Research Article: Epigenetic Silencing in Friedreich Ataxia Is Associated with Depletion of CTCF (CCCTC-Binding Factor) and Antisense Transcription

Date Published: November 19, 2009

Publisher: Public Library of Science

Author(s): Irene De Biase, Yogesh K. Chutake, Paul M. Rindler, Sanjay I. Bidichandani, Amanda Ewart Toland.

Abstract: Over 15 inherited diseases are caused by expansion of triplet-repeats. Friedreich ataxia (FRDA) patients are homozygous for an expanded GAA triplet-repeat sequence in intron 1 of the FXN gene. The expanded GAA triplet-repeat results in deficiency of FXN gene transcription, which is reversed via administration of histone deacetylase inhibitors indicating that transcriptional silencing is at least partially due to an epigenetic abnormality.

Partial Text: Friedreich ataxia (FRDA), the most common inherited ataxia, is an autosomal recessive disease characterized by progressive sensory ataxia, cardiomyopathy, diabetes, and premature death [1]. FRDA is most commonly caused by inheriting an expanded GAA triplet-repeat sequence in intron 1 of both copies of the FXN gene [2]. The size of the expanded repeat tract can range from 66–1700 triplets, which results in a deficiency of FXN gene transcription [3], [4]. This in turn causes a deficiency of the mitochondrial protein frataxin, which is essential for iron-sulfur cluster biogenesis, and thereby results in mitochondrial dysfunction [1].

The expanded GAA triplet-repeat sequence results in deficiency of FXN transcript via at least two mechanisms: deficient transcriptional elongation through the expanded repeat tract [3], [16], [17] and epigenetic silencing [6]–[8]. Previous studies detected evidence of heterochromatin formation in the immediate vicinity of the expanded GAA triplet-repeat in intron 1 in FRDA [6]–[8], however, it has remained unclear how this results in transcriptional silencing of the FXN gene. Our data are consistent with the model that CTCF depletion in the 5′UTR of the FXN gene in FRDA patients results in reduced FXN transcription via heterochromatin formation involving the critical +1 nucleosome, which offers a plausible mechanism for transcriptional silencing of the FXN gene, and is consistent with the observed transcriptional reactivation via administration of HDAC inhibitors [6]. It is interesting to note that previous unsuccessful attempts to detect heterochromatin formation in the upstream regions of the FXN gene in FRDA were directed to the nucleosome free region immediately upstream of TSS1 [6], [8]; the sequence we have analyzed here is ∼100 nucleotides downstream of this sequence, and represents the +1 nucleosome (Fig. 1A). The +1 nucleosome is an important regulator of transcription [18] and alteration of its chromatin organization in FRDA has the possibility of influencing FXN transcriptional initiation and/or elongation. It is also interesting to note that heterochromatin formation in the vicinity of the expanded GAA triplet-repeat in intron 1 of FRDA patients is different from what we have observed in the 5′UTR. The former is associated with increased CpG methylation at specific sites in intron 1, whereas we did not detect any alterations in DNA methylation in the 5′UTR. Instead, heterochromatin formation in the 5′UTR seems to be based on H3K9me3-mediated recruitment of HP1.



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