Trinucleotide repeats: triggers for genomic disorders?

Abstract

Among the various sequence repeats that shape the human genome, trinucleotide repeats have attracted special interest as a result of their involvement in a class of human genetic disorders known as triplet repeat expansion diseases. Recently, long TGG repeat tracts were shown to be implicated in a genomic disorder resulting from chromosome 14q32.2 deletion. Various different mechanisms might trigger this deletion, and looking at the problem from a structural biology perspective may help. Deeper insight into repeated sequences and their features may shed light on the mechanisms involved in this microdeletion and similar genomic rearrangements.

Figure 1

Triplet-repeat-mediated pathological mechanisms of human diseases. (a-c) Diseases associated with the expansion of triplet repeats (TREDs). (a) Expansion of CGG/CCG repeats over 200 repeats in exon 1 of the FMR1 gene located on chromosome X causes methylation of CpG islands in expanded repeats and flanking DNA, which results in the formation of heterochromatin and inhibition of transcription. Loss of FMR1 expression causes FXS in mutation-carrying males; FXS is thus a recessive disease. (b) Expanded CTG repeats (60 to a few thousand) in the 3' UTR of the DMPK gene are transcribed but not translated. Long CUG repeat hairpins cause a toxic dominant RNA gain-of-function effect mediated by sequestration of nuclear RNA-binding proteins, such as the alternative splicing regulator muscleblind-like 1 (MBNL1). There is clear evidence of an RNA gain-of-function effect in at least five TREDs: DM1, DM2 (expanded CCTG repeats), fragile X-associated tremor ataxia syndrome (FXTAS; expanded CGG repeats), Huntington's disease-like 2 (HDL2) and SCA8 (expanded CTG repeats). (c) The mutated HTT gene with expanded CAG repeats (40 to 100 repeats) in the coding region is transcribed and translated into a toxic protein containing an abnormally long polyglutamine domain. Intracellular aggregation of mutant protein is responsible for the pathogenesis of HD. A similar pathological mechanism is postulated for several dominant disorders known as polyglutamine expansion diseases: seven different spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 8 and 17), dentatorubral-pallidoluysian atrophy (DRPLA) and spinal and bulbar muscular atrophy (SBMA). (d) Diseases caused by long TGG repeat tracts. The dominant UPD(14)mat-like phenotype is caused by the deletion of a 1.11 Mb fragment of chromosome 14q32, which is mediated by two interrupted TGG repeat tracts (red boxes A and B). The deleted fragment contains about a dozen protein and short RNA coding genes, including paternally (green) and maternally (red) imprinted genes. The phenotype results from loss of function of two genes, DLK1 and RTL1, and haplo-insufficiency of the others.

Figure 2

Mechanism of TGG repeat-induced deletion. (a) Schematic representation of the 14q32.2 deletion (blue lines) and proximal and distal breakpoint sequences (red boxes A and B, respectively). Nucleotide sequences of A and B TGG repeat tracts are shown. Green indicates interruptions; pure repeat tracts (of at least 8 repeat units) are underlined. (b) Potential mechanisms that can explain the formation of TGG repeat-mediated deletion. NAHR requires homology between breakpoint sequences, NHEJ relies on joining dsDNA breaks induced by DNA structures at breakpoints, and FoSTeS depends on replication stalling and switching of the lagging strand to another replication fork. Both replication stalling and disengagement of the lagging strand can be facilitated by structures formed by template or synthesized DNA strands. (c) Frequency of different TNRs in the human genome. Blue bars indicate the number of pure TNR tracts with at least eight repeat units according to [4] (this is the length required for stable G-quadruplex formation); red bars indicate the number of interrupted TNR tracts with at least 100 units (the minimal sequence length required for catalyzing NAHR is 300 bp) according to Simple Repeat track, available on the UCSC Browser (hg18) (our unpublished data). (d) G-quadruplex structure formed by eight GGA DNA repeats (GGA)₈ [21]. The most 5' and 3' nucleotides are shown and arrows indicate direction of DNA strand from 5' to 3' end. A similar structure can be expected for TGG repeats based on the results of an RNA study [23].