biostudies-literatureChaudhry GU.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)9688https://www.ebi.ac.uk/biostudies/studies/S-EPMC12583555biostudies-literatureUnknown16(1)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 pericentromereNature communicationsGenomic and epigenomic maps of mouse centromeres and pericentromeres.PMC125835551R35GM147558-01Bahl SChen JSnipes LLin XPackiaraj JThakur JChaudhry GfalseGenomic 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 pericentromere2025-01-01T00:00:00Z2025 Nov2026-06-05T11:47:00.053Z2026-05-16T03:12:52.713ZS-EPMC125835554118425810.1038/s41467-025-64689-0