RNA gain-of-function mechanisms in short tandem repeat diseases

Abstract

As adaptors, catalysts, guides, messengers, scaffolds, and structural components, RNAs perform an impressive array of cellular regulatory functions often by recruiting RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs). While this RNA-RBP interaction network allows precise RNP assembly and the subsequent structural dynamics required for normal functions, RNA motif mutations may trigger the formation of aberrant RNP structures that lead to cell dysfunction and disease. Here, we provide our perspective on one type of RNA motif mutation, RNA gain-of-function mutations associated with the abnormal expansion of short tandem repeats (STRs) that underlie multiple developmental and degenerative diseases. We first discuss our current understanding of normal polymorphic STR functions in RNA processing and localization followed by an assessment of the pathogenic roles of STR expansions in the neuromuscular disease myotonic dystrophy. We also highlight ongoing questions and controversies focused on STR-based insights into the regulation of nuclear RNA processing and export as well as the relevance of the RNA gain-of-function pathomechanism for other STR expansion disorders in both coding and noncoding genes.

Keywords: RNA; anticipation; neurological disease; neuromuscular disease; short tandem repeat.

FIGURE 1.

STR functions in pre-mRNA processing. STRs are distributed throughout genic coding and noncoding regions (gray boxes, constitutive exons; blue, alternative exon or 3′ss) and function as copy number dependent alternative processing signals based on RBP recruitment (red boxes, ISS and ESS; green, ISE and ESE). For this example, the top illustration depicts a hypothetical common pre-mRNA processing pattern in the general population. For splicing, exon 2 inclusion is driven by an intron 2 ISE composed of three tandem repeats with coordinate RBP-binding promoting U1 snRNP recruitment. For 3′-end cleavage and polyadenylation, the first polyadenylation site (pA) is selected since there are only two tandem repeats in the downstream region. The uncommon (bottom) splicing pattern shows that exon 2 is skipped due to an intron 2 ISE with only one repeat, while an intron 1 ISS contains four repeats that facilitate RBP recruitment resulting in a U2 snRNP block. This uncommon example also shows an increase in CAG repeats in intron 3 that promotes an alternative exon 4 3′ss together with 3′ UTR repeat number variations that increase RBP recruitment downstream from the proximal pA site leading to selection of the distal site.

FIGURE 2.

STR-mediated diseases. Shown are STRs (red font) in the promoter, 5′ untranslated (5' UTR), intron, coding, and 3′ untranslated (3' UTR) regions together with the disease acronym, gene name, and pathogenic repeat range (black font). Listed diseases are: amyotrophic lateral sclerosis (ALS); blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES); Baratela–Scott syndrome (BSS); C9orf72-linked ALS and frontotemporal dementia (C9-ALS/FTD); cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); cleidocranial dysplasia (CCD); congenital central hypoventilation syndrome (CCHS); congenital myotonic dystrophy (CDM); myotonic dystrophy type 1 (DM1) and type 2 (DM2); dentatorubral-pallidoluysian atrophy (DRPLA); early infantile epileptic encephalopathy 1 (EIEE1); progressive myoclonus epilepsy (EPM1); familial adult myoclonic epilepsy types 1–4,6,7 (FAME1-4,6,7); Fuchs endothelial corneal dystrophy (FECD); intellectual disability-associated fragile sites 2A, 7A, 10A*, 11A*, 11B, 12A, 16A* (FRA2A, FRA7A, FRA10A*, FRA11A*, FRA11B, FRA12A, FRA16A*) and fragile X syndromes A,E,F (FRAXA, FRAXE, FRAXF*), (*) indicates the disease link is questionable, and for FRA16A* a gene link has not been documented; fragile X-associated primary ovarian insufficiency (FXPOI); fragile X-associated tremor/ataxia syndrome (FXTAS); Friedreich's ataxia (FRDA); global developmental delay, progressive ataxia, elevated glutamine (GDPAG), Huntington's disease (HD); Huntington's disease-like 2 (HDL2); hand-foot genital syndrome (HFGS); holoprosencephaly (HPE); X-linked heterotaxy VACTERLX syndrome (HTX1); intellectual disability with growth hormone deficiency (IDGH); Jacobsen syndrome (JS); late-onset cerebellar ataxia/spinocerebellar ataxia 27B (LOCA/SCA27B); neuronal intranuclear inclusion disease (NIID); oculopharyngodistal myopathy types 1–5 (OPDM); oculopharyngeal muscular dystrophy (OPMD); oculopharyngeal myopathy with leukoencephalopathy (OPML1); pseudoachondroplasia/multiple epiphyseal dysplasia-1 (PSACH/EDM); Richieri-Costa-Pereira syndrome (not the common 5′-UTR pattern so noted as RCPS^#); recessive hereditary motor neuropathy (not the common CDS pattern so noted as RHMD^#); spinal-bulbar muscular atrophy (SBMA); spinocerebellar ataxia (SCA) types 1–3, 6–8, 10, 12, 17, 31, 36, 37 (SCA1–3, 6–8, 10, 12, 17, 31, 36, 37); synpolydactyly (SPD1); X-linked dystonia-parkinsonism (XDP). See Depienne and Mandel (2021), Malik et al. (2021), Mirceta et al. (2022) for references except ALS LRP12 (Kume et al. 2023), ALS NIPA1 (Tazelaar et al. 2019), FRA10A (Sarafidou et al. 2004), FRA11A (Debacker et al. 2007), FRA11B (Jones et al. 1995), FRAXF (Shaw et al. 2002), HTX1 (Wessels et al. 2010), LOCA/SCA27B (Pellerin et al. 2023; Rafehi et al. 2023), OPDM3 (Yu et al. 2021), OPDM4 (Yu et al. 2022; Zeng et al. 2022), OPDM5 (Cortese et al. 2024), RCPS (Favaro et al. 2014), and RHMD (Pagnamenta et al. 2021).

FIGURE 3.

RNA gain-of-function pathomechanism in DM1. Bidirectional transcription of DM1 DMPK produces sense CUG^exp RNAs that bind MBNL proteins (red ovals), which undergo RNA–RNA, RNA–protein, and protein–protein multivalent interactions to form RNA foci or condensates (1). In contrast to sense transcription, antisense transcription yields very low-abundance RNAs with/without CAG^exp repeats (Gudde et al. 2017). MBNL sequestration in these foci together with phosphorylated CELF (blue sphere with black P) overexpression promotes fetal splicing patterns for target RNAs in adult tissues, and in DM1 skeletal muscle, exon 7A inclusion in CLCN1 mRNA (fetal isoform) (2) results in nonsense-mediated decay (NMD), CLCN1 loss, and myotonia (3). Somatic CTG expansions result in extremely long CUG^exp tracts that deplete MBNL (4) from the dilute nucleoplasmic pool, leading to release of intact or fragmented mutant DMPK mRNAs into the cytoplasm where they undergo RAN translation, giving rise to toxic RAN proteins (green and brown/yellow beads) (5). Mutant DMPK antisense transcripts may be exported into the cytoplasm at a low level, resulting in RAN translation of polyGln (Zu et al. 2011), and possibly polySer and polyAla, proteins.