which results in deficiency of FXN transcript. Consistent with the expanded GAA-TR sequence as a cause of variegated gene silencing, evidence for heterochromatin has been detected in intron 1 in the immediate vicinity of the expanded GAA-TR mutation in FRDA. Transcriptional deficiency in FRDA is thought to result from deficient elongation through the expanded GAA-TR sequence because of repeat-proximal heterochromatin and abnormal DNA structures adopted by the expanded repeat. There is also evidence for deficient transcriptional initiation in FRDA, but its relationship to the expanded GAA-TR mutation remains unclear. We show that repressive chromatin extends from the expanded GAA-TR in intron 1 to the upstream regions of the FXN gene, involving the FXN transcriptional start site. Using a chromatin accessibility assay and a high-resolution nucleosome occupancy assay, we found that the major FXN transcriptional start site, which is normally in a nucleosome-depleted region, is rendered inaccessible by altered nucleosome positioning in FRDA. Consistent with the altered epigenetic landscape the FXN gene promoter, a typical CpG island promoter, was found to be in a transcriptionally non-permissive state in FRDA. Both metabolic labeling of nascent transcripts and an unbiased whole transcriptome analysis revealed a severe deficiency of transcriptional initiation in FRDA. Deficient transcriptional initiation, and not elongation, is the major cause of FXN transcriptional deficiency in FRDA, and it is related to the spread of repressive chromatin from the expanded GAA-TR mutation.
authors.affiliation: From the Departments of Pediatrics and.
authors.forename: Yogesh K
authors.initials: YK
authors.lastname: Chutake
authors.affiliation: From the Departments of Pediatrics and.
authors.forename: Whitney N
authors.initials: WN
authors.lastname: Costello
authors.affiliation: From the Departments of Pediatrics and.
authors.forename: Christina
authors.initials: C
authors.lastname: Lam
authors.affiliation: From the Departments of Pediatrics and Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104 Sanjay-Bidichandani@ouhsc.edu.
authors.forename: Sanjay I
authors.initials: SI
authors.lastname: Bidichandani
mesh_terms: D002460:Cell Line; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D005621:Friedreich Ataxia / Q000235:genetics*; D020869:Gene Expression Profiling; D006570:Heterochromatin / Q000502:physiology; D006801:Humans; D007438:Introns / Q000235:genetics; D033862:Iron-Binding Proteins / Q000235:genetics*; D009707:Nucleosomes / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D061805:Transcription Elongation, Genetic / Q000502:physiology*; D024363:Transcription Initiation Site / Q000502:physiology*; D014158:Transcription, Genetic / Q000235:genetics; D018911:Trinucleotide Repeats / Q000235:genetics; D000096923:Frataxin
chemical_list: D006570:Heterochromatin; D033862:Iron-Binding Proteins; D009707:Nucleosomes; D000096923:Frataxin
keywords: Expanded Triplet Repeat; Friedreich Ataxia; Gene Transcription; Heterochromatin; Neurological Diseases; Nucleosome Positioning; Nucleotide Repeat Disease; Transcription Promoter; Transcription Start Site
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