Gozashti L, Harringmeyer OS, Hoekstra HE.

Cell Rep. 2025 May 27;44(5):115644. doi:10.1016/j.celrep.2025.115644

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice.

Centromeres based on repeat analysis and methylation calls of PacBio HiFi data. “at least 14 [inversions] are likely pericentric [...] based on our predicted centromere locations” “[we] found examples of independently derived inversions sharing the same breakpoint (within 10 kb)”. “We found no evidence for the overrepresentation of LINE or SINE retrotransposons at the breakpoints of megabase-scale inversions [... where we observed ...] a 4-fold increase in SD occupancy with respect to random expectations.” “We also observed a strong enrichment of PMSat at the breakpoints of large inversions”. “the inversion breakpoints often coincide with contig boundaries from the initial hifi-asm contig-level assemblies”. “highly similar LINE copies [occupy] >1% of the deer mouse genome”. “9 [large] inversions had PMSat arrays at both breakpoints in at least one of the ancestral or derived haplotypes”