Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA

Abstract

Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. In this review, we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences.

Figure 1

(A) Types of repetitive DNA sequences are illustrated on two hypothetical chromosomes (blue and red): segmental duplications (green boxes), interspersed repeats (black boxes), satellites (yellow lines) present in eukaryotic genomes and NAHR events that involve repetitive sequences. These include interchromosomal (X), intrachromosomal and intersister rearrangements (curved X). (B) Types of GCRs resulting from NAHR in repetitive sequences. Interchromosomal rearrangements can result in gene conversions (non-crossovers), translocations (crossovers), or unstable acentric or dicentric chromosomes (crossovers, not shown). Intrachromosomal or intersister rearrangements surrounding a chromosomal locus (white arrow) can result in duplications, deletions, or inversions. A color version of the figure is available online.

Figure 2

Recombination mechanisms (DSBR, SDSA, BIR and SSA) that can use repetitive DNA sequences as substrates. (A) DSBR and (B) BIR can result in crossovers and non-crossovers, SDSA (C) creates only non-crossovers, and SSA (D) creates only deletions or chromosome fusions (not shown). See the text for further details. A color version of the figure is available online.

Figure 3

Model for how NAHR is initiated during replication. (A) Repetitive sequences form secondary structures that block progression of the replication fork and induce fork reversal which can result in sequence duplications. Physical stress on a stalled replication fork can also cause breakage of the fork (a DSB) and subsequent repair by homologous recombination (not shown). (B) Replication across single-strand gaps may also produce DSBs that may initiate homologous recombination by using the adjacent sister chromatid as a template. A color version of the figure is available online.

Figure 4

A model for how mismatch and double-strand break repair factors can collaborate to reject recombination between divergent DNA sequences during SSA. After annealing of divergent sequences, Msh proteins (i.e. Msh2-Msh6, pink ovals) can recognize base mismatches (red star) in the heteroduplex intermediate and changes conformation to begin a search for Sgs1-Top3-Rmi1 (yellow oval, light green oval, blue oval). Sgs1-Top3-Rmi1 can load onto the junction between the heteroduplex and the 3′ non-homologous tail and is stimulated by Msh2-Msh6 to unwind the duplex. A color version of the figure is available online.

Figure 5

Heteroduplex rejection within a D-loop. Similarly to rejection during SSA (Figure 4), Msh2-Msh6 (pink ovals) will locate a mismatch (red star) and switch to searching mode. Msh2-Msh6 may either (1.) find Sgs1-Top3-Rmi1 (yellow oval, light green oval, blue oval, or another helicase such as Srs2, not shown) loaded at the duplex junction to stimulate unwinding, or instead may (2.) find an active replication fork (represented as Pol δ, purple hexagon) through a direct interaction with PCNA (dark blue square) to stimulate nucleolytic degradation. In a third alternative (3.), Mlh1-Pms1(dark green ring) may accompany activated Msh2-Msh6 during the search and may recruit an exonuclease such as Exo1 (blue pac-man) to either stimulate repair of the mismatch, or to disrupt the D-loop by a nucleolytic mechanism. A color version of the figure is available online.

Figure 6

(A) Model for the nuclear organization of chromatin in mammalian and budding yeast nuclei. Fractal-globule models (Mirny, 2011) predict that individual chromosomes (distinguished by color) in mammalian nuclei (left) are folded into distinct, untangled territories with heterochromatin domains associated with the nuclear lamina and euchromatin in the center of the nucleus. The nucleolus is a distinct heterochromatin domain that houses ribosomal DNA which is distributed among multiple chromosomes in humans. The yeast nucleus (right), which is 100 times smaller than an average mammalian nucleus (3 versus 300 μm³), is predicted to be less tolerable of a fractal globule model so that chromosomal territories are more closely entwined. 3C modeling by Duan et al., (2010) show protrusion of the rDNA locus on chromosome 12 into a distinct heterochromatin domain and also clustering of other heterochromatin regions such as centromeres and telomeres. (B) Heterochromatin is more compact than euchromatin and is associated with specific marks such as methylated (Me) histones and HP1 protein. Histones in euchromatin are usually acetylated (Ac). Nucleosomes (purple circles). A color version of the figure is available online.

Figure 7

(A) DSB repair by homologous recombination requires chromatin modifications and nucleosome remodeling within approximately 50 KB on each side of the DSB to facilitate loading of HR proteins that are excluded from heterochromatin (i.e. Rad51 and Rad52). During S and G2 phase, break-induced loading of cohesin (orange lines) occurs within the region of the DSB to facilitate sister chromatid recombination and this is dependent on γH2AX (yellow stars) and the resection initiator MRX (not shown). This panel is based on Figure 2 of Lee and Myung (2009). (B) Model for movement of DSBs within heterochromatin to the heterochromatin periphery, as described by Chiolo et al., (2010). DSBs (yellow) within heterochromatin domains (gray) move, by an unknown mechanism, toward the periphery of the heterochromatin (dotted line) accompanied by a global expansion of the heterochromatin domain. Finally, DSBs protrude into the euchromatin domain (light blue) where the Rad51 protein (red) is available for homologous recombination. A color version of the figure is available online.