Synergistic role of Alu and core duplicon sequences in driving genomic instability at the disease-associated 16p12.3–p13.11 region

Human chromosome 16p is a hotspot of interspersed segmental duplications (SDs), which have served as row material for gene innovation while also increasing susceptibility to recurrent pathogenic rearrangements. These SDs are organized around a high-copy, ancestral core duplicon known as LCR16a (Low Copy Repeat 16a), and are characterized by an enrichment of Alu elements at their boundaries. In this study, we investigated the molecular mechanisms underlying SD formation across four clusters within the 16p12.3–p13.11 region. Analysis of 94 genome assemblies showed 12 and 8 alternative structures in clusters 1-2 and 3-4, respectively. These include at least 10 duplication/deletion events and 5 inversions. Breakpoint mapping revealed that 13 out of 15 events arose via nonallelic homologous recombination (NAHR). In particular, 6 had breakpoints in duplicons associated with LCR16a, 2 occurred within the LCR16a sequence itself, and 5 were mediated by Alu elements—one of which located within LCR16a. The last mechanism contributes to multiallelic, tandem copy-number variation involving two distinct LCR16a-duplicon pairs. We identified an interspersed, inverted duplicative transposition, possibly driven by double template switches at homologous sites— specifically, Alu elements located within inverted copies of LCR16a and an associated duplicon. Comparative analyses using nonhuman primate T2T genome assemblies suggest that clusters 3 and 4 originated ∼6 million years ago in the human-chimpanzee common ancestor through double template switching involving Alu repeats. Clusters 1 and 2 primarily formed more recently through human-specific LCR16a-associated duplicative transpositions. These findings highlight a synergistic interplay between Alu elements and LCR16a in driving 16p12.3–p13.11 SD formation and genomic instability, through both recombination-and replication-based mechanisms.