R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome

Abstract

Friedreich ataxia (FRDA) and Fragile X syndrome (FXS) are among 40 diseases associated with expansion of repeated sequences (TREDs). Although their molecular pathology is not well understood, formation of repressive chromatin and unusual DNA structures over repeat regions were proposed to play a role. Our study now shows that RNA/DNA hybrids (R-loops) form in patient cells on expanded repeats of endogenous FXN and FMR1 genes, associated with FRDA and FXS. These transcription-dependent R-loops are stable, co-localise with repressive H3K9me2 chromatin mark and impede RNA Polymerase II transcription in patient cells. We investigated the interplay between repressive chromatin marks and R-loops on the FXN gene. We show that decrease in repressive H3K9me2 chromatin mark has no effect on R-loop levels. Importantly, increasing R-loop levels by treatment with DNA topoisomerase inhibitor camptothecin leads to up-regulation of repressive chromatin marks, resulting in FXN transcriptional silencing. This provides a direct molecular link between R-loops and the pathology of TREDs, suggesting that R-loops act as an initial trigger to promote FXN and FMR1 silencing. Thus R-loops represent a common feature of nucleotide expansion disorders and provide a new target for therapeutic interventions.

Author Summary

Friedreich ataxia and Fragile X syndrome are among 40 human diseases associated with expansion of repeated sequences. In both disorders repeat expansion leads to gene silencing, the molecular mechanism of which is not well understood, impeding the development of specific therapies to treat these disorders. It is proposed that formation of unusual DNA structures (RNA/DNA hybrids, or R-loops) over repeat regions may play a role, but their molecular function has not been investigated in vivo. We show that R-loops form on expanded repeats of FXN and FMR1 genes in cells from FRDA and FXS patients. These R-loops are stable, correlate with repressive chromatin marks and hinder FXN transcription in patient cells. We studied the relationship between repressive chromatin and R-loops. Decrease in the amount of repressive chromatin has no effect on R-loop levels. In contrast, increase in the R-loops leads to transcriptional silencing of FXN gene and formation of repressive chromatin, providing a direct molecular link between R-loops and pathology of expansion diseases. This discovery is important for understanding the basic molecular mechanism underlying the pathology of expansion diseases. The ability of R-loops to trigger transcriptional silencing makes them an attractive target for future therapeutic approaches to treat these diseases.