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Oryza sativa Japonica Group

ABSTRACT: Regulation of histone methylation and gene expression reprogramming in rice inflorescence meristem

PROVIDER: PRJNA282397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1999340_1.fastq.gz	Fastqsanger.gz
	SRR1999340_2.fastq.gz	Fastqsanger.gz
	SRR1999350_1.fastq.gz	Fastqsanger.gz
	SRR1999350_2.fastq.gz	Fastqsanger.gz
	SRR1999341_1.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Oryza sativa Japonica Group

Project description:Genome-wide DNA methylation profile in mutants of a rice HISTONE DEACETYLASE (HDA705)

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Oryza sativa Japonica Group

Project description:Cooperation between H3K27me3 and non-CG methylation in epigenetic regulation of genes in rice.

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Oryza sativa Japonica Group

Project description:Histone acetyltransferase OsGCN5 palys an important role in establishing programs of cell proliferation of crown root meristem

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Oryza sativa Japonica Group

Project description:Identification and analysis of adenine N6-methylation sites in the rice genome

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Project description:Gene expression profile of inflorescence at early developmental stage

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Project description:Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.

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Project description:Host transcriptional reprogramming across diverse strains of the rice bacterial leaf streak pathogen Xanthomonas oryzae pv.oryzicola

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The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.

Project description:The Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific PRC2 functions in other plant species, especially the cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis PRC2 gene EMBRYONIC FLOWER2 (EMF2). Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss of function mutants in rice E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 that are involved in floral development as differentially expressed in the emf2b mutant compared to wild type. OsMADS1 and OsMADS6 are known to be required for meristem determinacy in rice, and are down-regulated in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was up-regulated. Chromatin immunoprecipitation for H3K27me3 followed by deep sequencing showed that all three genes are amongst the presumptive targets of PRC2 in the meristem. We propose that the PRC2 operates through a mechanism that involves regulation of E-function genes to play a major role in floral organ specification and floral meristem determinacy in rice, and possibly in other cereals. RNA-seq: The transcriptome of WT and emf2b rice panicles were compared via RNA-seq.

2014-10-31 | E-GEOD-49633 | biostudies-arrayexpress

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