Epigenetic profiling of heterochromatic satellite DNA |
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Authors: | Falk Zakrzewski Bernd Weisshaar Jörg Fuchs Ekaterina Bannack André E Minoche Juliane C Dohm Heinz Himmelbauer Thomas Schmidt |
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Institution: | (1) Department of Biology, Dresden University of Technology, 01062 Dresden, Germany;(2) Institute of Genome Research, University of Bielefeld, 33594 Bielefeld, Germany;(3) Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany;(4) Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain;(5) Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; |
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Abstract: | Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of
two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic
regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical
analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families.
Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites,
with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin.
We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone
H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary
heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA
library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which
originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA
and histone methylation for maintaining heterochromatin. |
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