Transcription, Histone Modification, and CENH3 Nucleosome Positioning in Maize Centromeres

Centromere is epigenetically identified by nucleosomes containing centromere specific histone H3  (cenH3), a variation of canonical histone H3. The structure and organization of cenH3 nucleosomes in centromeres is densely studied in yeast and animals. Here, we use maize cenH3 antibody and paired-end high throughput sequencing technology to investigate the cenH3 nucleosomes in maize at single-base resolution. The positions and boundaries of centromeres were determined. CenH3 nucleosomes occupied the majority of centromeres and organized into blocks which intermingled with regions bound by canonical nucleosomes.  We detected expressed genes in centromeric regions and gene transcription was highly repulsive to occupancy of cenH3 nucleosomes. The expansion of maize centromeres in oat background frequently avoided regions with high level H3K36me3. CenH3 nucleosomes were phased on CentC arrays and aligned with 156-bp CentC monomers. Interestingly, we identified two occupancies of cenH3 nucleosomes on CentC and protect different length of DNA. Our results suggest conserved organization of cenH3 nucleosomes and dynamics of chromatin architecture in centromeres.