When genomes collide: aberrant seed development following maize interploidy crosses

Background and Aims: The results of wide- or interploidy crosses in angiosperms areunpredictable and often lead to seed abortion. The consequencesof reciprocal interploidy crosses have been explored in maizein detail, focusing on alterations to tissue domains in themaize endosperm, and changes in endosperm-specific gene expression. Methods: Following reciprocal interploidy crosses between diploid andtetraploid maize lines, development of endosperm domains wasstudied using GUS reporter lines, and gene expression in resultingkernels was investigated using semi-quantitative RT-PCR on endospermsisolated at different stages of development. Key Results: Reciprocal interploidy crosses result in very small, largelyinfertile seeds with defective endosperms. Seeds with maternalgenomic excess are smaller than those with paternal genomicexcess, their endosperms cellularize earlier and they accumulatesignificant quantities of starch. Endosperms from the reciprocalcross undergo an extended period of cell proliferation, andaccumulate little starch. Analysis of reporter lines and geneexpression studies confirm that functional domains of the endospermare severely disrupted, and are modified differently accordingto the direction of the interploidy cross. Conclusions: Interploidy crosses affect factors which regulate the balancebetween cell proliferation and cell differentiation within theendosperm. In particular, unbalanced crosses in maize affecttransfer cell differentiation, and lead to the temporal deregulationof the ontogenic programme of endosperm development.     

Cell cycle progression during endosperm development in Zea mays depends on parental dosage effects

Interploidy crosses in flowering plants often cause seed abortion. Studies in maize have shown that failure of kernel development results from dosage effects among products of imprinted but as-yet-unknown genes in the endosperm, and that the operative stoichiometry is established for a ratio of two maternal genomes to one paternal genome. In this study, we used flow cytometry to monitor cell cycle activities in developing endosperms obtained after reciprocal crosses between diploid and tetraploid maize individuals. Our data show that dosage effects alter critical events involved in the establishment of endoreduplication during maize endosperm development. Particularly, maternal genomic excess (4x x 2x crosses) forces endosperm cells to enter early into endoreduplication while paternal genomic excess (2x x 4x crosses) prevents its establishment. Our results also suggest that altering mechanisms depend on two different sets of cell cycle regulatory genes--one imprinted through the female that is required for mitotic arrest, and another responsible for re-entry into S phase that is imprinted through the male. Further, molecular and physiological analyses should provide insights into the interaction of parental imprinting action and cell cycle regulation during endosperm development.     

Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm

Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome‐wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular‐type endosperm development are lacking. Using laser‐assisted microdissection, we characterized parent‐specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear‐type endosperm. Forty‐two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression‐level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular‐ and nuclear‐type endosperm.     

Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax

Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.     

Genomic imprinting in mammals-epigenetic parental memories

Genomic imprinting is an epigenetic phenomenon that brings the difference of expression between paternally or maternally derived alleles and is specific for mammals in vertebrates. This imprint is established in the parental germlines and then inherited to the next generation to regulate expression of imprinted genes that are essential to support proper embryonic development. More than one hundred imprinted genes have been identified in mice and humans. Some are essential for embryonic development, especially placental formation, and others regulate metabolism, behavior and physiological functions. In humans, disruption of genomic imprinting causes several diseases, including cancer. Recently, the molecular mechanisms of genomic imprinting are getting clarified. How do parents regulate gene expression of their children? Why and how is genomic imprinting evolved in mammals? The review offers a handful of recent progress in this area.     

Balance between maternal and paternal alleles sets the timing of resource accumulation in the maize endosperm

Key aspects of seed development in flowering plants are held to be under epigenetic control and to have evolved as a result of conflict between the interests of the male and female gametes (kinship theory). Attempts to identify the genes involved have focused on imprinted sequences, although imprinting is only one mechanism by which male or female parental alleles may be exclusively expressed immediately post-fertilization. We have studied the expression of a subset of endosperm gene classes immediately following interploidy crosses in maize and show that departure from the normal 2 : 1 ratio between female and male genomes exerts a dramatic effect on the timing of expression of some, but not all, genes investigated. Paternal genomic excess prolongs the expression of early genes and delays accumulation of reserves, while maternal genomic excess foreshortens the expression period of early genes and dramatically brings forward endosperm maturation. Our data point to a striking interdependence between the phases of endosperm development, and are consonant with previous work from maize showing progression from cell proliferation to endoreduplication is regulated by the balance between maternal and paternal genomes, and from Arabidopsis suggesting that this ‘phasing’ is regulated by maternally expressed imprinted genes. Our findings are discussed in context of the kinship theory.     

Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division

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.     

DNA methylation and imprinting in plants: machinery and mechanisms

Imprinting is an epigenetic phenomenon in which genes are expressed selectively from either the maternal or paternal alleles. In plants, imprinted gene expression is found in a tissue called the endosperm. Imprinting is often set by a unique epigenomic configuration in which the maternal chromosomes are less DNA methylated than their paternal counterparts. In this review, we synthesize studies that paint a detailed molecular portrait of the distinctive endosperm methylome. We will also discuss the molecular machinery that shapes and modifies this methylome, and the role of DNA methylation in imprinting.     

Reproductive barrier and genomic imprinting in the endosperm of flowering plants

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.     

Autonomous endosperm development in flowering plants: how to overcome the imprinting problem?

In the vast majority of sexually reproducing flowering plants, a ratio of 2 maternally derived genomes to 1 paternally derived genome (2m:1p) is essential for normal endosperm development, and therefore ultimately for seed development. Even in many pseudogamous apomicts, where the embryo develops without a paternal contribution, fertilisation of the endosperm to obtain the correct 2m:1p parental ratio is still necessary. How do autonomous apomicts, where both embryo and endosperm develop autonomously, circumvent this requirement? The background for the 2m:1p requirement is that the parental genomes are epigenetically different; in either genome, a set of genes is silenced in a sex-specific way by genomic imprinting. Removal of the imprints from the maternally derived endosperm genome leads to expression of normally maternally silenced genes, and effectively supplies the missing paternal genome. In Arabidopsis, we propose that a combination of the fie mutation and hypomethylation of the genome creates such a situation in the endosperm genome. As a result, in a fie mutant, hypomethylated ovule complete autonomous endosperm development takes place in the absence of fertilisation.     

Genomic imprinting and mammalian reproduction

Among animals, genomic imprinting is a uniquely mammalian phenomenon in which certain genes are monoallelically expressed according to their parent of origin. This silencing of certain alleles often involves differential methylation at regulatory regions associated with imprinted genes and must be recapitulated at every generation with the erasure and reapplication of these epigenetic marks in the germline. Imprinted genes encode regulatory proteins that play key roles in fetal growth and development, but they also exert wider effects on mammalian reproduction. Genetic knockout experiments have shown that certain paternally expressed imprinted genes regulate post-natal behavior in offspring as well as reproductive behaviors in males and females. These deficits involve changes in hypothalamic function affecting multiple areas and different neurochemical pathways. Paternally expressed genes are highly expressed in the hypothalamus which regulates growth, metabolism and reproduction and so are well placed to influence all aspects of reproduction from adults to the resultant offspring. Coadaptation between offspring and mother appears to have played an important role in the evolution of some paternally expressed genes, but the influence of these genes on male reproductive behavior also suggests that they have evolved to regulate their own transmission to successive generations via the male germline.     

Aberrant endosperm development in interploidy crosses reveals a timer of differentiation

The common assumption that the seed failure in interploidy crosses of flowering plants is due to parental genomic imprinting is based on vague interpretations and needs reevaluation since the general question is involved, how differentiation is timed so that cell progenies, while specializing, pass through proper numbers of amplification divisions before proliferation ceases. As recently confirmed, endosperm differentiation is accelerated or de-accelerated, depending upon whether polyploid females are crossed with diploid males, or vice-versa. Unlike the zygote, the first cell of the endosperm is determined to produce a tissue that successively induces growth of maternal tissues, stimulates and nourishes the embryo, and finally ceases cell cycling. Altered timing of endosperm differentiation, thus, perturbs seed development. During fertilization, only the female genomes contribute cytoplasmic equivalents to endosperm development so that in interploidy crosses, the initial amount of cytoplasm per chromosome set is altered, and due to semi-autonomy of cytoplasmic growth, altered numbers of division cycles are needed to provide the amount of cytoplasmic organelles required for differentiation. Cytoplasmic semi-autonomy and dependence of differentiation on an increase in cytoplasm has been shown in other tissues of plants and animals, thus, revealing a common mechanism for intracellular timing of differentiation. As demonstrated, imprinted genes can alter the extent of cell proliferation by interfering with this mechanism.     

