Systems seed biology to understand and manipulate rice grain quality and nutrition.

Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.

Methylation profile of imprinted genes provides evidence for teratomatous origin of a subset of mucinous ovarian tumours.

Mucinous ovarian tumours are sometimes associated with mature teratomas. It is suggested that the mucinous tumours in this setting are derived from teratomas, but there remains the possibility of collision or metastasis from extra-ovarian sites. Because mature ovarian teratomas are considered to be parthenogenetic tumours that arise from a single oocyte/ovum, they have only a maternal genome and therefore show maternal genome imprinting. If mucinous ovarian tumours originate from teratomas, their genome imprinting is theoretically maternal. One of the most important mechanisms of genome imprinting is DNA methylation. In the present study, we analysed a total of 28 mucinous ovarian tumours (7 with teratomas, 21 without teratomas; 14 malignant, 14 borderline) to clarify the methylation profiles of their imprinted genes using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) of 21 imprinting control regions (ICRs) of nine imprinted genes/gene clusters using formalin-fixed, paraffin-embedded samples. All cases lacked evidence of an extra-ovarian primary mucinous tumour. In all seven mucinous tumours with teratomas, the overall methylation profile of mucinous tumours was comparable to that of teratomas, although some ICRs showed aberrant methylation. In contrast, all but one of the mucinous tumours without teratomas showed somatic or irregular methylation patterns. Morphologically, there was little teratomatous tissue in some mucinous tumours carrying teratoma-type methylation profiles, suggesting that mucinous tumours overwhelmed ancestral teratomas. In conclusion, the methylation profile of imprinted genes provides evidence that a subset of mucinous ovarian tumours originated from mature teratomas. Genome imprinting-based analysis is a promising strategy to verify the teratomatous origin of human tumours. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

A Genomic Imprinting Model of Termite Caste Determination: Not Genetic but Epigenetic Inheritance Influences Offspring Caste Fate.

Eusocial insects exhibit the most striking example of phenotypic plasticity. There has been a long controversy over the factors determining caste development of individuals in social insects. Here we demonstrate that parental phenotypes influence the social status of offspring not through genetic inheritance but through genomic imprinting in termites. Our extensive field survey and genetic analysis of the termite Reticulitermes speratus show that its breeding system is inconsistent with a genetic caste determination model. We therefore developed a genomic imprinting model, in which queen- and king-specific epigenetic marks antagonistically influence sexual development of offspring. The model accounts for all known empirical data on caste differentiation of R. speratus and other related species. By conducting colony-founding experiments and additively incorporating relevant socio-environmental factors into our genomic imprinting model, we show the relative importance of genomic imprinting and environmental factors in caste determination. The idea of epigenetic inheritance of sexual phenotypes solves the puzzle of why parthenogenetically produced daughters carrying only maternal chromosomes exclusively develop into queens and why parental phenotypes (nymph- or worker-derived reproductives) strongly influence caste differentiation of offspring. According to our model, the worker caste is seen as a "neuter" caste whose sexual development is suppressed due to counterbalanced maternal and paternal imprinting and opens new avenues for understanding the evolution of caste systems in social insects.

Mature and immature ovarian teratomas share methylation profiles of imprinted genes: a MS-MLPA analysis.

Immature teratomas are a subset of ovarian teratomas, and the pathogenic relationship between mature and immature ovarian teratomas is unclear. Mature ovarian teratomas are parthenogenetic tumors that arise from a single oocyte/ovum, whereas the origin of immature ovarian teratomas has not been extensively investigated. Since parthenogenetic tumors contain only maternal genomes, genome imprinting in these tumors usually follows a maternal pattern. DNA methylation is among the most important mechanisms of genome imprinting. Therefore, we analyzed the methylation profile of imprinted genes by performing methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) of 25 imprinting control regions (ICRs) in 10 imprinted genes/gene clusters from formalin-fixed, paraffin-embedded samples obtained from 4 immature ovarian teratomas, 8 mature ovarian teratomas, and 4 ovarian yolk sac tumors (YSTs). Both the immature and mature components showed similar methylation levels in each ICR in immature teratomas. Overall, immature ovarian teratomas showed maternal methylation patterns of imprinted genes in concordance with their parthenogenetic origin. However, they also showed aberrant methylation levels in a few imprinted genes, suggesting that genome imprinting in immature teratomas may partially differ from that in mature teratomas. Microscopic foci of YST were seen in one immature teratoma; the YST component also showed a maternal methylation pattern, unlike the pure YSTs that showed irregular patterns. Thus, teratoma-associated YST and pure YST may have different pathogenic mechanisms.

