Publisher：Research Square Platform LLC  

Abstract

In the offspring, imprinted genes show differential expression from the maternal and paternal alleles. Our time-course analysis in rice (Oryza sativa) revealed persistent and stage-specific classes of imprinted genes, including over a hundred novel genes, especially in the early stage of endosperm development. In the persistent maternally expressed genes (MEGs), CG and CHG sequences are heavily methylated, while these sites are less methylated in the stage-specific MEGs. Similarly, differences in H3K27me3 defined the two classes of paternally expressed genes (PEGs). The imprinting for MEGs involves activating silent genes. By contrast, many PEGs are active in various tissues and carry gene body DNA methylation (gbM); the maternally inherited alleles of these PEGs undergo silencing via gbM demethylation and deposition of H3K27me3. Stage-specific imprinting indicates that parental marks can be differentially interpreted during development. Its developmental variability contrasts the robustness of persistent imprinting, revealing the dynamic layering of parental effects and suggesting new mechanisms for evolution and manipulation of rice endosperm development.

DOI： 10.21203/rs.3.rs-2403620/v1

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Other Link： https://www.researchsquare.com/article/rs-2403620/v1.html

Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

Apomixis, defined as the transfer of maternal germplasm to offspring without fertilization, enables the fixation of F1-useful traits, providing advantages in crop breeding. However, most apomictic plants require pollination to produce endosperm. Endosperm is essential for embryogenesis and its development is suppressed until fertilization. We show that expression of a chimeric repressor of the Elongation of Siliques without Pollination 3 (ESP3) gene (Pro35S:ESP3-SRDX) induces ovule enlargement without fertilization in Arabidopsis thaliana. The ESP3 gene encodes a protein similar to the FWA homeodomain transcription factor containing a StAR-related lipid-transfer (START) domain. However, ESP3 lacks the homeobox-encoding region. Genes related to the cell cycle and sugar metabolism were upregulated in unfertilized Pro35S:ESP3-SRDX ovules similar as in fertilized seeds, while those related to autophagy were downregulated similar to fertilized seeds. Unfertilized Pro35S:ESP3-SRDX ovules partially nourished embryos when only the egg was fertilized, accumulating hexoses without central cell proliferation. ESP3 may regulate nutrient flow during seed development, and ESP3-SRDX could be a useful tool for complete apomixis that does not require pseudo-fertilization.

DOI： 10.1093/pcp/pcac151

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Publisher：Cold Spring Harbor Laboratory  

Pollen tube attraction is a key event of sexual reproduction in flowering plants. In the ovule, two synergid cells neighboring the egg cell control pollen tube arrival via the active secretion of attractant peptides such as AtLURE1 and XIUQIU from the filiform apparatus facing toward the micropyle. Distinctive cell polarity together with longitudinal F-actin and microtubules are hallmarks of the synergid cell in various species, though functions of these cellular structures are still unclear. In this study we used genetic and pharmacological approaches to elucidate the roles of cytoskeletal components in filiform apparatus formation and pollen tube guidance in Arabidopsis thaliana. Inhibition of microtubule formation reduced invaginations of the plasma membrane but did not abolish micropylar AtLURE1.2 accumulation. In contrast, the expression of a dominant-negative form of ACTIN8 induced disorganization of the filiform apparatus and loss of polar AtLURE1.2 distribution toward the filiform apparatus. Interestingly, after pollen tube reception, F-actin became unclear for a few hours in the persistent synergid cell, which may be involved in pausing and resuming pollen tube attraction during early polytubey block. Our data propose the central role of F-actin in the maintenance of cell polarity and function of male-female communication in the synergid cell.

DOI： 10.1101/2022.06.14.496136

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>During the double fertilization process, pollen tubes deliver two sperm cells to an ovule containing the female gametes. In the pollen tube, the vegetative nucleus and sperm cells move together to the apical region where the vegetative nucleus is thought to play a crucial role in controlling the direction and growth of the pollen tube. Here, we report the generation of pollen tubes in <italic>Arabidopsis thaliana</italic> whose vegetative nucleus and sperm cells are isolated and sealed by callose plugs in the basal region due to apical transport defects induced by mutations in the WPP domain-interacting tail-anchored proteins (WITs) and sperm cell-specific expression of a dominant mutant of the CALLOSE SYNTHASE 3 protein. Through pollen-tube guidance assays, we show that the physiologically anuclear mutant pollen tubes maintain the ability to grow and enter ovules. Our findings provide insight into the sperm cell delivery mechanism and illustrate the independence of the tip-localized vegetative nucleus from directional growth control of the pollen tube.

DOI： 10.1038/s41467-021-22661-8

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Other Link： http://www.nature.com/articles/s41467-021-22661-8

Publisher：Cold Spring Harbor Laboratory  

The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we used a custom microarray to survey the transcripts generated from TEs during the rice endosperm development and at selected timepoints in the embryo as a control. The expression patterns of TE transcripts are dynamically up- and downregulated during endosperm development, especially for miniature inverted-repeat transposable elements (MITEs). Surprisingly, some TE transcripts were directionally controlled, while the other DNA transposons and retrotransposons were not. We also discovered the NF-Y binding motif, CCAAT, in the region near the 5′ terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.

DOI： 10.1101/2021.09.27.461986

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Company of Biologists  

Nutrient transfer from mother to the embryo is essential for reproduction in viviparous animals. In the viviparous teleost Xenotoca eiseni belonging to the family Goodeidae, the intraovarian embryo intakes the maternal component secreted into the ovarian fluid via the trophotaenia. Our previous study reported that the epithelial layer cells of the trophotaenia incorporate a maternal protein via vesicle trafficking. However, the molecules responsible for the absorption were still elusive. Here, we focused on Cubam (Cubilin-Amnionless) as a receptor involved in the absorption, and cathepsin L as a functional protease in the vesicles. Our results indicated that the Cubam receptor is distributed in the apical surface of the trophotaenia epithelium and then is taken into the intracellular vesicles. The trophotaenia possesses acidic organelles in epithelial layer cells and cathepsin L-dependent proteolysis activity. This evidence does not conflict with our hypothesis that receptor-mediated endocytosis and proteolysis play roles in maternal macromolecule absorption via the trohotaenia in viviparous teleosts. Such nutrient absorption involving endocytosis is not a specific trait in viviparous fish. Similar processes have been reported in the larval stage of oviparous fish or the suckling stage of viviparous mammals. Our findings suggest that the viviparous teleost acquired trophotaenia-based viviparity from a modification of the intestinal absorption system common in vertebrates. This is a fundamental study to understand the strategic variation of the reproductive system in vertebrates.

