Epigenetic landscape of synthetic human centromere core regions: CENP-A assembly and euchromatic modifications interdependently antagonize heterochromatin accumulation.

Centromeres are specialized chromatin structures essential for equal chromosome segregation. The human centromeres are organized on a portion of homogeneously repeated DNA sequence and contains nucleosomes including centromere specific histone H3 variant CENP-A. Histone modifications around the CENP-A dense region are also thought to have important roles in centromere function. Here, we used human artificial chromosome (HAC) system based on synthetic centromeric repeat DNA to enable structural and chromatin analysis at ∼2-kb resolution within defined centromere core domains. Analysis using this HAC centromere showed that the CENP-A dense regions span approximately 18-50 kb in size and coexisted with euchromatic histone modifications in an interdependent manner. We further found that when DNA replication reduced CENP-A density, a heterochromatin modification H3K9me3 transiently accumulated in the CENP-A-dense regions. This accumulation was suppressed by the CENP-A deposition factor HJURP and the histone acetyltransferase KAT7, suggesting that CENP-A assembly and euchromatic modifications interdependently antagonize heterochromatin accumulation. The synthetic centromere DNA generated in this study elucidates the epigenetic landscape within the centromere core regions and provides a more precise framework for understanding the dynamic balance between CENP-A assembly and histone modifications.