title: Epigenetic promoter silencing in Friedreich ataxia is dependent on repeat length.
abstract: OBJECTIVE
  Friedreich ataxia (FRDA) is caused by an expanded GAA triplet-repeat (GAA-TR) mutation in the FXN gene. Patients are typically homozygous for expanded alleles containing 100 to 1,300 triplets, and phenotypic severity is significantly correlated with the length of the shorter of the 2 expanded alleles. Patients have a severe deficiency of FXN transcript, which is predominantly caused by epigenetic silencing of the FXN promoter. We sought to determine whether the severity of FXN promoter silencing is related to the length of the expanded GAA-TR mutation in FRDA.
  
  
  METHODS
  Patient-derived lymphoblastoid cell lines bearing a range of expanded alleles (200-1,122 triplets) were evaluated for FXN transcript levels by quantitative reverse transcriptase polymerase chain reaction. FXN promoter function was directly measured by quantitative analysis of transcriptional initiation via metabolic labeling of newly synthesized transcripts in living cells.
  
  
  RESULTS
  FXN transcriptional deficiency was significantly correlated with the length of the shorter of the 2 expanded alleles, which was noted both upstream (R(2)  = 0.84, p = 0.014) and downstream (R(2)  = 0.89, p = 0.002) of the expanded GAA-TR mutation, suggesting that FXN promoter silencing in FRDA is related to repeat length. A bilinear regression model revealed that length dependence was strongest when the shorter of the 2 expanded alleles contained <400 triplets. Direct measurement of FXN promoter activity in patients with expanded alleles containing <400 versus >400 triplets in the shorter of the 2 expanded alleles revealed a significantly greater deficiency in individuals with longer GAA-TR alleles (p < 0.05).
  
  
  CONCLUSIONS
  FXN promoter silencing in FRDA is dependent on the length of the expanded GAA-TR mutation.
authors.affiliation: Department of Pediatrics, University of Oklahoma College of Medicine, Oklahoma City, OK.
authors.forename: Yogesh K
authors.initials: YK
authors.lastname: Chutake
authors.forename: Christina
authors.initials: C
authors.lastname: Lam
authors.forename: Whitney N
authors.initials: WN
authors.lastname: Costello
authors.forename: Michael
authors.initials: M
authors.lastname: Anderson
authors.forename: Sanjay I
authors.initials: SI
authors.lastname: Bidichandani
mesh_terms: D000483:Alleles; D044127:Epigenesis, Genetic / Q000235:genetics*; D005260:Female; D005621:Friedreich Ataxia / Q000235:genetics* / Q000473:pathology; D005838:Genotype; D006801:Humans; D033862:Iron-Binding Proteins / Q000235:genetics*; D016014:Linear Models; D008297:Male; D011401:Promoter Regions, Genetic / Q000235:genetics*; D019680:Trinucleotide Repeat Expansion / Q000235:genetics*; D000096923:Frataxin
chemical_list: D033862:Iron-Binding Proteins; D000096923:Frataxin
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