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.
Highlights
More than half a century has passed since the concept and practice of plant cell culture was first introduced [1]
We investigated the epigenomic consequences of long-term plant cell culture and found that some genes show an increase in DNA methylation, reminiscent of immortalized animal cell lines and cancer cells
The reactivated transposable elements (TE) in culture are accompanied by a production of 21-nucleotide small RNAs
Summary
More than half a century has passed since the concept and practice of plant cell culture was first introduced [1]. Plant cells can change from one differentiated state, representing a committed developmental program, to a completely different one via a transition through a dedifferentiated state typical of callus tissue [2]. This process is achieved by varying concentrations and relative proportions of two major plant growth regulators (auxin and cytokinin) in the growth medium [3]. The epigenetic nature of this shift is demonstrated by the fact that upon plant regeneration from habituated cell culture and reculturing, the original requirement for growth factors is present again in the reestablished cell culture. In addition to the reversibility, this switch occurs at rates that are orders of magnitude higher than mutations rates in plants [5]
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