Fwa-pollen-Effect of DNA hypomethylation on gene expression
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE10717 | GEO | 2008/06/07
SECONDARY ACCESSION(S): PRJNA107603
REPOSITORIES: GEO
Similar Datasets
Project description:au05-02_fwa - fwa-pollen - Which gene are upregulated in a hypomethylated mutant? - Compare gene expression between WT pollen and mutant pollen Keywords: gene knock out 4 dye-swap - CATMA arrays
2010-05-26 | E-GEOD-10717 | biostudies-arrayexpress
Project description:au05-02_fwa - fwa-leaves - Which gene are upregulated in a hypomethylated mutant? - Compare gene expression between WT leaves and hypomethylated leaves Keywords: gene knock out
2008-03-12 | GSE10724 | GEO
Project description:Polyadenylation of mRNAs is critical for their export from the nucleus, stability and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, their distinct mutant phenotypes and transcriptome studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the two very similar PAPS2 and PAPS4 proteins. Such functional specialization raises the possibility of modulating the balance of activities between the isoforms to alter poly(A) lengths of sets of transcripts, providing an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression more strongly than in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes germinate and grow at the same rates as wild-type pollen tubes, they are compromised in locating the micropyles of ovules. Transcriptomic analyses indicate that previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A)-tail lengths of transcripts in mutant and wild-type pollen tubes suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 upregulation during pollen-tube growth through the style plays a key role in the acquisition of competence and support the notion that plants can modulate the balance of activity between PAPS isoforms to regulate gene expression.
2023-02-21 | GSE207285 | GEO
Project description:In tomato, there are seven ethylene receptors, ETR1, ETR2, ETR3, ETR4, ETR5, ETR6, and ETR7. In our laboratory, we have ETR3, ETR4, and ETR7, loss-of-function single mutants, in this study we compare the pollen tube length of ETR mutant KO with WT and NR (never rip) gain of function mutant. We found the pollen tube length in ETR3, ETR4, and ETR7 (KO) was more than WT; on the other hand, NR was less than WT, and the treatment by ethylene (ET) increase the length of pollen tube in all ETRs KO and WT but not in NR. The treatment by MCP-1 decreases the pollen tube length slightly in WT, 20% in ETR (KO) and no effect in NR. In conclusion, our results suggest that ethylene receptors (ETRs) in the active state inhibit pollen tube growth; therefore the ethylene is an essential factor for male gametophyte growth.
2020-10-23 | E-MTAB-9660 | biostudies-arrayexpress
Project description:Polyadenylation of mRNAs is critical for their export from the nucleus, stability and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, their distinct mutant phenotypes and transcriptome studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the two very similar PAPS2 and PAPS4 proteins. Such functional specialization raises the possibility of modulating the balance of activities between the isoforms to alter poly(A) lengths of sets of transcripts, providing an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression more strongly than in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes germinate and grow at the same rates as wild-type pollen tubes, they are compromised in locating the micropyles of ovules. Transcriptomic analyses indicate that previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A)-tail lengths of transcripts in mutant and wild-type pollen tubes suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 upregulation during pollen-tube growth through the style plays a key role in the acquisition of competence and support the notion that plants can modulate the balance of activity between PAPS isoforms to regulate gene expression.
2023-02-21 | GSE207509 | GEO
Project description:Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes are causal for the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement of the epigenetic Polycomb Repressive Complex 2 (PRC2) in the endosperm. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that hypomethylated pollen causes redistribution of CHG methylation to PRC2 target genes, revealing that different epigenetic modifications can functionally substitute for each other. Our work presents a method and the underlying mechanism for the generation of viable triploids, providing an impressive example for the potential of epigenome manipulations for plant breeding. Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen, and gene expression in seeds
2014-09-22 | E-GEOD-53642 | biostudies-arrayexpress
Project description:We isolated tricellular pollen (TCP) and pollen mother cells (PMC) of rice using laser microdissection, and did microarray analysis with Agilent 44k rice array.
2010-07-31 | GSE17098 | GEO
Project description:rs09-10_fwa - wt vs mutants 09. Impact of loss of DNA methylation and small interference RNAs (siRNAs) in gene expression. Determination of the genes misregulated upon ectopic expression of the FWA imprinted gene. Mutants impaired for the DNA methylation maintenance pathway and RNA interference machinery were compared to mutants simultaneously impaired for both. Impact of FWA and SDC ectopic expression. 15 dye-swaps. fwa-d, gain of function epimutation, gene knock-in (transgenic), gene knockout.
2011-03-31 | E-GEOD-26844 | biostudies-arrayexpress
Project description:fwa-pollen-Effect of DNA hypomethylation on gene expression
| PRJNA107603 | ENA
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). We have identified and characterized a T-DNA insert rice mutant (Osfuct) with loss of α1,3-fucosyltransferase function. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycan revealed the lack of α1,3-fucose in the N-glycan structure of rice Osfuct mutant. The mutant displayed the pleiotropic developmental defects such as diminished growth, shorter plant height, less number of tillers, shorter panicle lengths and internode, impaired anther and pollen development. In addition, the anther was curved, pollen grains shapes were shriveled, pollen viability and pollen number per anther was dramatically decreased in Osfuct mutant. The complementation test of Osfuct mutant clearly exhibited that the phenotype is caused by the loss of α1,3-fucosyltransferase function bescause complementation line is rescued. Transcriptome profiling data revealed that several genes essential in plant developmental processes were significantly altered in Osfuct mutant including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis and hypothetical proteins. Moreover, Osfuct mutant exhibited the enhanced salt insensitivity. Taken together, these findings demonstrated that Osfuct plays a critical role in growth, anther, pollen development and salt stress response.
2018-06-06 | GSE110873 | GEO