IC4R008-Epigenomic-2012- 22835977

Project Title

• Epigenomic Modification and Epigenetic Regulation in Rice

The Background of This Project

• Epigenomes define gene expression profiles in specific cell types or in response to specific environmental cues in higher eukaryotes. Rice is the largest food plant in the world and becomes as a model plant for cereal genomics because of its small genome size (430 Mb). Whole-genome sequences are available for japonica and indica, two of the three subspecies of rice that have been independently domesticated from wild relatives. Recent studies have accumulated a large set of rice transcriptomic, small RNA, DNA methylation and histone modification data obtained by high throughput analyses (http://rice.plantbiology. msu.edu/cgi-bin/gbrowse/rice/). Work in plants including rice has revealed specific mechanisms involved in acquisition, inheritance and resetting of epigenetic information. In this review, the researchers will summarize recent development in rice epigenomic and epigenetic research by focussing on epigenetic regulation of rice transposon repression, plant development, stress adaptation, and gene expression related to heterosis.

Research Findings

• The role of epigenomic modifications in rice plant development can be illustrated by the function of genes involved in histone modification and DNA methylation (Fig. 1A). In addition to DNA methylation, histone modification seems to also play a primary role in TE repression in rice (Fig. 1B).

Fig. 1. Models of epigenetic mark changes over genes induced by environmental signals (A), and transposons induced by stresses in rice (B). Histone modification marks associated with gene activation may be induced by inductive signals, whereas marks associated with gene repression (i.e., H3K27me3) may remain unchanged during gene activation. The role of histone H3K9 methyltransferases SDG714 and SDG718, DNA demethylase DNG701 and histone H3K9 deacetylase SRT701 in transposon repression/activation is indicated.

• Epigenomic variation that gives rise to stable or transgenerational heritable epialleles related to variation of important agronomical traits or stress responses is being characterized in rice. The expression level of SPL14 is essential for panicle size. In Nipponbare, the epigenetic state of SPL14 allows a moderate expression level of the gene. In the ST- 12 that was derived from Nipponbare, the SPL14 locus shows a distinct and inheritable chromatin modification change that is associated with the higher expression level of gene. The different epigenetic states ofthe locus are stably inherited in the two rice varieties (Fig. 2). Therefore epigenetic mutations may be an important source for variation of important agronomic traits in rice.

Fig. 2. Variation of inheritable epigenetic states on key regulatory genes leads to agronomic trait variation.

• More generally, epigenetic reprogramming may be a key mechanism in the interaction between the different genomes in hybrids (Ishikawa and Kinoshita, 2009) (Fig. 3). Allelic interaction may lead to resetting of the epigenetic states over the locus in the hybrid, such that the DNA methylation of one parental allele may induce the methylation of the other (left), or allelic or non-allelic interactions may enrich activation or repression marks over the locus, leading to higher or lower than mid-parent expression levels in the hybrid.

Fig. 3. Differential epigenetic modifications over parental alleles may contribute to non-additive gene expression in the hybrid.

Labs working on this Project

• National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
• Institut de Biologie des Plantes, Universite´ Paris sud, Orsay 91405, France

Corresponding Author

• D.-X. Zhou: dao-xiu.zhou@u-psud.fr