pericentromere chromatin
Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation, and H3 chromatin modifications
In this study, we compared siRNA abundance across centromere/pericentromere regions of maize chromosomes by Illumina sequencing a library of small RNAs (selecting for species with 5' and 3' ends already compatible for ligation, i.e., 5' monophosphates and 3' hydroxyls). We also compared DNA methylation across centromere/pericentromere regions of maize chromosomes by bisulfite sequencing of DNA fragments generated by micrococcal nuclease. These fragments, mainly corresponding to single nucleosome cores, were enriched for centromeres by chromatin immunoprecipitation with CENH3 antibodies prior to bisulfite treatment and Illumina library preparation.
Both kinetochore function and sister chromatid cohesion can depend upon pericentromere chromatin structure, and factors associated with heterochromatin have been proposed to have general, conserved roles in distinguishing centromeres and pericentromeres and in conferring pericentromere-intrinsic functions. We applied sequencing approaches to quantify RNA expression, DNA methylation, and histone modification distributions genome-wide in maize (Zea mays), focusing on centromeres and pericentromeres. Aside from the presence of the Histone H3 variant common to all centromeres, Centromeric Histone H3 (CENH3), we found no RNA expression or chromatin modifications that clearly differentiate centromeres from the immediate flanking regions. In general, both RNA expression and chromatin modification frequencies were a function of distance from the centromere, either peaking or dipping toward arms, with the vertices within the centromere. These results do not lend themselves well to models suggesting that specialized heterochromatic regions are required to enable centromere function. Our data suggest that visible pericentromeric heterochromatin in maize and many other species reflects the sharp transition between CENH3 chromatin and H3 chromatin and gradual distance-correlated changes similar to the frequency of recombination in flanking regions.