Strain level centromere variation influences CENP-A association dynamics and centromere function

Centromeres are rapidly evolving chromatin domains that fulfill essential roles in chromosome segregation. Rapid centromere sequence evolution imposes strong selection for compensatory changes in centromere-associated kinetochore proteins, leading to striking co-evolutionary trends across species. However, it remains unknown whether within species centromere sequence diversity leads to functional differences in kinetochore protein association. House mice (Mus musculus) exhibit significant variation in centromere satellite array size and sequence heterogeneity, but the amino acid sequence of CENP-A, a centromere-specific histone variant that specifies centromere identity, is conserved. We hypothesize that centromere satellite sequence variation leads to differences in the localization of CENP-A among house mice, with potential consequences for meiotic drive and genome stability. Using CENP-A chromatin immunoprecipitation with a customized k-mer based, reference-blind bioinformatic analysis strategy, we compare the CENP-A sequence association landscape in four diverse inbred mouse strains (C57BL/6J, CAST/EiJ, LEWES/EiJ, and PWK/PhJ). We uncover significant strain-level diversity in CENP-A associated sequences, with more closely related strains exhibiting more similar CENP-A association profiles. LEWES/EiJ and CAST/EiJ show mild association of CENP-A with the pericentromeric satellite repeat, countering the prevailing notion that functional centromere size is solely determined by the size of the minor satellite array. Strain-specific CENP-A association profiles are enriched for unique suites of transcription factor motifs, hinting at strain differences in centromere transcription. Given the importance of centromere-CENP-A association and centromere transcription for both kinetochore assembly and chromosome segregation fidelity, our findings suggest a potential mechanism for centromere-mediated variation in genome stability among inbred mouse strains.