Chromatin remodeling in the noncoding repeat expansion diseases

Abstract

Friedreich ataxia, myotonic dystrophy type 1 and 3 forms of intellectual disability, fragile X syndrome, FRAXE mental retardation, and FRA12A mental retardation are repeat expansion diseases caused by expansion of CTG.CAG, GAA.TTC, or CGG.CCG repeat tracts. These repeats are transcribed but not translated. They are located in different parts of different genes and cause symptoms that range from ataxia and hypertrophic cardiomyopathy to muscle wasting, male infertility, and mental retardation, yet recent reports suggest that, despite these differences, the repeats may share a common property, namely the ability to initiate repeat-mediated epigenetic changes that result in heterochromatin formation.

FIGURE 1.

A, organization of the human DMPK locus. Panel i, the region shown encompasses the sequence of chromosome 19 from ∼50,960,300 to ∼50,988,000 using the numbering from the March 2006 build of the UCSC Genome Bioinformatics Human Genome Database. Panel ii, shown is the expansion of the region between the end of the DMPK open reading frame (ORF) and the start of SIX5 transcription. The location of the CTG·CAG repeat is indicated by the arrowhead. The two CTCF sites are shown as stippled ovals (28). The black box indicates the DNase I hypersensitive site that contains the promoter for the antisense transcript (28). nt, nucleotide. B, organization of the human FMR1 locus. Panel i, the numbering used in this diagram is relative to the major FMR1 sense transcription start site in cells from normal individuals. The arrowhead indicates the location of the CGG·CCG repeat. CTCF sites are shown as stippled ovals. Panel ii, shown are sense and antisense transcripts produced from the FMR1 gene. The sense transcripts initiate from one of three major transcription start sites located close to exon 1. Start site usage changes with increasing repeat number, with start sites II and III being used more heavily as repeat number increases (44). Two major promoters are used for the production of antisense transcripts, one in the promoter of the sense transcript and one >10 kb downstream. Transcripts initiating at this second promoter predominate in carriers of long but still active alleles. C, organization of the human FXN locus. Panel i, the numbering used in this diagram is relative to the major FXN sense transcription start site in cells from normal individuals. The arrowhead indicates the location of the GAA·TTC repeats. The arrows indicate the orientation of the two Alu elements in intron 1. Panel ii, shown are the sense and hypothetical antisense transcripts from the FXN gene. The gray dashed line illustrates the potential antisense transcript originating from the upstream AluSp element.

FIGURE 2.

Schematic representation of potential mechanisms of heterochromatin formation at loci containing long CGG·CCG, CTG·CAG, and GAA·TTC repeats. The green segments of the DNA and RNA represent the repeat-containing region. The nucleosome octamer is shown in pale blue. The orange and blue lines emerging from each nucleosome represent a histone H3 and H4 tail, respectively. For simplicity, only one tail is shown per nucleosome. The acetyl groups (purple circles) represent those attached to H3K9 and H4K16 as seen on the active FMR1 and FXN alleles. Many other potentially acetylatable residues exist. H3K9 methylation seen on all three disease alleles is indicated by blue circles. A, RNA-based models. In the mechanism illustrated on the left-hand side of A, sense and antisense transcripts from the affected gene generate a region of dsRNA that is a substrate for Dicer. The region of overlap may or may not include the repeat. On the right-hand side of A, the repeats in the transcript form an RNA hairpin that is a Dicer substrate. Irrespective of the source of the dsRNA, the small Dicer products become loaded into the RITS complex and target the complex to the affected gene. The RITS complex then facilitates hypoacetylation of histones H3 and H4, methylation of H3K9, and DNA methylation. These and presumably other epigenetic changes are then propagated to the surrounding regions perhaps because they abolish the activity of an insulator element like CTCF (not shown). B, DNA-based model. Repeat-binding proteins may bind to the expanded repeat and recruit proteins like HP1 that lead to heterochromatin formation. RITS, RNA-induced initiation of transcriptional gene-silencing complex; HDACs, histone deacetylases; HMTs, histone methyltransferases that establish repressive chromatin marks; DMNT, de novo DNA methyltransferase.