DOI： 10.1242/jeb.242613

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.pbi.2021.102032

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Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>
In angiosperms, endosperm development comprises a series of developmental transitions controlled by genetic and epigenetic mechanisms that are initiated after double fertilization. Polycomb repressive complex 2 (PRC2) is a key component of these mechanisms that mediate histone H3 lysine 27 trimethylation (H3K27me3); the action of PRC2 is well described in Arabidopsis thaliana but remains uncertain in cereals. In this study, we demonstrate that mutation of the rice (Oryza sativa) gene EMBRYONIC FLOWER2a (OsEMF2a), encoding a zinc-finger containing component of PRC2, causes an autonomous endosperm phenotype involving proliferation of the central cell nuclei with separate cytoplasmic domains, even in the absence of fertilization. Detailed cytological and transcriptomic analyses revealed that the autonomous endosperm can produce storage compounds, starch granules, and protein bodies specific to the endosperm. These events have not been reported in Arabidopsis. After fertilization, we observed an abnormally delayed developmental transition in the endosperm. Transcriptome and H3K27me3 ChIP-seq analyses using endosperm from the emf2a mutant identified downstream targets of PRC2. These included &amp;gt;100 transcription factor genes such as type-I MADS-box genes, which are likely required for endosperm development. Our results demonstrate that OsEMF2a-containing PRC2 controls endosperm developmental programs before and after fertilization.

DOI： 10.1093/plcell/koaa006

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Other Link： http://academic.oup.com/plcell/advance-article-pdf/doi/10.1093/plcell/koaa006/36138656/koaa006.pdf

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Karyogamy is a prerequisite event for plant embryogenesis, in which dynamic changes in nuclear architecture and the establishment of appropriate gene expression patterns must occur. However, the precise role of the male and female gametes in the progression of karyogamy still remains elusive. Here, we show that the sperm cell possesses the unique property to drive steady and swift nuclear fusion. When we fertilized egg cells with sperm cells in vitro, the immediate fusion of the male and female nuclei in the zygote progressed. This rapid nuclear fusion did not occur when two egg cells were artificially fused. However, the nuclear fusion of two egg nuclei could be accelerated by additional sperm entry or the exogenous application of calcium, suggesting that possible increase of cytosolic Ca2+ level via sperm entry into the egg cell efficiently can facilitate karyogamy. In contrast to zygotes, the egg-egg fusion cells failed to proliferate beyond an early developmental stage. Our transcriptional analyses also revealed the rapid activation of zygotic genes in zygotes, whereas there was no expression in fused cells without the male contribution. Thus, the male sperm cell has the ability to cause immediate karyogamy and to establish appropriate gene expression patterns in the zygote.

DOI： 10.1093/pcp/pcz077

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Language：English   Publishing type：Research paper (scientific journal)  

Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the hst1 gene, transferring salinity tolerance from "Kaijin" into high-yielding "Yukinko-mai" (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC3F3 population, named "YNU31-2-4", in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC3F2 genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC3F2 variants along with field assessment data indicated that "YNU31-2-4" plants carrying the hst1 gene had similar agronomic traits to the WT under normal growth condition. "YNU31-2-4" seedlings subjected to salt stress (125 mM NaCl) had a significantly higher survival rate and increased shoot and root biomasses than the WT. At the tissue level, quantitative and electron probe microanalyzer studies indicated that "YNU31-2-4" seedlings avoided Na+ accumulation in shoots under salt stress. The "YNU31-2-4" plants showed an improved phenotype with significantly higher net CO2 assimilation and lower yield decline than WT under salt stress at the reproductive stage. "YNU31-2-4" is a potential candidate for a new rice cultivar that is highly tolerant to salt stress at the seedling and reproductive stages, and which might maintain yields under a changing global climate.

DOI： 10.3390/ijms20102585

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Language：English  

Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.

DOI： 10.1073/pnas.1821435116

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Language：English   Publisher：Palgrave Macmillan Ltd.  

Seeds are products of successful fertilization involving the merging of maternal and paternal gametes. Interspecific pollination can often produce viable seeds but, on germination, these unwanted offspring are generally rejected by an epigenetic barrier, mediated by the endosperm.

DOI： 10.1038/s41477-018-0179-9

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：National Academy of Sciences  

The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

DOI： 10.1073/pnas.1713333115

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media S.A.  

Chloroplasts, which perform photosynthesis, are one of the most important organelles in green plants and algae. Chloroplasts maintain an independent genome that includes important genes encoding their photosynthetic machinery and various housekeeping functions. Owing to its non-recombinant nature, low mutation rates, and uniparental inheritance, the chloroplast genome (plastome) can give insights into plant evolution and ecology and in the development of biotechnological and breeding applications. However, efficient methods to obtain high-quality chloroplast DNA (cpDNA) are currently not available, impeding powerful sequencing and further functional genomics research. To investigate effects on rice chloroplast genome quality, we compared cpDNA extraction by three extraction protocols: liquid nitrogen coupled with sucrose density gradient centrifugation, high-salt buffer, and Percoll gradient centrifugation. The liquid nitrogen–sucrose gradient method gave a high yield of high-quality cpDNA with reliable purity. The cpDNA isolated by this technique was evaluated, resequenced, and assembled de novo to build a robust framework for genomic and genetic studies. Comparison of this high-purity cpDNA with total DNAs revealed the read coverage of the sequenced regions
next-generation sequencing data showed that the high-quality cpDNA eliminated noise derived from contamination by nuclear and mitochondrial DNA, which frequently occurs in total DNA. The assembly process produced highly accurate, long contigs. We summarize the extent to which this improved method of isolating cpDNA from rice can provide practical progress in overcoming challenges related to chloroplast genomes and in further exploring the development of new sequencing technologies.

DOI： 10.3389/fpls.2018.00266

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Blackwell Publishing Ltd  

In most eudicot and monocot species, interspecific and interploidy crosses generally display abnormalities in the endosperm that are the major cause of a post-zygotic hybridization barrier. In some eudicot species, however, this type of hybridization barrier can be overcome by the manipulation of ploidy levels of one parental species, suggesting that the molecular mechanisms underlying the species hybridization barrier can be circumvented by genome dosage. We previously demonstrated that endosperm barriers in interspecific and interploidy crosses in the genus Oryza involve overlapping but different mechanisms. This result contrasts with those in the genus Arabidopsis, which shows similar outcomes in both interploidy and interspecific crosses. Therefore, we postulated that an exploration of pathways for overcoming the species hybridization barrier in Oryza endosperm, by manipulating the ploidy levels in one parental species, might provide novel insights into molecular mechanisms. We showed that fertile hybrid seeds could be produced by an interspecific cross of female tetraploid Oryza sativa and male diploid Oryza longistaminata. Although the rate of nuclear divisions did not return to normal levels in the hybrid endosperm, the timing of cellularization, nucellus degeneration and the accumulation of storage products were close to normal levels. In addition, the expression patterns of the imprinted gene MADS87 and YUCCA11 were changed when the species barrier was overcome. These results suggest that the regulatory machinery for developmental transitions and imprinted gene expression are likely to play a central role in overcoming species hybridization barriers by genome dosage in the genus Oryza.

DOI： 10.1111/tpj.13803

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Company of Biologists Ltd  

Cell fusion is a pivotal process in fertilization and multinucleate cell formation. A plant cell is ubiquitously surrounded by a hard cell wall, and very few cell fusions have been observed except for gamete fusions. We recently reported that the fertilized central cell (the endosperm) absorbs the persistent synergid, a highly differentiated cell necessary for pollen tube attraction. The synergid-endosperm fusion (SE fusion) appears to eliminate the persistent synergid from fertilized ovule in Arabidopsis thaliana. Here, we analyzed the effects of various inhibitors on SE fusion in an in vitro culture system. Different from other cell fusions, neither disruption of actin polymerization nor protein secretion impaired SE fusion. However, transcriptional and translational inhibitors decreased the SE fusion success rate and also inhibited endosperm division. Failures of SE fusion and endosperm nuclear proliferation were also induced by roscovitine, an inhibitor of cyclin-dependent kinases (CDK). These data indicate unique aspects of SE fusion such as independence of filamentous actin support and the importance of CDK-mediated mitotic control.

DOI： 10.1242/jcs.204123

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELIFE SCIENCES PUBLICATIONS LTD  

Mature seed dormancy is a vital plant trait that prevents germination out of season. In Arabidopsis, the trait can be maternally regulated but the underlying mechanisms sustaining this regulation, its general occurrence and its biological significance among accessions are poorly understood. Upon seed imbibition, the endosperm is essential to repress the germination of dormant seeds. Investigation of genomic imprinting in the mature seed endosperm led us to identify a novel set of imprinted genes that are expressed upon seed imbibition. Remarkably, programs of imprinted gene expression are adapted according to the dormancy status of the seed. We provide direct evidence that imprinted genes play a role in regulating germination processes and that preferential maternal allelic expression can implement maternal inheritance of seed dormancy levels.

DOI： 10.7554/eLife.19573

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN SOC CELL BIOLOGY  

In flowering plants, fertilization of the central cell gives rise to an embryo-nourishing endosperm. Recently, we reported that the endosperm absorbs the adjacent synergid cell through a cell-fusion, terminating the pollen tube guidance by a rapid inactivation of the synergid cell. Although this synergid-endosperm fusion (SE fusion) initiates soon after fertilization, it was still unknown whether the triggers of SE fusion are stimuli during fertilization or other seed developmental processes. To further dissect out the SE fusion process, we investigated the SE fusion in an Arabidopsis mutant defective for MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a subunit of the polycomb repressive complex 2 (PRC2). The mutant msi1 develops autonomous endosperm without fertilization. Time-lapse imaging revealed a rapid efflux of the synergid contents during the autonomous endosperm development, indicating that the initiation of SE fusion is under the control of some of the events triggered by fertilization of the central cell distinct from the discharge of pollen tube contents and plasma membrane fusion.

DOI： 10.1247/csf.16010

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Language：English   Publisher：FRONTIERS RESEARCH FOUNDATION  

The polycomb repressive complex 2 (PRC2) is an evolutionarily conserved multimeric protein complex in both plants and animals. In contrast to animals, plants have evolved a range of different components of PRC2 and form diverse complexes that act in the control of key regulatory genes at many stages of development during the life cycle. A number of studies, particularly in the model species Arabidopsis thaliana, have highlighted the role of PRC2 and of epigenetic controls via parent-of-origin specific gene expression for endosperm development. However, recent research in cereal plants has revealed that although some components of PRC2 show evolutionary conservation with respect to parent-of-origin specific gene expression patterns, the identity of the imprinted genes encoding PRC2 components is not conserved. This disparity may reflect the facts that cereal plant genomes have undergone different patterns of duplication during evolution compared to A. thaliana and that the endosperm development program is not identical in monocots and eudicots. In this context, we focus this review on the expression of imprinted PRC2 genes and their roles in endosperm development in cereals.

DOI： 10.3389/fpls.2015.00144

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The endosperm of cereal grains represents the most important source of human nutrition. In addition, the endosperm provides many investigatory opportunities for biologists because of the unique processes that occur during its ontogeny, including syncytial development at early stages. Rice endospermless 1 (enl1) develops seeds lacking an endosperm but carrying a functional embryo. The enl1 endosperm produces strikingly enlarged amoeboid nuclei. These abnormal nuclei result from a malfunction in mitotic chromosomal segregation during syncytial endosperm development. The molecular identification of the causal gene revealed that ENL1 encodes an SNF2 helicase family protein that is orthologous to human Plk1-Interacting Checkpoint Helicase (PICH), which has been implicated in the resolution of persistent DNA catenation during anaphase. ENL1-Venus (enhanced yellow fluorescent protein (YFP)) localizes to the cytoplasm during interphase but moves to the chromosome arms during mitosis. ENL1-Venus is also detected on a thread-like structure that connects separating sister chromosomes. These observations indicate the functional conservation between PICH and ENL1 and confirm the proposed role of PICH. Although ENL1 dysfunction also affects karyokinesis in the root meristem, enl1 plants can grow in a field and set seeds, indicating that its indispensability is tissue-dependent. Notably, despite the wide conservation of ENL1/PICH among eukaryotes, the loss of function of the ENL1 ortholog in Arabidopsis (CHR24) has only marginal effects on endosperm nuclei and results in normal plant development. Our results suggest that ENL1 is endowed with an indispensable role to secure the extremely rapid nuclear cycle during syncytial endosperm development in rice.

DOI： 10.1111/tpj.12705

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Language：English   Publisher：OXFORD UNIV PRESS  

In contrast to the majority of animal species, plants are sessile organisms and are, therefore, constantly challenged by environmental perturbations. Over the past few decades, our knowledge of how plants perceive environmental stimuli has increased considerably, e.g. the mechanisms for transducing environmental stress stimuli into cellular signaling cascades and gene transcription networks. In addition, it has recently been shown that plants can remember past environmental events and can use these memories to aid responses when these events recur. In this mini review, we focus on recent progress in determination of the epigenetic mechanisms used by plants under various environmental stresses. Epigenetic mechanisms are now known to play a vital role in the control of gene expression through small RNAs, histone modifications and DNA methylation. These are inherited through mitotic cell divisions and, in some cases, can be transmitted to the next generation. They therefore offer a possible mechanism for stress memories in plants. Recent studies have yielded evidence indicating that epigenetic mechanisms are indeed essential for stress memories and adaptation in plants.

DOI： 10.1093/pcp/pcu125

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

On fertilization in Arabidopsis thaliana, one maternal gamete, the central cell, forms a placenta-like tissue, the endosperm. The DNA glycosylase DEMETER (DME) excises 5-methylcytosine via the base excision repair pathway in the central cell before fertilization, creating patterns of asymmetric DNA methylation and maternal gene expression across DNA replications in the endosperm lineage (EDL). Active DNA demethylation in the central cell is essential for transcriptional activity in the EDL of a set of genes, including FLOWERING WAGENINGEN (FWA). A DME-binding motif for iron-sulfur (Fe-S) cluster cofactors is indispensable for its catalytic activity. We used an FWA-GFP reporter to find mutants defective in maternal activation of FWA-GFP in the EDL, and isolated an allele of the yeast Dre2/ human antiapoptotic factor CIAPIN1 homolog, encoding an enzyme previously implicated in the cytosolic Fe-S biogenesis pathway (CIA), which we named atdre2-2. We found that AtDRE2 acts in the central cell to regulate genes maternally activated in the EDL by DME. Furthermore, the FWA-GFP expression defect in atdre2-2 was partially suppressed genetically by a mutation in the maintenance DNA methyltransferase MET1; the DNA methylation levels at four DME targets increased in atdre2-2 seeds relative to WT. Although atdre2-2 shares zygotic seed defects with CIA mutants, it also uniquely manifests dme phenotypic hallmarks. These results demonstrate a previously unidentified epigenetic function of AtDRE2 that may be separate from the CIA pathway.

DOI： 10.1073/pnas.1404058111

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS INC  

In flowering plants, the tapetum, the innermost layer of the anther, provides both nutrient and lipid components to developing microspores, pollen grains, and the pollen coat. Though the programmed cell death of the tapetum is one of the most critical and sensitive steps for fertility and is affected by various environmental stresses, its regulatory mechanisms remain mostly unknown. Here we show that autophagy is required for the metabolic regulation and nutrient supply in anthers and that autophagic degradation within tapetum cells is essential for postmeiotic anther development in rice. Autophagosome-like structures and several vacuole-enclosed lipid bodies were observed in postmeiotic tapetum cells specifically at the uninucleate stage during pollen development, which were completely abolished in a retrotransposon-insertional OsATG7 (autophagy-related 7)-knockout mutant defective in autophagy, suggesting that autophagy is induced in tapetum cells. Surprisingly, the mutant showed complete sporophytic male sterility, failed to accumulate lipidic and starch components in pollen grains at the flowering stage, showed reduced pollen germination activity, and had limited anther dehiscence. Lipidomic analyses suggested impairment of editing of phosphatidylcholines and lipid desaturation in the mutant during pollen maturation. These results indicate a critical involvement of autophagy in a reproductive developmental process of rice, and shed light on the novel autophagy-mediated regulation of lipid metabolism in eukaryotic cells.

DOI： 10.4161/auto.28279

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Language：English   Publishing type：Part of collection (book)   Publisher：ELSEVIER ACADEMIC PRESS INC  

Genomic imprinting refers to the unequal expression of maternal and paternal alleles according to the parent of origin. This phenomenon is regulated by epigenetic controls and has been reported in placental mammals and flowering plants. Although conserved characteristics can be identified across a wide variety of taxa, it is believed that genomic imprinting evolved independently in animal and plant lineages. Plant genomic imprinting occurs most obviously in the endosperm, a terminally differentiated embryo-nourishing tissue that is required for seed development Recent studies have demonstrated a close relationship between genomic imprinting and the development of elaborate defense mechanisms against parasitic elements during plant sexual reproduction. In this chapter, we provide an introductory description of genomic imprinting in plants, and focus on recent advances in our understanding of its role in endosperm development, the frontline of maternal and paternal epigenomes.

DOI： 10.1016/B978-0-12-800222-3.00001-2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. In Arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. Therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. However, these two types of hybridization barrier may be initiated by different intrinsic cues: the interspecific cross barrier arises after hybridization of genomes with differences in DNA sequences, while the interploidy cross barrier arises after hybridization of genomes with the same DNA sequences but differences in ploidy levels. In this study, we performed interploidy crosses to identify components of the post-hybridization barrier in the endosperm of rice. We performed an intra-cultivar cross of autotetraploid (4n)xdiploid (2n) rice, and found precocious cellularization and a decreased rate of nuclear division in the syncytial endosperm. By contrast, seeds from the reciprocal cross showed delayed cellularization and an increased rate of nuclear division. This differential effect on nuclear division rates contrasts with the outcome of rice interspecific crosses, which were previously shown to have altered timing of cellularization without any change in nuclear division rates. Thus, we propose that the post-zygotic hybridization barrier in rice endosperm has two separable components, namely control of the timing of cellularization and control of the nuclear division rates in the syncytial stage of endosperm development.

DOI： 10.1111/tpj.12333

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Iron-sulfur proteins have iron-sulfur clusters as a prosthetic group and are responsible for various cellular processes, including general transcriptional regulation, photosynthesis and respiration. The cytosolic iron-sulfur assembly (CIA) pathway of yeast has been shown to be responsible for regulation of iron-sulfur cluster assembly in both the cytosol and the nucleus. However, little is known about the roles of this pathway in multicellular organisms.
In a forward genetic screen, we identified an Arabidopsis thaliana mutant with impaired expression of the endosperm-specific gene Flowering Wageningen (FWA). To characterize this mutant, we carried out detailed phenotypic and genetic analyses during reproductive and vegetative development.
The mutation affects NAR1, which encodes a homolog of a yeast CIA pathway component. Comparison of embryo development in nar1-3 and other A. thaliana mutants affected in the CIA pathway showed that the embryos aborted at a similar stage, suggesting that this pathway potentially functions in early seed development. Transcriptome analysis of homozygous viable nar1-4 seedlings showed transcriptional repression of a subset of genes involved in 'iron ion transport' and 'response to nitrate'. nar1-4 also exhibited resistance to the herbicide paraquat.
Our results indicate that A. thaliana NAR1 has various functions including transcriptional regulation in gametophytes and abiotic stress responses in vegetative tissues.

DOI： 10.1111/nph.12350

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Language：English   Publishing type：Research paper (scientific journal)  

In mammals and plants, parental genomic imprinting restricts the expression of specific loci to one parental allele. Imprinting in mammals relies on sex-dependent de novo deposition of DNA methylation during gametogenesis but a comparable mechanism was not shown in plants. Rather, paternal silencing by the maintenance DNA methyltransferase 1 (MET1) and maternal activation by the DNA demethylase DEMETER (DME) cause maternal expression. However, genome-wide studies suggested other DNA methylationdependent imprinting mechanisms. Here, we show that de novo RNA-directed DNA methylation (RdDM) regulates imprinting at specific loci expressed in endosperm. RdDM in somatic tissues is required to silence expression of the paternal allele. By contrast, the repression of RdDM in female gametes participates with or without DME requirement in the activation of the maternal allele. The contrasted activity of DNA methylation between male and female gametes appears sufficient to prime imprinted maternal expression. After fertilization, MET1 maintains differential expression between the parental alleles. RdDM depends on small interfering RNAs (siRNAs). The involvement of RdDM in imprinting supports the idea that sources of siRNAs such as transposons and de novo DNA methylation were recruited in a convergent manner in plants and mammals in the evolutionary process leading to selection of imprinted loci. © 2013. Published by The Company of Biologists Ltd.

DOI： 10.1242/dev.092981

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

DOI： 10.1270/jsbbr.15.42

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Other Link： https://jlc.jst.go.jp/DN/JALC/10021164544?from=CiNii

Language：English   Publisher：OXFORD UNIV PRESS  

DOI： 10.1093/pcp/pcs061

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In Arabidopsis, DEMETER (DME) DNA demethylase contributes to reprogramming of the epigenetic state of the genome in the central cell. However, other aspects of the active DNA demethylation processes remain elusive. Here we show that Arabidopsis SSRP1, known as an HMG domain-containing component of FACT histone chaperone, is required for DNA demethylation and for activation and repression of many parentally imprinted genes in the central cell. Although loss of DNA methylation releases silencing of the imprinted FWA-GFP, double ssrp1-3;. met1-3 mutants surprisingly showed limited activation of maternal FWA-GFP in the central cell, and only became fully active after several nuclear divisions in the endosperm. This behavior was in contrast to the dme-1;. met1 double mutant in which hypomethylation of FWA-GFP by met1 suppressed the DNA demethylation defect of dme-1. We propose that active DNA demethylation by DME requires SSRP1 function through a distinctly different process from direct DNA methylation control. © 2011 Elsevier Inc.

DOI： 10.1016/j.devcel.2011.08.013

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Oryza sativa is widely used as a model organism for many aspects of research in monocots and cereals. However, it has certain disadvantages as a model species compared with Arabidopsis thaliana, the eudicot species most widely used in plant sciences: first, it has a long cultivation time; and second, it requires considerably more space for growth. Here, we introduce a biotron breeding system, which allows rapid and reliable rice cultivation using a well-equipped artificial environmental chamber. This system involves use of regulation of CO 2 levels, removal of tillers and embryo rescue to overcome the disadvantages of rice cultivation. The rice cultivars Nipponbare, Koshihikari, Taichung 65 and Kasalath all showed vigorous growth and sufficient seed production in the biotron breeding system with accelerated flowering time. Nipponbare, which was the earliest among these cultivars, flowered at about 50 d after sowing. The life cycle of these plants could be further shortened using an embryo rescue technique on immature seeds at 7 d after pollination, thereby avoiding the lengthy process of seed maturation. Overall, it was possible to shorten the life cycle of Nipponbare to about 2 months under the controlled conditions. Furthermore, controlled crosses, which can be difficult with conventional cultivation methods, were easy to perform as we could control the exact timing of anther dehiscence. Thus, our biotron breeding system offers a valuable new approach to genetic and breeding studies in rice. © 2011 The Author.

DOI： 10.1093/pcp/pcr066

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Summary In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested as under-proliferation or over-proliferation of endosperm. Recent analyses using crosses between Arabidopsis thaliana and its related species with different ploidy levels have shown that interspecific hybridization causes delayed developmental transition and increased mitotic activity in the endosperm. In this study, we investigated endosperm development in interspecific crosses between diploid Oryza species. In a cross between female O. sativa and male O. punctata, we found that the hybrid endosperm was reduced in size and this cross was associated with precocious developmental transition. By contrast, the cross between O. sativa and O. longistaminata generated enlarged hybrid endosperm at the mid-point of seed development and this cross was associated with delayed developmental transition. Subsequently, the hybrid endosperm displayed a shriveled appearance at the seed maturation stage. We found that the accumulation of storage products and the expression patterns of several marker genes were also altered in the hybrid endosperm. By contrast, the rate of syncytial mitotic nuclear divisions was not significantly affected. The gene OsMADS87 showed a maternal origin-specific expression pattern in rice endosperm, in contrast to its Arabidopsis homologue PHERES1, which shows paternal origin-specific expression. OsMADS87 expression was decreased or increased depending on the type of developmental transition change in the hybrid rice endosperm. Our results indicate that one of the interspecies hybridization barriers in Oryza endosperm is mediated by precocious or delayed developmental alterations and de-regulation of OsMADS87, without change to the rate of syncytial mitotic nuclear division in the hybrid endosperm. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

DOI： 10.1111/j.1365-313X.2010.04466.x

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Publisher：The Japanese Society of Plant Physiologists  

The rice <I>enl1</I> mutant bears seeds without endosperm. We mapped the <I>enl1</I> locus at a region close to the telomere of the Chromosome 4 long arm and identified a deletion of several nucleotides and substitutions in an exon of a predicted gene in this region. Transgenic introduction of a wild type genomic fragment containing this gene completely complemented the mutant phenotype, concluding this gene to be <I>ENL1</I>. <I>ENL1</I> encodes a protein belonging to the SNF2 class helicase family, which harbors an SNF2 domain and a HELICc domain. Orthologs of ENL1 are conserved among most of eukaryotes. The human ortholog, PICH, is reported to be required for chromosome condensation, chromosome arm architecture, and sister chromatid segregation. Laser confocal microscopic observation of PI-stained syncytial endosperms revealed the presence of giant endosperm nuclei with many nucleoli in the mutant. The abnormality of mutant nuclei appeared to derive from failure in chromosome separation. These results suggest that the errors in the chromosome cycle at the syncytial stage in the <I>enl1</I> mutant result in the inability of further endosperm development.

DOI： 10.14841/jspp.2011.0.0060.0

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In many organisms, the genomes of individual species are isolated by a range of reproductive barriers that act before or after fertilization. Successful mating between species results in the presence of different genomes within a cell (hybridization), which can lead to incompatibility in cellular events due to adverse genetic interactions. In addition to such genetic interactions, recent studies have shown that the epigenetic control of the genome, silencing of transposons, control of non-additive gene expression and genomic imprinting might also contribute to reproductive barriers in plant and animal species. These genetic and epigenetic mechanisms play a significant role in the prevention of gene flow between species. In this review, we focus on aspects of epigenetic control related to hybrid incompatibility during species hybridization, and also consider key mechanism(s) in the interaction between different genomes.

DOI： 10.1093/mp/ssp028

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Gene silencing by DNA methylation is well documented and known to be essential for various biological phenomena in many organisms. In contrast, the processes that convert the silent state of a gene whose DNA is methylated and predicted to form facultative heterochromatin to the actively transcribed state remain elusive. In Arabidopsis, recent studies have shown that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING1 (ROS1) participate in DNA demethylation. DME is necessary for genomic imprinting in the endosperm, while ROS1 is involved in pruning DNA methylation patterns in transposons and genic regions of vegetative tissues. These findings provide us with molecular clues for understanding the underlying mechanisms of DNA demethylation and gene activation. In this review, we will consider and discuss the processes of controlling gene activation through DNA demethylation, which are predicted to include the recognition of target sequences, DNA demethylation, the transformation of the chromatin to the active state, and transcription. Many of these processes remain poorly understood at this stage. © Springer-Verlag 2008.

DOI： 10.1007/s00412-008-0183-3

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Publisher：The Japanese Society of Plant Physiologists  

Abnormal endosperm development is observed in inter-specific or inter-ploidy crosses of many plant species. Several reports suggested that the endosperm failure is caused either by promotion or suppression of the endosperm development and this can be due to the functional difference between parental genomes. One of the possible molecular mechanisms underlying this phenomenon can be genomic imprinting, an epigenetic mechanism with parent-of-origin dependent mono-allelic gene expression. <br>We conducted inter-specific crosses between several cultivated and wild rice species and found abnormality in hybrid endosperm. In these crosses, the rate of nuclear division of the endosperm was not affected but the timing of cellularization was found to be delayed or advanced. We also carried out the microarray analysis using hybrid endosperm of <I>O. sativa</I> and <I>O. longistaminata</I>, and identified the candidate genes related to the endosperm failure. Possible involvement of these genes and their effects on the endosperm development will be discussed.

DOI： 10.14841/jspp.2009.0.0114.0

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Maternally and paternally derived chromosomes might be expected to contribute equally to the various cellular and developmental processes in placental mammals and flowering plants. However, this is not true even in the case of the self-pollinated plant, Arabidopsis, which has identical DNA sequences in both parental genomes. The reason for this is that some genes, called "imprinted genes", are expressed exclusively from paternally or maternally inherited chromosomes. As a result, parental chromosomes express a distinct set of genes and play different roles in biological processes. Here, we review and compare roles of genomic imprinting in flowering plants and placental mammals. © 2008 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.semcdb.2008.07.018

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Parental imprinting is important for seed development, but few imprinted genes have been identified in plants. The four known imprinted genes in Arabidopsis thaliana encode transcriptional regulators. Here, we describe a novel imprinted gene, MATERNALLY EXPRESSED PAB C-TERMINAL (MPC), which encodes the C-terminal domain of poly(A) binding proteins (PABPs). PABPs play roles in mRNA stability and translation. MPC interacts with proteins that also interact with the C-terminal domain of typical PABPs, suggesting that MPC may regulate translation by modulating PABP activity. In the endosperm, MPC is expressed only from the maternal allele. Reduction of MPC expression affects seed development. In dna methyltransferase1 (met1) mutants, MPC is ectopically expressed, and the paternal allele is active in the endosperm. CGs in the 5′ flanking region and gene body of MPC lose methylation in a met1 background. Both regions are required to confer imprinted reporter expression, suggesting that the gene body contains imprinting control region elements. In Arabidopsis, DEMETER (DME) activates expression of maternal alleles. MPC expression is reduced in flowers and seeds in a dme-4 mutant but only after fertilization in dme-1. We conclude that other factors along with DME promote MPC expression and that DME has indirect effects on imprinted gene expression in endosperm. © 2008 American Society of Plant Biologists.

DOI： 10.1105/tpc.108.061929

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

A central question in genomic imprinting is how a specific sequence is recognized as the target for epigenetic marking. In both mammals and plants, imprinted genes are often associated with tandem repeats and transposon-related sequences, but the role of these elements in epigenetic gene silencing remains elusive. FWA is an imprinted gene in Arabidopsis thaliana expressed specifically in the female gametophyte and endosperm. Tissue-specific and imprinted expression of FWA depends on DNA methylation in the FWA promoter, which is comprised of two direct repeats containing a sequence related to a SINE retroelement. Methylation of this element causes epigenetic silencing, but it is not known whether the methylation is targeted to the SINE-related sequence itself or the direct repeat structure is also necessary. Here we show that the repeat structure in the FWA promoter is highly diverse in species within the genus Arabidopsis. Four independent tandem repeat formation events were found in three closely related species. Another related species, A. halleri, did not have a tandem repeat in the FWA promoter. Unexpectedly, even in this species, FWA expression was imprinted and the FWA promoter was methylated. In addition, our expression analysis of FWA gene in vegetative tissues revealed high frequency of intra-specific variation in the expression level. In conclusion, we show that the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene. Rather, SINE-related sequence is sufficient for imprinting, vegetative silencing, and targeting of DNA methylation. Frequent independent tandem repeat formation events in the FWA promoter led us to propose that they may be a consequence, rather than cause, of the epigenetic control. The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed.

DOI： 10.1371/journal.pgen.1000048

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A central question in genomic imprinting is how a specific sequence is recognized as the target for epigenetic marking. In both mammals and plants, imprinted genes are often associated with tandem repeats and transposon-related sequences, but the role of these elements in epigenetic gene silencing remains elusive. FWA is an imprinted gene in Arabidopsis thaliana expressed specifically in the female gametophyte and endosperm. Tissue-specific and imprinted expression of FWA depends on DNA methylation in the FWA promoter, which is comprised of two direct repeats containing a sequence related to a SINE retroelement. Methylation of this element causes epigenetic silencing, but it is not known whether the methylation is targeted to the SINE-related sequence itself or the direct repeat structure is also necessary. Here we show that the repeat structure in the FWA promoter is highly diverse in species within the genus Arabidopsis. Four independent tandem repeat formation events were found in three closely related species. Another related species, A. halleri, did not have a tandem repeat in the FWA promoter. Unexpectedly, even in this species, FWA expression was imprinted and the FWA promoter was methylated. In addition, our expression analysis of FWA gene in vegetative tissues revealed high frequency of intra-specific variation in the expression level. In conclusion, we show that the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene. Rather, SINE-related sequence is sufficient for imprinting, vegetative silencing, and targeting of DNA methylation. Frequent independent tandem repeat formation events in the FWA promoter led us to propose that they may be a consequence, rather than cause, of the epigenetic control. The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed. © 2008 Fujimoto et al.

DOI： 10.1371/journal.pgen.1000048

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A unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressed specifically in the endosperm in an imprinted manner. Ectopic FWA expression and disruption of imprinting can be induced in mutants of a CG methyltransferase MET1 (methyltransferase 1) or a chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), suggesting that the proper FWA expression depends on cytosine methylation. However, critical methylated residues controlling FWA silencing are not pinpointed. Nor is it understood how the FWA gene is initially methylated and silenced in wild-type plants. Here we mapped sequences critical for FWA silencing by application of RdDM (RNA-directed DNA methylation) to a ddm1-induced stable fwa epiallele. Transcription of double-stranded RNA corresponding to the tandem direct repeats around the FWA transcription start site induced de novo DNA methylation, transcriptional suppression and phenotypic reversion. The induced changes were heritable even without the transgene, which correlates with inheritance of CG methylation in the direct repeats. The newly silenced FWA allele was transcribed in an endosperm-specific and imprinted manner, as is the case for the wild-type FWA gene. The results indicate that methylation of the direct repeats, which presumably originated from a short interspersed nuclear element (SINE), is sufficient to induce proper epigenetic control of the FWA gene. © 2007 The Authors.

DOI： 10.1111/j.1365-313X.2006.02936.x

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In flowering plants, success or failure of seed development is determined by various genetic mechanisms. During sexual reproduction, double fertilization produces the embryo and endosperm, which both contain maternally and paternally derived genomes. In endosperm, a reproductive barrier is often observed in inter-specific crosses. Endosperm is a tissue that provides nourishment for the embryo within the seed, in a similar fashion to the placenta of mammals, and for the young seedling after germination. This review considers the relationship between the reproductive barrier in endosperm and genomic imprinting. Genomic imprinting is an epigenetic mechanism that results in mono-allelic gene expression that is parent-of-origin dependent. In Arabidopsis, recent studies of several imprinted gene loci have identified the epigenetic mechanisms that determine genomic imprinting. A crucial feature of genomic imprinting is that the maternally and paternally derived imprinted genes must carry some form of differential mark, usually DNA methylation and/or histone modification. Although the epigenetic marks should be complementary on maternally and paternally imprinted genes within a single species, it is possible that neither the patterns of epigenetic marks nor expression of imprinted genes are the same in different species. Moreover, in hybrid endosperm, the regulation of expression of imprinted genes can be affected by upstream regulatory mechanisms in the male and female gametophytes. Species-specific variations in epigenetic marks, the copy number of imprinted genes, and the epigenetic regulation of imprinted genes in hybrids might all play a role in the reproductive barriers observed in the endosperm of interspecific and interploidy crosses. These predicted molecular mechanisms might be related to earlier models such as the "endosperm balance number" (EBN) and "polar nuclei activation" (PNA) hypotheses.

DOI： 10.1266/ggs.82.177

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Imprinted genes are expressed predominantly from either their paternal or their maternal allele. To date, all imprinted genes identified in plants are expressed in the endosperm. In Arabidopsis thaliana, maternal imprinting has been clearly demonstrated for the Polycomb group gene MEDEA (MEA) and for FWA. Direct repeats upstream of FWA are subject to DNA methylation. However, it is still not clear to what extent similar cis-acting elements may be part of a conserved molecular mechanism controlling maternally imprinted genes. In this work, we show that the Polycomb group gene FERTILIZATION-INDEPENDENT SEED2 (FIS2) is imprinted. Maintenance of FIS2 imprinting depends on DNA methylation, whereas loss of DNA methylation does not affect MEA imprinting. DNA methylation targets a small region upstream of FIS2 distinct from the target of DNA methylation associated with FWA. We show that FWA and FIS2 imprinting requires the maintenance of DNA methylation throughout the plant life cycle, including male gametogenesis and endosperm development. Our data thus demonstrate that parental genomic imprinting in plants depends on diverse cis-elements and mechanisms dependent or independent of DNA methylation. We propose that imprinting has evolved under constraints linked to the evolution of plant reproduction and not by the selection of a specific molecular mechanism. © 2006 American Society of Plant Biologists.

DOI： 10.1105/tpc.106.041178

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The Arabidopsis FWA gene was initially identified from late-flowering epigenetic mutants that show ectopic FWA expression associated with heritable hypomethylation of repeats around transcription starting sites. Here, we show that wild-type FWA displays imprinted (maternal origin-specific) expression in endosperm. The FWA imprint depends on the maintenance DNA methyltransferase MET1, as is the case in mammals. Unlike mammals, however, the FWA imprint is not established by allele-specific de novo methylation. It is established by maternal gametophyte-specific gene activation, which depends on a DNA glycosylase gene, DEMETER. Because endosperm does not contribute to the next generation, the activated FWA gene need not be silenced again. Double fertilization enables plants to use such "one-way" control of imprinting and DNA methylation in endosperm.

DOI： 10.1126/science.1089835

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Publishing type：Research paper (international conference proceedings)  

DOI： 10.1101/sqb.2004.69.139

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All plants flower late in their life cycle. For example, in Arabidopsis, the shoot undergoes a transition and produces reproductive flowers after the adult phase of vegetative growth. Much is known about genetic and environmental processes that control flowering time in mature plants. However, little is understood about the mechanisms that prevent plants from flowering much earlier during embryo and seedling development. Arabidopsis embryonic flower (emf1 and emf2) mutants flower soon after germination, suggesting that a floral repression mechanism is established in wild-type plants that prevents flowering until maturity. Here, we show that polycomb group proteins play a central role in repressing flowering early in the plant life cycle. We found that mutations in the Fertilization Independent Endosperm (FIE) polycomb gene caused the seedling shoot to produce flower-like structures and organs. Flower-like structures were also generated from the hypocotyl and root, organs not associated with reproduction. Expression of floral induction and homeotic genes was derepressed in mutant embryos and seedlings. These results suggest that FIE-mediated polycomb complexes are an essential component of a floral repression mechanism established early during plant development.

DOI： 10.1073/pnas.241507798

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In flowering plants, two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus, which replicates to generate the endosperm, a tissue that supports embryo development. The FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) and MEDEA (MEA) genes encode WD and SET domain polycomb proteins, respectively. In the absence of fertilization, a female gametophyte with a loss-of-function fie or mea allele initiates endosperm development without fertilization, fie and mea mutations also cause parent-of-origin effects, in which the wild-type maternal allele is essential and the paternal allele is dispensable for seed viability. Here, we show that FIE and MEA polycomb proteins interact physically, suggesting that the molecular partnership of WD and SET domain polycomb proteins has been conserved during the evolution of flowering plants. The overlapping expression patterns of FIE and MEA are consistent with their suppression of gene transcription and endosperm development in the central cell as well as their control of seed development after fertilization. Although FIE and MEA interact, differences in maternal versus paternal patterns of expression, as well as the effect of a recessive mutation in the DECREASE IN DNA METHYLATION1 (DDM1) gene on mutant allele transmission, indicate that fie and mea mutations cause parent-of-origin effects on seed development by distinct mechanisms.

DOI： 10.1105/tpc.12.12.2367

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In flowering plants, two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, which is a tissue that supports embryo development. MEDEA (MEA) encodes an Arabidopsis SET domain Polycomb protein. Inheritance of a maternal loss-of-function mea allele results in embryo abortion and prolonged endosperm production, irrespective of the genotype of the paternal allele. Thus, only the maternal wild-type MEA allele is required for proper embryo and endosperm development. To understand the molecular mechanism responsible for the parent-of-origin effects of mea mutations on seed development, we compared the expression of maternal and paternal MEA alleles in the progeny of crosses between two Arabidopsis ecotypes. Only the maternal MEA mRNA was detected in the endosperm from seeds at the torpedo stage and later. By contrast, expression of both maternal and paternal MEA alleles was observed in the embryo from seeds at the torpedo stage and later, in seedling, leaf, stem, and root. Thus, MEA is an imprinted gene that displays parent-of-origin-dependent monoallelic expression specifically in the endosperm. These results suggest that the embryo abortion observed in mutant mea seeds is due, at least in part, to a defect in endosperm function. Silencing of the paternal MEA allele in the endosperm and the phenotype of mutant mea seeds supports the parental conflict theory for the evolution of imprinting in plants and mammals.

DOI： 10.1105/tpc.11.10.1945

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Vacuolar processing enzyme (VPE) has been shown to be responsible for maturation of various seed proteins in protein-storage vacuoles. Arabidopsis has three VPE homologues; βVPE is specific to seeds and αVPE and γVPE are specific to vegetative organs. To investigate the activity of the vegetative VPE, we expressed the γVPE in a pep4 strain of the yeast Saccharomyces cerevisiae and found that γVPE has the ability to cleave the peptide bond at the carbonyl side of asparagine residues. An immunocytochemical analysis revealed the specific localization of the γVPE in the lytic vacuoles of Arabidopsis leaves that had been treated with wounding. These findings indicate that γVPE functions in the lytic vacuoles as the βVPE does in the protein-storage vacuoles. The βVPE promoter was found to direct the expression of the β-glucuronidase reporter gene in seeds and the root tip of transgenic Arabidopsis plants. On the other hand, both the αVPE and γVPE promoters directed the expression in senescent tissues, but not in young intact tissues. The mRNA levels of both αVPE and γVPE were increased in the primary leaves during senescence in parallel with the increase of the mRNA level of a senescence-associated gene (SAG2). Treatment with wounding, ethylene and salicylic acid up-regulated the expression of αVPE and γVPE, while jasmonate slightly up-regulated the expression of γVPE. These gene expression patterns of the VPEs were associated with the accumulation of vacuolar proteins that are known to respond to these treatments. Taken together, the results suggest that vegetative VPE might regulate the activation of some functional proteins in the lyric vacuoles.

