Human Structural Variation: Mechanisms of Chromosome Rearrangements

Abstract

Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.

Keywords: chromothripsis; copy-number variation; inverted duplication; structural variation; translocation; triplication.

Figure 1

Signatures of mutational mechanisms. DNA sequence that spans the translocation breakpoint junction is aligned to the pink reference chromosome A (chrA) and blue reference chromosome B (chrB). The breakpoints are located where the junction (Jxn) sequence transitions from chrA to chrB. (a) Jxn with blunt ends at the breakpoints points to repair by non-homologous end-joining (NHEJ) or fork stalling and template switching (FoSTeS). (b) Homology, shown in purple, >1 kb in length and shared between chrA and chrB breakpoints suggests non-allelic homologous recombination (NAHR) between paralogous human endogenous retroviruses (HERVs), long interspersed nuclear elements (LINEs), or segmental duplications (SDs). (c) The presence of inverted and/or inserted sequences (shown in black) at the breakpoints are signatures of replicative mechanisms such as FoSTeS and microhomology-mediated break-induced replication (MMBIR). (d) 1–15 bp of microhomology between chromosome breakpoints is common and may be due to NHEJ, FoSTeS, or MMBIR.

Figure 2

Simple chromosome rearrangements. (a) Two nonhomologous chromosomes shown in blue and pink. Segments are labeled with letters A–E. Black arches indicate structural variation (SV) breakpoint junctions. (b) Intrachromosomal rearrangements include inversions, interstitial and terminal deletions, and interstitial duplications. (c) Simple translocations between two different chromosome ends. Balanced translocations do not result in copy-number variation (CNV), but unbalanced translocations have partial monosomy (segment E) and partial trisomy (segments B,C).

Figure 3

Complex chromosome rearrangements. Complex rearrangements and their array comparative genome hybridization (CGH) signatures are shown relative to the blue reference chromosome (top) divided into segments A–F. (a) Inverted duplications adjacent to terminal deletions have a short disomic spacer region (segment E) between inverted duplications. (b) A duplication-normal-duplication (DUP-NML-DUP) appears by array CGH as two copy-number gains (segments B and D). The duplications may be in direct orientation, or one duplicated segment (D) may be inverted between two copies of the other (B). (c) Triplication type I has three direct copies of B. In triplication type II the triplication (C) is embedded within a duplicated region (B–D). The triplicated segment may be in direct or inverted orientation. (d) Complex interchromosomal rearrangements occur between the blue and pink chromosomes. An insertional translocation involves the interstitial insertion of one chromosome segment (D) into another chromosome. Some complex translocations have multiple chromosome segments and/or inversion at the breakpoint junction. (e) An inverted duplication with terminal deletion may end with the translocated end of a nonhomologous chromosome.

Figure 4

DUP-TRP/INV-DUP (duplication-inverted triplication-duplication) formation. (a) Copy-number changes are detected relative to the black reference chromosome. 2x indicates normal disomic copy number, while 3x genomic copies of A and C are duplications, and 4x total copies of segment B represents a triplication. Inverted repeats (grey arrows) are present at the edges of segment C. (b) At a collapsed replication fork, sequence homology drives strand invasion from one inverted repeat into one from the opposite strand. DNA synthesis is reinitiated until the occurrence of a second collapsed replication fork. (c) This second junction may arise from a non-homologous end-joining (NHEJ) or microhomology-mediated break-induced replication (MMBIR) mechanism. In NHEJ, a double-strand break (DSB) occurs on the original DNA strand and is repaired by joining the to end of the replicated strand. In MMBIR, the lagging strand disengages, invades upstream sequence, and synthesizes DNA along the rest of the chromosome. (d) The resulting structure is a duplication, inverted triplication, and duplication. Orientation of the triplicated 'B' is confirmed by sequencing across junctions Jxn1 and Jxn2. Figure adapted with permission from [71].

Figure 5

Massive genomic reorganization. (a) Chromothripsis shatters three nonhomologous chromosomes. The only copy-number variations (CNVs) are deletions of B and D, but translocating segments and inversions have shuffled the contents of the three chromosomes. The 12 breakpoint junctions have blunt ends or short microhomology. (b) Chromoanagenesis leads to triplication (B) and duplications (D and F) across one chromosome. These breakpoint junctions contain microhomology and insertions that suggest a DNA replication-based mechanism of repair.