漆树胚,胚乳发育及花果生长的相关性研究

漆树为倒生胚珠,双珠被,厚珠心,具承珠盘及拟珠孔塞,胚囊发育为蓼型,核型胚乳,胚发育为柳叶菜型,后历经棒状形胚、心形胚、鱼雷形胚和成熟胚各期。花和果实生长与胚及胚乳发育有密切的相关性,胚内具原始的乳汁道系统为重要特征。一些胚珠内无胚或胚乳早期退化引起胚败育是造成种子空籽原因之一。     

Genomic imprinting in plants: observations and evolutionary implications

The epigenetic phenomenon of genomic imprinting occurs among both plants and animals. In species where imprinting is observed, there are parent-of-origin effects on the expression of imprinted genes in offspring. This review focuses on imprinting in plants with examples from maize, where gene imprinting was first described, and Arabidopsis. Our current understanding of imprinting in plants is presented in the context of cytosine methylation and imprinting in mammals, where developmentally essential genes are imprinted. Important considerations include the structure and organization of imprinted genes and the role of regional, differential methylation. Imprinting in plants may be related to other epigenetic phenomena including paramutation and transgene silencing. Finally, we discuss the role of gene structure and evolutionary implications of imprinting in plants.     

西瓜胚和胚乳的发育

应用显微技术对西瓜胚和胚乳的发育过程进行了观察并分析了西瓜胚珠败育的原因。西瓜胚发育属紫菀型。合子第一次分裂为不均等分裂 ,形成的基细胞体积明显较顶细胞大 ,两细胞均含有多个液泡。原胚发育过程中没有明显的胚柄。最外层的原胚细胞 ,与胚乳细胞相邻的壁上被胼胝质物质包围 ,且无外连丝存在 ;与胚囊壁相接的壁上无壁内突结构。胚的子叶体积增长的同时 ,子叶细胞内积累蛋白质和脂类物质 ,多糖物质的含量下降。胚乳发育属核型 ,在球形胚期开始自珠孔端向合点端细胞化 ,胚子叶分化出后开始自珠孔端向合点端退化。胚乳合点端在球形胚早期形成发达的胚乳吸器 ,开始呈游离核状态 ,后细胞化 ,在心型胚期之后退化。     

Histone H1 affects gene imprinting and DNA methylation in Arabidopsis

Imprinting, i.e. parent-of-origin expression of alleles, plays an important role in regulating development in mammals and plants. DNA methylation catalyzed by DNA methyltransferases plays a pivotal role in regulating imprinting by silencing parental alleles. DEMETER (DME), a DNA glycosylase functioning in the base-excision DNA repair pathway, can excise 5-methylcytosine from DNA and regulate genomic imprinting in Arabidopsis. DME demethylates the maternal MEDEA (MEA) promoter in endosperm, resulting in expression of the maternal MEA allele. However, it is not known whether DME interacts with other proteins in regulating gene imprinting. Here we report the identification of histone H1.2 as a DME-interacting protein in a yeast two-hybrid screen, and confirmation of their interaction by the in vitro pull-down assay. Genetic analysis of the loss-of-function histone h1 mutant showed that the maternal histone H1 allele is required for DME regulation of MEA, FWA and FIS2 imprinting in Arabidopsis endosperm but the paternal allele is dispensable. Furthermore, we show that mutations in histone H1 result in an increase of DNA methylation in the maternal MEA and FWA promoter in endosperm. Our results suggest that histone H1 is involved in DME-mediated DNA methylation and gene regulation at imprinted loci.     

Genomic imprinting in the development and evolution of psychotic spectrum conditions

I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader‐Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith‐Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted‐gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively‐slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting.     

基因组印迹的起动与沉默

在配子中基因组印迹起动复合物的结合引发印迹现象,印迹起动复合物中有多种可鉴定成分,存在结合的精确时间和机制,印迹起动复合物似乎仅出现在生殖细胞系,而甲基CpG结合蛋白则能延续增殖印迹,因此基因组印迹调节着发育基因或组织特异性单等位基因的瞬时表达及大染色体结构域中基因之间的相互作用 。     

Genomic imprinting and chromatin insulation in beckwith-wiedemann syndrome

Genes are recognized as undergoing genomic imprinting when they are capable of being expressed only from the paternal or only from the maternal chromosome. The process can occur coordinately within large physical domains in mammalian chromosomes. One interesting facet of the study of genomic imprinting is that it offers insight into the regulation of large chromosomal regions. Understanding this regulation involves elucidating the cis-acting regulators of gene expression and defining the elements that maintain chromatin insulation, both required for understanding more practically applicable areas of biological research, such as efficient transgene production. This review is focused on the regulation of the imprinted domain of human chromosome 11p15.5, responsible for Beckwith-Wiedemann syndrome (BWS). Recent findings indicate that the maintenance of imprinting within this domain is critically dependent on the stable maintenance of chromatin insulation.