Long non-coding RNAs: Mechanism of action and functional utility.

Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.

Epigenetic disorders and altered gene expression after use of Assisted Reproductive Technologies in domestic cattle.

The use of Assisted Reproductive Technologies (ARTs) in modern cattle breeding is an important tool for improving the production of dairy and beef cattle. A frequently employed ART in the cattle industry is in vitro production of embryos. However, bovine in vitro produced embryos differ greatly from their in vivo produced counterparts in many facets, including developmental competence. The lower developmental capacity of these embryos could be due to the stress to which the gametes and/or embryos are exposed during in vitro embryo production, specifically ovarian hormonal stimulation, follicular aspiration, oocyte in vitro maturation in hormone supplemented medium, sperm handling, gamete cryopreservation, and culture of embryos. The negative effects of some ARTs on embryo development could, at least partially, be explained by disruption of the physiological epigenetic profile of the gametes and/or embryos. Here, we review the current literature with regard to the putative link between ARTs used in bovine reproduction and epigenetic disorders and changes in the expression profile of embryonic genes. Information on the relationship between reproductive biotechnologies and epigenetic disorders and aberrant gene expression in bovine embryos is limited and novel approaches are needed to explore ways in which ARTs can be improved to avoid epigenetic disorders.

Involvement of IGF2 and H19 imprinting in choriocarcinoma development.

Complete hydatidiform mole is an abnormal pregnancy characterized by grossly swollen villi in the absence of a fetus (Kajii and Ohama 1997, Wake et al., 1978, Jacobs et al., 1980). It is well known that this abnormal pregnancy product is androgenetic in origin. The entire genome of the molar conceptus is paternally derived. The majority of moles result from fertilization of an empty egg by haploid sperm. The paternally derived haploid set then duplicated without cytokinesis and restores diploidy. Invariably, this class of moles has a 46, XX karyotype and is completely homozygous for genetic markers. Fertilization of an empty egg by two sperms is responsible for the remaining case. These moles show a mixture of homozygous and heterozygous patterns of paternally derived genetic markers. Although complete mole is usually a benign process, 10 to 20 percent of cases leads to either invasive mole or choriocarcinoma. This propensity to malignancy has to associate with the genetic features shown in the mole, that imply the formation of homozygosity and the selective inheritance of paternal genome. It has been described in various human malignancies that both genetic features associate with the inactivation of tumor suppressor genes. Homozygosity would lead to the inactivation of tumor suppressor gene in the mole by a signal event occurred on sperm DNAs. In turn, paternal transmission would result in the silencing of particular tumor suppressor genes. Thus, tumor suppressor genes inactivated either by homozygosity formation or by paternal transmission would be involved in the pathogenesis of choriocarcinoma. Both the maternal and paternal genomes are necessary for normal embryonic development in mammals. Parental-origin-specific functional differences between two alleles, known as genomic imprinting, seem to be exploited for a regulatory mechanism crucial for the proper development of both embryonic and extraembryonic tissues. The list of imprinted genes identified is growing rapidly lately in mouse and man (DeChiara TM et al., 1991, Barlow et al., 1991, Bartolomei MS et al., 1991, Leff SE et al., 1992, Hatada I et al., 1993, Giddings SJ et al., 1994, Hayashizaki Y et al., 1994, Villar AJ et al., 1994, Guillemot F et al., 1995). Among these, IGF2 and H19 tightly linked on human chromosome 11 are of special interest because of their reciprocal imprinting and possible association with certain malignancy and congenital abnormalies. The IGF2 gene expressed from the paternally derived allele (Ohlsson et al., 1993, Giannoukalis et al., 1993), whereas the H19 gene is expressed from the maternally derived allele (Rachmilewitz et al., 1992, Zhang et al 1993, Ferguson-Smith et al., 1993).