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Cited by 218Epigenetics and DNA MethylationPlant Molecular Biology ResearchChromosomal and Genetic Variations

Epigenomic consequences of immortalized plant cell suspension culture

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Tanurdzic, Milos, Vaughn, Matthew W, Jiang, Hongmei, Lee, Tae-Jin, Slotkin, R. Keith, Sosinski, Bryon, Thompson, William F, Doerge, R. W +1 more·2008·PLoS Biology
DOI 10.1371/journal.pbio.0060302PMC PMC2596858
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Abstract

Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.

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  • In A. thaliana cells, TEs with the strongest reactivation were Athila retrotransposons and some members of the Helitron, Mu, Vandal, and En/Spm families; activation correlated with an increase of 21-nt siRNA; TEs that remained silenced generated 24-nt siRNAs at the same level as the mother's vegetative tissue.

    “Tanurdzic et al. (2008) [135] studied the epigenomic consequences of long-term culture on A. thaliana cells and identified that TEs with the strongest reactivation were Athila retrotransposons, and some members of the Helitron, Mu, Vandal, and En/Spm families of transposons. The activation of these TEs was correlated with an increase of 21-nt siRNA in the cultured cells. In contrast, TEs that”

    From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as Tanurdzic et al. (2008) [135]

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References 117 · Cited by 218

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Authors
Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., & Martienssen, R. A.
Affiliations
  • Cold Spring Harbor Laboratory (US)
  • Northwestern University (US)
  • North Carolina State University (US)
  • Purdue University West Lafayette (US)
ORCID
Venue
PLoS Biology
Publisher
Public Library of Science (PLoS)
Published
2008-12-09
Volume
6
Issue
12
Pages
e302
ISSN
  • 1544-9173 (ISSN-L)
  • 1545-7885
DOI
10.1371/journal.pbio.0060302
PMC
PMC2596858
OpenAlex
W1988935841
Cited by
218
References
117
Citations by year
2025: 6 · 2024: 7 · 2023: 6 · 2022: 9 · 2021: 16 · 2020: 8 · 2019: 8 · 2018: 13 · 2017: 13 · 2016: 14 · 2015: 14 · 2014: 17 · 2013: 15 · 2012: 24
FWCI
6.59
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Purdue e-Pubs (Purdue University System) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
National Science Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
plant cell suspension culture, epigenetic instability, DNA methylation, histone modifications, heterochromatin, transposable elements, siRNA, RNA interference, Arabidopsis thaliana, chromatin immunoprecipitation, DNA hypomethylation, genome rearrangement
MeSH terms
Base Sequence, Cells, Cultured, DNA Transposable Elements, Histones, Gene Expression, Genes, Plant, Arabidopsis, Plant Leaves, Genome, Plant, RNA, Plant, DNA Methylation, Chromosomes, Plant, RNA, Small Interfering, Epigenesis, Genetic, Chromatin Immunoprecipitation

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