Dynamic Chromatin Changes Associated with De Novo Centromere Formation in Maize Euchromatin 

Handong Su, Yalin Liu, Yong-Xin Liu, Zhenling Lv, Hongyao Li, Shaojun Xie, Zhi Gao, Junling Pang, Xiu-Jie Wang, Jinsheng Lai, James A. Birchler, Fangpu Han 

Plant Journal  

DOI:10.1111/tpj.13305  

Abstract  

The inheritance and function of centromere are not strictly dependent on any specific DNA sequence, but involve an epigenetic component in most species. CENH3, a centromere histone H3 variant, is one of the best described epigenetic factors in centromere identity. However, the required chromatin features during centromere formation have not been revealed yet. We previously identified two de novo centromeres on maize minichromosomes derived from euchromatic sites with high-density gene distributions but low-density transposons distributions. The distribution of gene location and gene expression in these sites indicates that transcriptionally active regions can initiate de novo centromere formation and CENH3 seeding shows preference for gene-free regions or regions with no gene expression. The locations of expressed genes detected were at relatively hypomethylated loci, and the altered gene expression was due to the de novo centromere formation but not to the additional copy of minichromosome. The initial overall DNA methylation level of the two de novo regions was at a low level, but increased substantially to that of native centromeres after centromere formation. These results illustrate the dynamic chromatin changes during euchromatin-originated de novo centromere formation, which provides insight into the mechanism of de novo centromere formation and regulation of subsequent consequences.