E-GEOD-42410 - Plants regenerated from tissue culture contain stable epigenome changes in rice

Released on 26 March 2013, last updated on 14 March 2016
Oryza sativa Japonica Group
Samples (37)
Protocols (7)
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA). Whole genome expression maps of rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).
Experiment types
methylation profiling by high throughput sequencing, RNA-seq of coding RNA, RNA-seq of non coding RNA 
Hume Stroud <geo@ncbi.nlm.nih.gov>, Blake C Meyers, Stacey Simon, Steven E Jacobsen, Suhua Feng
Plants regenerated from tissue culture contain stable epigenome changes in rice. Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE. , Europe PMC 23539454
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-42410.idf.txt
Sample and data relationshipE-GEOD-42410.sdrf.txt
Processed data (28)Click to browse processed data