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Comparison of transcriptome profile between wild-type and Epi-df mutant plants

ABSTRACT: We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df. For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Liguo Zhang 

PROVIDER: E-GEOD-39298 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice.

Zhang Liguo L   Cheng Zhijun Z   Qin Ruizhen R   Qiu Yang Y   Wang Jiu-Lin JL   Cui Xiekui X   Gu Lianfeng L   Zhang Xin X   Guo Xiuping X   Wang Dan D   Jiang Ling L   Wu Chuan-yin CY   Wang Haiyang H   Cao Xiaofeng X   Wan Jianmin J  

The Plant cell 20121113 11

DNA methylation and histone H3 Lys 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and for regulating gene expression. However, the mechanistic relationship to other repressive marks, such as histone H3 Lys 27 trimethylation (H3K27me3) is unclear. FERTILIZATION-INDEPENDENT ENDOSPERM1 (FIE1) encodes an Esc-like core component of the Polycomb repressive complex 2, which is involved in H3K27me3-mediated gene repression. Here, we ident  ...[more]

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