Break-induced replication links microsatellite expansion to complex genome rearrangements

Abstract

The instability of microsatellite DNA repeats is responsible for at least 40 neurodegenerative diseases. Recently, Mirkin and co-workers presented a novel mechanism for microsatellite expansions based on break-induced replication (BIR) at sites of microsatellite-induced replication stalling and fork collapse. The BIR model aims to explain single-step, large expansions of CAG/CTG trinucleotide repeats in dividing cells. BIR has been characterized extensively in Saccharomyces cerevisiae as a mechanism to repair broken DNA replication forks (single-ended DSBs) and degraded telomeric DNA. However, the structural footprints of BIR-like DSB repair have been recognized in human genomic instability and tied to the etiology of diverse developmental diseases; thus, the implications of the paper by Kim et al. (Kim JC, Harris ST, Dinter T, Shah KA, et al., Nat Struct Mol Biol 24: 55-60) extend beyond trinucleotide repeat expansion in yeast and microsatellite instability in human neurological disorders. Significantly, insight into BIR-like repair can explain certain pathways of complex genome rearrangements (CGRs) initiated at non-B form microsatellite DNA in human cancers.

Keywords: DNA repair; DNA replication; FoSTeS; break-induced replication; chromothripsis; genome instability; microsatellite instability.

Figure 1

Hairpin formation during DNA replication or repair. A) Polymerase stuttering at microsatellite repeats leads to excess nascent strand microsatellite sequence (expansion). B) Terminal transferase-like nontemplated synthesis (dashed line) across a hairpin abasic gap [–120] or C) Template hairpin isomerization following destabilization of a stalled polymerase [121] leads to contraction. D) Polymerase stalling leads to replication stress, fork collapse, single-ended DSB (seDSB).

Figure 2

Model of break-induced replication. A) A single-ended DSB leads to BIR. A break in the lagging strand template is shown for simplicity, but other causes of fork collapse or nuclease cleavage (e.g. HO endonuclease [68] and camptothecin inhibition of topoisomerase I [85], have been used to produce seDSB. B) Displacement of the lagging strand template allows leading strand ligation to form an intact chromatid. The seDSB is subject to 5′ end resection and RPA binding. C) RPA is replaced by RAD51 to form and invading (acceptor) filament. The acceptor DNA released by branch migration of the unstable D-loop is a template for lagging strand conservative DNA synthesis.

Figure 3

Model for (CAG/CTG) microsatellite expansion by break-induced replication. A) Replication stalling at a (CAG/CTG) repeat tract (green). B) DNA cleavage (MUS81-EME2) at the site of stalling leads to a single-ended double strand break, fork collapse (replisome dissociation), resection of the 5′ end of the seDSB and binding of RPA to the extended 3′ ssDNA. C) Replacement of RPA by RAD51 and homology-dependent invasion of the sister chromatid repeat forms a displacement loop (D-loop). Misalignment of the acceptor (CAG) and donor (CTG) repeats at the start or middle of the template repeat tract leads to large expansions. D) Repeat expansions larger than the initial repeat tract length arise after continued template misalignment, mutation-prone replication fork slippage and hairpin formation across the repeat. The acceptor DNA released from the unstable D-loop is a template for conservative lagging strand replication. Break-induced replication is subsequently terminated by fusion with a leftward moving replication fork and/or resolvase (MUS81, YEN1) cleavage.

Figure 4

Template switching and the transition from BIR to MMBIR. A) Fork stalling within or beyond microsatellite sequences causes fork collapse/breakage. B) TLS polymerases (Polζ/Rev1) enable microhomology-mediated BIR (MMBIR). TLS polymerase synthesis is not processive and fork collapse leads to template switching and microhomology-mediated BIR at a new site. C) Successive cycles of fork stalling and template switching (FoSTeS) lead to complex genomic rearrangements (CGRs). D) Self-annealing and DNA synthesis at microhomologies in nascent DNA. E) DSBs at simultaneously broken microsatellites may recombine by nonhomologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ).