Comment[ArrayExpressAccession]	E-GEOD-40674
MAGE-TAB Version	1.1			
Public Release Date	2013-12-04
Investigation Title	Genome-wide maps of H3K27me3 in WT (wild type) and Epi-df (mutant) rice			
Comment[Submitted Name]	Genome-wide maps of H3K27me3 in WT (wild type) and Epi-df (mutant) rice
Experiment Description	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.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Zhang	Zhang	Wan	
Person First Name	Liguo	Liguo	Jianmin	
Person Email	liguozhang83@gmail.com			
Person Affiliation	Chinese Academy of Agricultural Sciences			
Person Address	Chinese Academy of Agricultural Sciences, South Zhongguancun Street, Beijing, China			
Person Roles	submitter			
Protocol Name	P-GSE40674-4	P-GSE40674-1	P-GSE40674-3	P-GSE40674-2
Protocol Description	Basecalls were performed using CASAVA version 1.4. Clean: After completing the sequencing, we removed the low-quality sequences, the adaptor sequences, and the pollutants. Alignment: Sequence reads were obtained and mapped to the rice (Orazy JP_6.1) genome using Bowtie (Langmead et al., 2009) allowing up to two mismatches. Reads with unique locations were retained for further analysis. Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm. The default parameters were bandwidth, 200bp; mfold, 32; P-value of 1.00e-05. Genome_build: Orazy JP_6.1 Supplementary_files_format_and_content: WIG files were generated using the MACS program.	No treatment.	Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K27me3 antibody (Millipore,cat no. 07-449). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 100-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.	Surface-sterilized seeds of the WT and Epi-df plants were soaked in water for 3 d and then placed in artificial soil for three weeks.
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	GENOTYPE			
Experimental Factor Type	genotype			
Publication Title	Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice.			
Publication Author List	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			
PubMed ID	23150632			
Publication DOI	10.1105/tpc.112.102269			
Comment[SecondaryAccession]	GSE40674			
Comment[GEOReleaseDate]	2013-12-04			
Comment[ArrayExpressSubmissionDate]	2012-09-06			
Comment[GEOLastUpdateDate]	2013-12-04			
Comment[AEExperimentType]	ChIP-seq			
Comment[SecondaryAccession]	SRP015763			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR570427-SRR570428			
SDRF File	E-GEOD-40674.sdrf.txt