Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics

Abstract

Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.

Fig. 1. DNA secondary structures

All panels: repetitive DNA portions pictured in color, non-repetitive DNA pictured in black. A) Cruciform structure, consisting of hairpin structures on the top and bottom strands. B) Slipped-strand DNA, here shown with loop-outs on either end stabilized by hairpin structures. The loop-outs can also remain unpaired, or can be stabilized by a different secondary structure. C) H-DNA, one of several potential secondary structures involving triplex or triple-helical DNA. The triplex is stabilized by Hoogsteen or Reverse-Hoogsteen basepairs (illustrated as *). The fourth strand can remain unpaired, as shown, or can potentially incorporate into further secondary structures. D) G-quadruplex DNA (top strand), also known as G4 or tetrahelical DNA. Several different folding patterns are possible, in addition to the one shown here, involving different arrangements of parallel or anti-parallel strand orientations. Typically, only one of the two strands will contain the regularly-spaced Gs that permit G4 folding, while the other strand can remain unpaired or fold into a different secondary structure, such as a hairpin (bottom strand as pictured).

Fig. 2. “Ori-switch” hypothesis

Top panel: Repetitive DNA (colored) sits between two different replication origins. Middle panel: Replication proceeds bi-directionally from each origin. In this case, the upstream origin reaches the repeats first. The top strand serves as the lagging strand template, while the bottom strand serves as the leading strand template. Bottom panel: The upstream origin is inactivated, either by a mutation of the binding site, or due to epigenetic changes such as DNA methylation. As a consequence, the downstream origin replicates through the repeats, flipping the orientation such that the top strand now serves as the leading strand template, while the bottom strand serves as the lagging strand template.

Fig. 3. Small-scale instability due to replication slippage

Top panel: Secondary structures, here shown as hairpins, form within a repetitive region on either template strand during replication. As a result, the nascent strand skips a small portion of the template, leading to a contraction. Bottom panel: Secondary structures form on either nascent strand during replication, leading to a small expansion in the newly-generated DNA. Both panels: Lagging strand synthesis is discontinuous by nature, providing regular opportunities for slippage. Leading strand synthesis is generally continuous, but may occasionally slip while encountering DNA lesions or previously-formed secondary structures.

Fig. 4. Instability due to template-switch events

Top panel: During replication, the leading strand may stall after encountering a barrier, including DNA lesions, secondary structures or bound proteins. To bypass the barrier, replication may temporarily switch to use the nascent lagging strand as a template. After reaching the end of the Okazaki fragment, replication re-invades the leading strand template ahead of the lesion. However, within a repetitive region, this re-invasion can occur out-of-register, potentially leading to a large-scale expansion. Bottom panel: The lagging strand can also encounter a barrier to replication, leading to use of the nascent leading strand as a template. Within a repetitive region, this invasion step can be variable. If it occurs close to the border of the repeat (left panel) the Okazaki fragment will contain non-repetitive sequence, leading to a contraction after re-invasion. If the Okazaki fragment contains only repetitive DNA, reinvasion can occur at any point within the repeat, potentially leading to a large-scale expansion.

Fig. 5. Instability due to break-induced replication (BIR)

A stalled replication fork (top panel) that cannot be restarted by other means may lead to fork reversal, resulting in a chicken-foot structure (second panel). Together, the two template strands are intact, while the two nascent strands make up a one-ended double strand break (third panel). The nascent leading strand can then invade the template via homologous recombination to initiate BIR. If the invading end consists of repeats, invasion can occur anywhere within the repetitive tract. This can lead to a large-scale expansion – as much as a doubling of the repeat tract – if invasion occurs near the beginning of the repeats (left). In the opposite case (right), invasion can occur towards the end of the repetive tract, skipping a large portion of the repeat and leading to a large-scale contraction. Synthesis of this strand continues (bottom panel), potentially until reaching the end of the chromosome, before the remaining strand is filled in, resulting in conservative DNA replication.

Fig. 6. Instability due to DNA damage and repair

A) Sources of single strand breaks (SSBs): In addition to spontaneous DNA damage (*), R-loops (extended RNA-DNA hybrids) can expose long stretches of single-stranded DNA, which can increase the rate of DNA damage, including oxidative damage and cytosine deamination. DNA damage undergoes base excision repair, leading to single-strand breaks. Secondary structure formation in repetitive tracts occurs in ssDNA exposed on the non-template strand while the R-loop is present, and can lead to slipped-strand structures when the R-loop is removed. Secondary structures can be recognized and cleaved by various enzymes, potentially leading to contractions, and also leading to SSBs. B) If SSBs occur only on one strand, repair can occur via strand displacement synthesis, creating a flap that can form secondary structures. The flap can be stabilized by mismatch repair enzymes and incorporated into the repaired DNA strand, causing a repeat expansion. C) If SSBs occur on both strands, this results in a double strand break. DSB repair can occur by a number of mechanisms, including non-homologous end joining (not shown), BIR (see Fig. 5), single-strand annealing between repetitive tracts, which can result in contractions, and sister chromatid invasion and recombination, which can potentially result in expansions or contractions.