Availability of DNA-packaging proteins explains rapid expansion of repetitive DNA

Spindle microtubules attach to centromeric chromatin regions to segregate chromosomes during cell division. Despite this conserved function, centromeres are composed of rapidly evolving repetitive satellite DNA that changes in both size and sequence. Divergent satellites emerge from a library of shorter repeats via stochastic expansions. However, it remains unclear how divergent satellites expand rapidly without interfering with chromosome segregation. We recently found that the satellite sequence defines the shape of the DNA molecule, which dictates its packaging during chromosome segregation. We proposed that divergent satellites rapidly expand via DNA shape-recognizing, conserved architectural proteins that package them, explaining rapid satellite evolution. Here, we tested a key prediction of our model: a satellite with DNA shape recognized by an architectural protein uses that protein for its own packaging. We leveraged M. musculus × spretus hybrid mouse oocytes, in which divergent centromeric satellites (major and minor) are present within the same cell. We analyzed the localization of selected DNA shape-recognizing architectural proteins to divergent satellites using molecular biology techniques and fluorescence microscopy. We found that high mobility group AT-hook 2 (HMGA2) binds preferentially to major satellite, where its levels are higher in M. musculus than in hybrid oocytes. Remarkably, HMGA2 depletion disrupts the packaging of the major satellite only in M. musculus but not in hybrid oocytes, indicating that the availability of HMGA2 dictates major satellite packaging. Our results are consistent with centromeric satellites using available DNA shape-recognizing architectural proteins for packaging, allowing them to expand without interfering with chromosome segregation.