[Pao-Yang Chen] Rice transformation treatments leave specific epigenome changes beyond tissue culture
POST:
A. Scheme showing the processes of transgenic rice production, mainly separating into two steps (tissue culture and transformation). B. Scheme depicting nine transformation components composed of different combinations of transformation treatments. C. Heatmap showing the module-component association. D. Total numbers of differentially methylated regions (DMRs) in the CHH contexts. E. Proportion of promoters with CHH-hypomethylated DMRs overlapping with MITEs.
During transgenic plant production, tissue culture often carries epigenetic and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes towards transcriptional variations remain unknown. Here, the impact from individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were co-localized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is way beyond the tissue culture effect.
The first author Jo-Wei Allison Hsieh is a Ph.D. student from Academia Sinica - NTU Genome and Systems Biology Degree Program. The study is published in Plant Physiology, and the research was generously supported by both Academia Sinica and the National Science and Technology Council in Taiwan.
Jo-Wei Allison Hsieh, Pearl Chang, Lin-Yun Kuang, Yue-Ie Hsing, Pao-Yang Chen (2023) Rice transformation treatments leave specific epigenome changes beyond tissue culture Plant Physiology. Jul 3:kiad382. doi: 10.1093/plphys/kiad382. Epub ahead of print. PMID: 37394940.