Conservation of chromatin organization within human and primate centromeres

The focal attachment of the kinetochore to the centromere core is essential for genome maintenance, yet the highly repetitive nature of human centromeres limits our understanding of their chromatin organization. We demonstrate that single-molecule chromatin fiber sequencing can uniquely resolve chromatin organization within centromeres at single-molecule and single-nucleotide resolution. We find that the centromere core contains a dichotomous chromatin organization not found elsewhere in the genome, which is characterized by highly accessible chromatin patches heterogeneously punctuated amongst tightly compacted nucleosome arrays. These highly accessible chromatin patches correspond to sites of kinetochore attachment, and clustered CENP-B occupancy within these patches phase nucleosome arrays to the alpha-satellite repeat. This dichotomous chromatin organization is conserved between humans despite the marked divergence of the underlying alpha-satellite organization and is similarly conserved in primate centromeres that lack alpha-satellite repeats, indicating that functional conservation within centromeres is mediated at the level of chromatin, not DNA. Fiber-seq on cell lines from different individuals. CHM13 cells and CHM1 cells are complete hydatidiform mole cell lines derived from separate humans. GM14385 cells are lymphoblastoid cells derived from a different human. HLE cells are lymphoblastoid cells derived from a gibbon. Fiber-seq was performed as indicated below.