Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27 & mapping maize centromeres and centormere evolution
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Taking advantage of 3D light microscopy and the fine cytological resolution of maize pachytene chromosomes, we compared the distribution of individual methylation events to each other and to DNA staining intensity. The data reveal that three marks (H3K9me1, H3K27me1, and H3K27me2) are associated with heterochromatin. Contrary to expectations, we found that in maize H3K9me2 is not localized to heterochromatin, but mostly distributed in euchromatic regions along with H3K4me2. Other data demonstrate that centromere chromatin contains H3K9me2 and H3K9me3, that H3K27me3 occurs at several focused euchromatic domains, and that H4K20 methylation is rare or absent. We describe a novel ChIP-display method that maps kinetochore footprints over high-resolution recombination maps. The centromeric retroelement CRM2 was used as the basis for an AFLP strategy that was combined with chromatin immunoprecipitation to yield a display of markers associated with CENH3 (a kinetochore-specific histone H3 variant). Each of the ten centromeres was mapped precisely using a combined set of 264 CRM markers, 57.2% of which interact with CENH3. The novel set of markers provides genetic anchor points throughout centromere cores. We can estimate that within-centromere gene conversion is roughly 10-3. Our data suggest that frequent conversion is an important mechanism for spreading sequence variants among homologous centromeres. We also provide a first measure of linkage disequilibrium (LD) within maize centromere 2. The data reveal that the tandem repeat CentC has been under selection in recent history. FISH analyses show the abundance of CentC in the closest relatives of maize further suggest that CentC has been the major DNA sequences selected by meiotic drive in the genus Zea.