The Polycomb Group Gene EMF2B modulates protein coding and non-coding RNAs in developing rice panicles.
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE62550 | GEO | 2018/05/31
REPOSITORIES: GEO
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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
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.
2014-10-31 | GSE49633 | GEO
Project description:Oryza sativa VIN3-LIKE2 (OsVIL2) acts as an epigenetic regulator together with Polycomb Repressive Complex2 (PRC2), which mediates trimethylation of histone H3 lysine 27 (H3K27me3) on target chromatin. T-DNA mutants of OsVIL2 displayed abnormal spikelet development. To understand function of OsVIL2 during spikelet development, RNA-sequencing was conducted in developing panicles of wild-type (WT) and osvil2 mutants.
2017-12-26 | GSE108538 | GEO
Project description:OsMADS1 in rice is an important transcription factor in controlling flower development, not only in flower organs development, but also in floral meristem determinacy. Early flower panicle we used is a high expression stage for OsMADS1. We used microarrays to detail the global gene expression underlying functions of OsMADS1 in rice flower development. Rice panicles in length of 2 mm and 5-7 mm were collectecd for RNA extraction and hybridization on Affymetrix microarrays.Rice panicles in length of 2 mm is the stage for the initiation of inner floral organ development and in length of 5-7 mm is the late stages for floral organ development.Though comparing the microarray data of osmads1 and wild-type (control) at these two stages, we can find the functions of OsMADS1 in the early and late flower development stages. Three biological repeats were used. And totally 12 samples were analyzed.
2014-10-06 | E-GEOD-62078 | biostudies-arrayexpress
Project description:To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3’-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats.
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Project description:Accumulating evidence highlights the role of long non-coding RNAs (lncRNA) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, an unbiased and comprehensive method to map its interactome has not yet been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting HOTAIR has functions independent of its (post-)transcriptional mode-of-action.
2022-02-15 | PXD029057 | Pride
Project description:To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3M-bM-^@M-^Y-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats. Expression profiling was conducted using a Rice 3M-bM-^@M-^Y-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3M-bM-^@M-^Y-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 M-BM-0C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in Ubi1:AtJMT, drought-treated NT, and untreated NT plants. Cy3-labeled target cDNA fragments were synthesized from S1 panicles using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2009-07-09 | E-GEOD-14508 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Conclusions: Our study represents the detailed analysis of panicles transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.
2021-08-12 | GSE181713 | GEO
Project description:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 31,439 rice genes was used to elucidate gene expression in leaf and panicles of non-transgenic and HMB4 over-expression line. The analyses show that transgenic rice induces early flowering due to an enhancement of stress response.
2014-09-01 | GSE55984 | GEO
Project description:RNA-sequencing analysis of wild-type and osvil2 mutant panicles
| PRJNA427581 | ENA