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  Epigenetic profiling of heterochromatic satellite DNA

Zakrzewski, F., Weisshaar, B., Fuchs, J., Bannack, E., Minoche, A. E., Dohm, J. C., et al. (2011). Epigenetic profiling of heterochromatic satellite DNA. Chromosoma, 120(4), 409-22. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/21594600 http://www.springerlink.com/content/y01473t88235r463/fulltext.pdf.

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Zakrzewski, F., Author
Weisshaar, B., Author
Fuchs, J., Author
Bannack, E., Author
Minoche, A. E., Author
Dohm, J. C.1, Author              
Himmelbauer, H.1, Author              
Schmidt, T., Author
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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Free keywords: *Beta vulgaris/genetics/metabolism; Blotting, Southern; Centromere/*chemistry/genetics/metabolism; Chromosomes, Plant/*chemistry/genetics/metabolism; Cluster Analysis; DNA Methylation; DNA, Satellite/*chemistry/genetics/metabolism; Epigenomics/*methods; Euchromatin/*chemistry/genetics/metabolism; Heterochromatin/*chemistry/genetics/metabolism; Histones/genetics/metabolism; In Situ Hybridization, Fluorescence; RNA, Small Interfering/*chemistry/genetics; Sequence Analysis, DNA; Small Molecule Libraries/chemistry
 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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 Dates: 2011
 Publication Status: Published in print
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Title: Chromosoma
Source Genre: Journal
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Pages: - Volume / Issue: 120 (4) Sequence Number: - Start / End Page: 409 - 22 Identifier: ISSN: 1432-0886 (Electronic) 0009-5915 (Linking)