Advanced search
1 file | 2.61 MB Add to list

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

(2017) PLANT JOURNAL. 90(6). p.1156-1175
Author
Organization
Abstract
The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.
Keywords
TOMATO FRUIT-DEVELOPMENT, BASE RESOLUTION MAPS, TISSUE-CULTURE, EPIGENETIC INHERITANCE, CYTOSINE METHYLATION, ARABIDOPSIS-THALIANA, GENOME SIZE, PLANTS, RICE, IDENTIFICATION, methylome, cytosine methylation, bisulfite sequencing, transposable, elements, Beta vulgaris, sugar beet, callus

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 2.61 MB

Citation

Please use this url to cite or link to this publication:

MLA
Zakrzewski, Falk et al. “DNA Methylation of Retrotransposons, DNA Transposons and Genes in Sugar Beet (Beta Vulgaris L.).” PLANT JOURNAL 90.6 (2017): 1156–1175. Print.
APA
Zakrzewski, F., Schmidt, M., Van Lijsebettens, M., & Schmidt, T. (2017). DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.). PLANT JOURNAL, 90(6), 1156–1175.
Chicago author-date
Zakrzewski, Falk, Martin Schmidt, Maria Van Lijsebettens, and Thomas Schmidt. 2017. “DNA Methylation of Retrotransposons, DNA Transposons and Genes in Sugar Beet (Beta Vulgaris L.).” Plant Journal 90 (6): 1156–1175.
Chicago author-date (all authors)
Zakrzewski, Falk, Martin Schmidt, Maria Van Lijsebettens, and Thomas Schmidt. 2017. “DNA Methylation of Retrotransposons, DNA Transposons and Genes in Sugar Beet (Beta Vulgaris L.).” Plant Journal 90 (6): 1156–1175.
Vancouver
1.
Zakrzewski F, Schmidt M, Van Lijsebettens M, Schmidt T. DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.). PLANT JOURNAL. 2017;90(6):1156–75.
IEEE
[1]
F. Zakrzewski, M. Schmidt, M. Van Lijsebettens, and T. Schmidt, “DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.),” PLANT JOURNAL, vol. 90, no. 6, pp. 1156–1175, 2017.
@article{8526859,
  abstract     = {The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.},
  author       = {Zakrzewski, Falk and Schmidt, Martin and Van Lijsebettens, Maria and Schmidt, Thomas},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keywords     = {TOMATO FRUIT-DEVELOPMENT,BASE RESOLUTION MAPS,TISSUE-CULTURE,EPIGENETIC INHERITANCE,CYTOSINE METHYLATION,ARABIDOPSIS-THALIANA,GENOME SIZE,PLANTS,RICE,IDENTIFICATION,methylome,cytosine methylation,bisulfite sequencing,transposable,elements,Beta vulgaris,sugar beet,callus},
  language     = {eng},
  number       = {6},
  pages        = {1156--1175},
  title        = {DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)},
  url          = {http://dx.doi.org/10.1111/tpj.13526},
  volume       = {90},
  year         = {2017},
}

Altmetric
View in Altmetric
Web of Science
Times cited: