GC-rich repeat expansions: associated disorders and mechanisms

Abstract

Noncoding repeat expansions are a well-known cause of genetic disorders mainly affecting the central nervous system. Missed by most standard technologies used in routine diagnosis, pathogenic noncoding repeat expansions have to be searched for using specific techniques such as repeat-primed PCR or specific bioinformatics tools applied to genome data, such as ExpansionHunter. In this review, we focus on GC-rich repeat expansions, which represent at least one third of all noncoding repeat expansions described so far. GC-rich expansions are mainly located in regulatory regions (promoter, 5' untranslated region, first intron) of genes and can lead to either a toxic gain-of-function mediated by RNA toxicity and/or repeat-associated non-AUG (RAN) translation, or a loss-of-function of the associated gene, depending on their size and their methylation status. We herein review the clinical and molecular characteristics of disorders associated with these difficult-to-detect expansions.

Keywords: DNA methylation; GC-rich repeats; RAN translation; RNA foci; RNA structure; RNA toxicity; aggregation; histone modifications; long-read sequencing; monogenic disorders; nuclear inclusion; regulatory regions; repeat expansion; tandem repeat.

Figure 1

Main pathogenic mechanisms associated with GC-rich repeat expansions. (A) Nonpathogenic situation (e. g., less than 50 GCC repeats in FMR1) associated with normal transcription and canonical translation. (B) Epigenetic gene silencing. Full-length GC-rich expansions in gene promoters and/or 5′ untranslated regions (e. g., >200 CGG repeats in 5′UTR of FMR1 causing Fragile X syndrome) are associated with DNA methylation at CpG sites. Expanded methylated alleles are locked in a chromatin configuration preventing gene transcription and protein expression. (C) Sequestration of RNA-binding splicing factors. Intermediate CGG expansions (55 to 200 repeats) causing Fragile X-associated tremor ataxia syndrome (FXTAS) can form stable RNA secondary structures able to bind specific RNA-binding proteins with high affinity. These RNA molecules accumulate to form inclusions in the nucleus and sequester bound RNA-binding proteins. (D) Repeat-associated non-AUG (RAN) translation is a noncanonical protein synthesis process in which peptide synthesis is initiated at the site of the expanded repeats in absence of an AUG codon. In the case of FXTAS, RAN translation leads to the synthesis of toxic polyglycine peptides that accumulate and form protein aggregates. Gain-of-function mechanisms described in (C) and (D) are mutually nonexclusive and can occur at the same time.