Genomic and epigenomic maps of mouse centromeres and pericentromeres

Satellite DNA comprises ~11% of the mouse genome and is primarily located in centromeres and pericentromeres. We present comprehensive genomic and epigenomic maps of these regions utilizing Hifiasm assemblies, CUT&RUN-seq, DNA methylation analysis, and RNA-seq alongside recent mouse telomere-to-telomere assembly drafts. We show that 120-mer Minor satellites (MiSats) occupy core centromeres, while MiSat length variants localize at centromere-pericentric junctions. Pericentromeres contain mostly homogeneous Major satellites (MaSats), with divergent MaSats concentrated near pericentric non-satellite repeat islands and pericentric-chromosomal junctions. Most centromeres contain higher-order repeats (HORs), with shorter HORs more common. Centromeres are hypomethylated compared to pericentromeres, and transcripts are detected from a small subset of satellites with lower DNA methylation. CENP-A is highly enriched at 120-mer MiSats but reduced at MiSat length variants. Homogeneous MaSats are enriched with H3K9me3, whereas divergent MaSats are associated with H3K9me3 and H3K27me3. Finally, the density and type of satellite sequence motifs correlate with chromatin signatures.