Epigenomic consequences of immortalized plant cell suspension culture

Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T. J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., Martienssen, R. A. (December 2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS biology, 6 (12). pp. 2880-95. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/19071958
DOI: 10.1371/journal.pbio.0060302

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.

Item Type: Paper
Uncontrolled Keywords: Arabidopsis cytology genetics growth & development Base Sequence Cells Cultured Chromatin Immunoprecipitation Chromosomes Plant physiology DNA Methylation DNA Transposable Elements genetics Epigenesis Genetic genetics Gene Expression Genes Plant genetics Genome Plant Histones metabolism Plant Leaves chemistry RNA Plant chemistry RNA Small Interfering metabolism
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
Investigative techniques and equipment > cell culture
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics

organism description > plant
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: Matt Covey
Date: 9 December 2008
Date Deposited: 26 Feb 2013 21:21
Last Modified: 26 Feb 2013 21:21
PMCID: PMC2596858
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27523

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