Recurrent Activation of a Latent Centromere in the Pericentromeric Region of Maize Chromosome 3

In most eukaryotes, centromere identity is determined by the presence of nucleosomes containing CENH3, a centromere-specific histone H3 variant. New centromeres can form de novo at non-centromeric regions, which are known as “neocentromeres”. Some chromosomal regions are prone to neocentromere formation, suggesting that neocentromere activation is non-random process. However, the determinants of neocentromere formation have remained elusive. We discovered that a pericentromeric region of maize chromosome 3 two megabases away from the centromere (Cen3) underwent at least three independent neocentromere activation events. We analyzed the genomic and epigenomic features associated with Cen3, the neocentromeres and an inactivated centromere of an ancestral chromosome 3. We find that the neocentromeric region lacks genes and is associated with low levels of transcription and relatively high levels of DNA methylation. These genomic and epigenomic features may provide a favorable chromatin environment for recurrent neocentromere activation.