Population and subspecies diversity at mouse centromere satellites

Abstract

Background: Mammalian centromeres are satellite-rich chromatin domains that execute conserved roles in kinetochore assembly and chromosome segregation. Centromere satellites evolve rapidly between species, but little is known about population-level diversity across these loci.

Results: We developed a k-mer based method to quantify centromere copy number and sequence variation from whole genome sequencing data. We applied this method to diverse inbred and wild house mouse (Mus musculus) genomes to profile diversity across the core centromere (minor) satellite and the pericentromeric (major) satellite repeat. We show that minor satellite copy number varies more than 10-fold among inbred mouse strains, whereas major satellite copy numbers span a 3-fold range. In contrast to widely held assumptions about the homogeneity of mouse centromere repeats, we uncover marked satellite sequence heterogeneity within single genomes, with diversity levels across the minor satellite exceeding those at the major satellite. Analyses in wild-caught mice implicate subspecies and population origin as significant determinants of variation in satellite copy number and satellite heterogeneity. Intriguingly, we also find that wild-caught mice harbor dramatically reduced minor satellite copy number and elevated satellite sequence heterogeneity compared to inbred strains, suggesting that inbreeding may reshape centromere architecture in pronounced ways.

Conclusion: Taken together, our results highlight the power of k-mer based approaches for probing variation across repetitive regions, provide an initial portrait of centromere variation across Mus musculus, and lay the groundwork for future functional studies on the consequences of natural genetic variation at these essential chromatin domains.

Keywords: Bioinformatics; CENP-A; Centromere; Evolution; Genetic diversity; Inbred mice; Mammalian genomics; Satellite DNA; Wild mice; k-mer.

Fig. 1

Significant differences in consensus centromere satellite copy number across Mus musculus. a Schematic overview of the approach used to quantify the frequencies of k-mers in centromere satellite repeats. b Boxplots showing the distribution of major (yellow) and minor (blue) satellite consensus 31-mer frequencies across inbred strains and wild-caught mouse populations

Fig. 2

Consensus centromere 15-mers are the most abundant and the most variable 15-mers in diverse Mus genomes. Heatmap displaying the observed frequencies of the 1000 most variable 15-mers (columns) across a sample of diverse Mus genomes (rows). The color scale represents the normalized frequency of 15-mers. 15-mers present in the Mus musculus minor and major satellite consensus sequences are noted by the blue and yellow boxes, respectively

Fig. 3

Quantitative FISH validates consensus centromere satellite copy number variation across inbred mouse strains. a Representative FISH images from four genetically diverse inbred strains: CAST/EiJ, WSB/EiJ, LEWES/EiJ, and PWK/PhJ. Individual color channels were manually manipulated using the Color Balance feature in FIJI for presentation purposes. Only raw, unedited images were used for quantification. Quantification of fluorescent intensity using DNA probes derived from the (b) major and (c) minor centromere satellite repeats across inbred strains. Points correspond to fluorescent intensity measurements for a single chromosome. A minimum of 40 centromeres from 36 cells were examined per strain. Fluorescent intensity is represented in arbitrary units (AU)

Fig. 4

Negative correlation between centromere satellite copy number and sequence diversity in Mus musculus. Estimated centromere satellite copy number and centromere diversity index for the (a) minor or (b) major satellite sequence. Copy number was estimated from the median frequency of consensus centromere 31-mers in each sample. The three primary house mouse subspecies are denoted by different colors: red - M. m. musculus, purple - M. m. domesticus, and green - M. m. castaneus, orange – M. m. molossinus. Shapes distinguish inbred strains (circles) from wild-caught mice (triangles)

Fig. 5

Landscape of nucleotide variation across centromere satellite repeats. Heatmap of non-consensus nucleotide usage for positions in the (a) minor satellite consensus sequence and (b) major satellite consensus sequence. Each row corresponds to a single sample with sample names colored by subspecies origin: green – M. m. castaneus, red – M. m. musculus, purple – M. m. domesticus, orange – M. m. molossinus

Fig. 6

Phylogenetic distribution of centromere satellite copy number and satellite heterogeneity in inbred strains and wild mice. a Maximum likelihood phylogenetic tree for 11 inbred house mouse strains and the outgroup, SPRET/EiJ. For each strain and for both the major and minor satellites, estimated satellite copy number and CDI are indicated by boxes shaded according to the corresponding color scales to the right of each heatmap. b Maximum likelihood phylogenetic tree for wild M. musculus samples and the outgroup of Mus spretus samples. The mouse subspecies and species are denoted by different colors: red - M. m. musculus, purple - M. m. domesticus, green - M. m. castaneus and black - M. spretus