Epigenetic landscape of synthetic human centromeres: Euchromatic modifications coexist interdependently at CENP-A dense regions and prevent intrusion of other modifications [RNA-seq]

Centromere is specialized chromatin structure essential for equal chromosome segregation. Human centromere is organized on a portion of homogeneously repeated DNA sequence, and contains nucleosomes including centromere specific histone H3, 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) technology to create functional centromeric chromatin on a synthetic centromeric repeat DNA sequence that allowed for structural analysis at 2-kb resolution. Analysis using this HAC centromere showed that the CENP-A dense regions are approximately 18–50 kb in size and coexisted with euchromatic histone modifications in a mutually dependent manner. We also find that when DNA replication reduces CENP-A density, a heterochromatin modification H3K9me3 transiently intrudes CENP-A-dense regions, and that both the CENP-A deposition factor HJURP and the histone acetyltransferase KAT7 are important for pushing back this intrusion. The synthetic centromere DNA generated in this study is more effective at elucidating centromere chromatin structure than relying on naturally occurring DNA mutations, allowing for a more precise understanding and manipulation of centromere function.