Epigenetic Profiling of Heterochromatic Satellite DNA in Sugar Beet

Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in intercalary and (peri)centromeric regions comprised of highly abundant satellite DNAs. Detailed epigenetic information about these regions regarding DNA methylation, histone modifications and the role of siRNAs is crucial for the understanding of the sugar beet epigenome. Particularly, the (peri)centromere is of outstanding importance because of its key role in chromosome stability and segregation through mitosis and meiosis. To uncover strand-specific DNA methylation at single-base resolution of intercalary and (peri)centromeric regions we performed bisulfite sequencing of more than one thousand satellite monomers. We found that strong methylated CG and CHG sites are only sparsely distributed while highly frequent CHH sites (with the exception of the CAA motif) are mostly unmethylated. Therefore, the sugar beet heterochromatin is DNA hypomethylated. The (peri)centromere shows even less DNA methylation than the intercalary heterochromatin because the frequency of CG and CHG sites is strongly reduced in these regions. The difference in DNA methylation intensity between both heterochromatic blocks is related to an unequal distribution of key histone H3 methylation marks. While clusters of H3K9me2 were absent in pericentromeric regions and restricted to intercalary heterochromatin only, H3K9me1 and H3K27me1 are enriched in all types of heterochromatin. To investigate a possible regulatory role of siRNAs in heterochromatin maintenance, we analyzed a sugar beet small RNA dataset consisting of 6,76 million sequences and identified 24 nt siRNAs originating from both strands of heterochromatic satellite DNAs suggesting a function in histone H3 and DNA methylation.