E-GEOD-40674 - Genome-wide maps of H3K27me3 in WT (wild type) and Epi-df (mutant) rice

Released on 4 December 2013, last updated on 30 November 2015
Oryza sativa
Samples (2)
Protocols (4)
DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and regulating gene expression in plant development. However, the mechanistic relationship to other repressive marks, such as histone H3 lysine 27 trimethylation (H3K27me3), is unclear. OsFIE1 (Fertilization Independent Endosperm 1) encodes an Esc-like core component of the Polycomb repressive complex 2 (PRC2), which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice OsFIE1; this allele exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in its nucleotide sequence, but is hypo-methylated in the promoter and the 5' region of OsFIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, OsFIE1 was ectopically expressed and its imprinting status was disrupted. OsFIE1 interacted with rice E(z) homologs, consistent with its role in H3K27me3 repression. Ectopic expression of OsFIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. Therefore, this work identifies a novel epi-allele involved in H3K27me3-mediated gene repression, that itself is highly regulated by histone H3K9me2, thereby shedding light on the link between two important epigenetic marks regulating rice development. We report the application of ChIP-Seq technology for high-throughput profiling of histone modifications in WT (wild type) and Epi-df (mutant). We demonstrate that the H3K27me3 status is perturbed at target genes and leads to mis-regulated expression in Epi-df.
Experiment type
Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Zhang L, Cheng Z, Qin R, Qiu Y, Wang JL, Cui X, Gu L, Zhang X, Guo X, Wang D, Jiang L, Wu CY, Wang H, Cao X, Wan J. , Europe PMC 23150632
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-40674.idf.txt
Sample and data relationshipE-GEOD-40674.sdrf.txt
Processed data (1)E-GEOD-40674.processed.1.zip