DOI： 10.1046/j.1365-313X.1999.00497.x

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Language：English   Publisher：Japanese Society of Plant Physiologists  

Vacuolar processing enzymes (VPEs) are responsible for the maturation of seed proteins. Southern blot analysis showed that a family of genes for VPEs in Arabidopsis thaliana was composed of three genes, for α-VPE, rβ-VPE and γ-VPE, respectively. The gene for γ-VPE was isolated from a genomic library. It was composed of nine exons and eight introns. The positions of the introns were fully conserved among the three genes, with the exception that the α-VPE gene was missing the fifth intron found in the rβ-VPE and γ-VPE genes. The predicted γ-VPE protein was 80% and 57% identical in terms of amino acid sequence to the α-VPE protein and rβ-VPE protein, respectively. Northern blot analysis demonstrated that the γ-VPE gene was expressed predominantly in the stems, with a lower level of expression in rosette and cauline leaves. However, the expression was not detected in roots, flowers plus buds, or green siliques, in contrast to the high-level expression of the rβ-VPE gene in the flowers plus buds. Thus, γ-VPE seems to be an isoform that is specific to vegetative organs. Members of the VPE family can be separated into two subfamilies, one that is specific to seeds and another that is specific to vegetative organs, such as leaves and stems. The members of the seed subfamily might function in the protein-storage vacuoles of seeds, while those of the vegetative subfamily might function in the lytic vacuoles of non-storage organs. Copyright © 1995. The Japanese Society of Plant Physiologists.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Kluwer Academic Publishers  

Vacuolar processing enzymes (VPEs) are responsible for the maturation of seed proteins. These processing enzymes belong to a novel group of cysteine proteinases with molecular masses of 37 to 39 kDa. We isolated two genes of VPEs from a genomic library of Arabidopsis. The gene products were designated α-VPE and β-VPE, and they were 56% identical in terms of amino acid sequence. The amino acid sequences of α-VPE and β-VPE were also 55% and 67% identical to that of castor bean VPE, respectively. The gene for α-VPE had 7 introns, while that of β-VPE had 8 introns. Northern blot analysis revealed that α-VPE is expressed in rosette leaves, cauline leaves and stems of Arabidopsis, while β-VPE is predominantly expressed in the flowers and buds. Neither α-VPE nor β-VPE is expressed in the siliques. This result strongly suggests that the isolated genes encode isozymes of VPE that are specific to vegetative organs. © 1995 Kluwer Academic Publishers.

DOI： 10.1007/BF00019120

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J-GLOBAL

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Publishing type：Research paper, summary (national, other academic conference)  

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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Language：Japanese   Publishing type：Meeting report  

DOI： 10.1270/jsbbr.19.35

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J-GLOBAL

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J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

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Language：Japanese   Publisher：The Japanese Society of Applied Glycoscience  

DOI： 10.5458/bag.4.3_215

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Language：Japanese   Publisher：The Japanese Society for Chemical Regulation of Plants  

Recent advances in the technologies for developing genetically modified crops have highlighted the importance of epigenetic controls in plants. Several studies have suggested that double-stranded RNA (dsRNA) can induce sequence-specific DNA methylation and silence expression of target genes. Moreover, DNA methylation-mediated gene silencing can be stably transmitted to the next generation without dsRNA trigger constructs. By exploring and elucidating the molecular mechanisms behind these phenomena, we have achieved a greater understanding of epigenetic molecular mechanisms and this knowledge has provided the foundation for new techniques, the so-called New Plant Breeding Techniques (NBT). Further advances in our understanding of the molecular mechanisms of RNA-directed DNA methylation (RdDM) will enable improvements to these new techniques.

DOI： 10.18978/jscrp.48.2_142

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Language：English   Publisher：SPRINGER  

Quantitative trait locus (QTL) analyses have greatly enhanced our understanding of complex traits in rice (Oryza sativa). In parallel, the development of introgression lines has provided a powerful tool for elucidation of complicated genetic networks and identification of QTL. We recently developed a biotron breeding system that allows rapid indoor cultivation of rice plants. The system, however, has two relatively weak points in its application to marker-assisted breeding in rice: first, variation in generation times among cultivars; second, the low number of seeds produced by crosses. To compensate for these weaknesses, we propose utilizing cytoplasmic male sterility (CMS) and restorer (Rf) lines with a cv. Nipponbare genetic background. Through use of the Nipponbare genetic background, rice generation times of 2 months can be achieved regardless of any differences in the genetic background of the donor rice plant. This CMS-Rf system confers a high yield of hybrid seeds, avoids the need for emasculation and precludes accidental crosses. Our results demonstrate that this new methodology can markedly accelerate many different aspects of rice research, especially in functional genomics. The combination of biotron breeding system, early flowering habit and CMS will be of great value for screening candidate genes associated with QTL and for introducing useful QTL into elite cultivars.

DOI： 10.1007/s11032-013-9910-4

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Language：Japanese  

J-GLOBAL

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Language：Japanese   Publisher：日本応用糖質科学会  

CiNii Books

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Language：Japanese  

J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Publishing type：Research paper, summary (national, other academic conference)  

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Language：Japanese  

DOI： 10.1270/jsbbr.14.95

J-GLOBAL

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Language：Japanese  

J-GLOBAL

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Language：Japanese  

J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Language：Japanese  

J-GLOBAL

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Language：Japanese  

CiNii Books

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Language：Japanese  

CiNii Books

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Language：Japanese  

DOI： 10.14841/jspp.2011.0.0238.0

J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Language：Japanese  

J-GLOBAL

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Language：Japanese  

DOI： 10.14841/jspp.2009.0.0421.0

J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Language：Japanese  

J-GLOBAL

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Language：Japanese  

J-GLOBAL

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Language：Japanese   Publisher：植物化学調節学会  

DOI： 10.18978/jscrp.43.1_29

CiNii Books

J-GLOBAL

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Language：Japanese  

DOI： 10.14841/jspp.2008.0.0612.0

J-GLOBAL

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Language：Japanese   Publisher：The Japanese Society of Plant Physiologists  

Defect of the endosperm development is observed in inter-specific crosses of many plant species. Abnormal endosperm development causes seed abortion, therefore, this phenomenon is known to be a reproductive barrier after fertilization. Several reports suggested that defect of endosperm development is caused by the functional difference between parental genome. One of the possible molecular mechanisms underlying this phenomenon can be genomic imprinting, an epigenetic mechanism resulting in mono-allelic gene expression by parent-of-origin dependent manner. Recent advances of the study of genomic imprinting in <I>Arabidopsis</I> are applied to understand the reproductive barrier of hybrid endosperm in rice.<br>To begin with, we analyzed how imprinted genes are involved in the development of hybrid endosperm. We conducted inter-specific cross between cultivated and wild rice and observed developmental defect in the hybrid endosperm. We also investigated the expression of imprinted gene. Possible involvement of genomic imprinting in the hybrid endosperm will be presented.

DOI： 10.14841/jspp.2008.0.0488.0

CiNii Research

J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

Web of Science

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

Web of Science

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Language：Japanese  

CiNii Books

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Language：Japanese  

CiNii Books

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Language：English  

CiNii Books

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Language：English  

CiNii Books

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Language：Japanese  

CiNii Books

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Language：Japanese  

CiNii Books

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Language：English  

CiNii Books

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