scholarly journals Characterization of imprinted genes in rice reveals post-fertilization regulation and conservation at some loci of imprinting in plant species

2017 ◽  
Author(s):  
Chen Chen ◽  
Tingting Li ◽  
Shan Zhu ◽  
Zehou Liu ◽  
Zhenyuan Shi ◽  
...  
Keyword(s):  
Plant Species ◽  
Genomic Imprinting ◽  
Biological Significance ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Dependent Manner ◽  
Cultivated Rice ◽  
Parental Allele ◽  
Intraspecific Variations ◽  
High Level

AbstractGenomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings inArabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.

scholarly journals Genomic imprinting and the social brain

2006 ◽  
Vol 361 (1476) ◽  
pp. 2229-2237 ◽  
Author(s):  
Anthony R Isles ◽  
William Davies ◽  
Lawrence S Wilkinson
Keyword(s):  
Genomic Imprinting ◽  
Parental Investment ◽  
Social Groups ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Epigenetic Mark ◽  
Parental Allele ◽  
Intragenomic Conflict ◽  
Starting Point ◽  
The Social

Genomic imprinting refers to the parent-of-origin-specific epigenetic marking of a number of genes. This epigenetic mark leads to a bias in expression between maternally and paternally inherited imprinted genes, that in some cases results in monoallelic expression from one parental allele. Genomic imprinting is often thought to have evolved as a consequence of the intragenomic conflict between the parental alleles that occurs whenever there is an asymmetry of relatedness. The two main examples of asymmetry of relatedness are when there is partiality of parental investment in offspring (as is the case for placental mammals, where there is also the possibility of extended postnatal care by one parent), and in social groups where there is a sex-biased dispersal. From this evolutionary starting point, it is predicted that, at the behavioural level, imprinted genes will influence what can broadly be termed bonding and social behaviour. We examine the animal and human literature for examples of imprinted genes mediating these behaviours, and divide them into two general classes. Firstly, mother–offspring interactions (suckling, attachment and maternal behaviours) that are predicted to occur when partiality in parental investment in early postnatal offspring occurs; and secondly, adult social interactions, when there is an asymmetry of relatedness in social groups. Finally, we return to the evolutionary theory and examine whether there is a pattern of behavioural functions mediated by imprinted genes emerging from the limited data, and also whether any tangible predictions can be made with regards to the direction of action of genes of maternal or paternal origin.

scholarly journals The influence of DNA methylation on monoallelic expression

2019 ◽  
Vol 63 (6) ◽  
pp. 663-676 ◽  
Author(s):  
Simão Teixeira da Rocha ◽  
Anne-Valerie Gendrel
Keyword(s):  
Dna Methylation ◽  
Expression Patterns ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Dependent Manner ◽  
Epigenetic Mechanisms ◽  
Cpg Sites ◽  
Mammalian Genomes ◽  
Parent Of Origin ◽  
Diploid Cells

Abstract Monoallelic gene expression occurs in diploid cells when only one of the two alleles of a gene is active. There are three main classes of genes that display monoallelic expression in mammalian genomes: (1) imprinted genes that are monoallelically expressed in a parent-of-origin dependent manner; (2) X-linked genes that undergo random X-chromosome inactivation in female cells; (3) random monoallelically expressed single and clustered genes located on autosomes. The heritability of monoallelic expression patterns during cell divisions implies that epigenetic mechanisms are involved in the cellular memory of these expression states. Among these, methylation of CpG sites on DNA is one of the best described modification to explain somatic inheritance. Here, we discuss the relevance of DNA methylation for the establishment and maintenance of monoallelic expression patterns among these three groups of genes, and how this is intrinsically linked to development and cellular states.

270 IN VITRO MATURATION ALTERS THE EXPRESSION OF SPECIFIC PUTATIVELY IMPRINTED GENES IN BOVINE MII OOCYTES

2007 ◽  
Vol 19 (1) ◽  
pp. 251
Author(s):  
M. G. Katz-Jaffe ◽  
B. R. McCallie ◽  
K. Preis ◽  
G. E. Seidel ◽  
D. K. Gardner
Keyword(s):  
Genomic Imprinting ◽  
In Vitro Maturation ◽  
Expression Profiles ◽  
Housekeeping Gene ◽  
Control Individual ◽  
Imprinted Genes ◽  
Parental Allele ◽  
Regulation Of Growth

Genomic imprinting is an epigenetic form of gene regulation resulting in only one parental allele being expressed. Imprinted genes have diverse functions including the regulation of growth and development in mammals. Errors in genomic imprinting have been associated with human disease (e.g. Beckwith-Wiedemann Syndrome) and large offspring syndrome of in vitro-produced ruminant fetuses. The aim of this study was to investigate the effect of in vitro maturation (IVM) on the expression of specific putatively imprinted genes in the bovine oocyte. Cumulus-enclosed immature oocytes were collected from cattle after 6 injections of 50 mg FSH with transvaginal aspiration (TVA) performed 48 h post-final FSH injection. The oocytes were cultured in groups of 10 for 23 h in a defined maturation medium (G-Mat) with 5 mg of HSA and 100 ng mL-1 of epidermal growth factor (EGF; group A) or with 20% serum and 100 ng mL-1 of EGF (group B) at 38.5�C in 6% CO2 in air. In vivo-matured oocytes (group C) were also collected via TVA after the administration of 6 FSH injections (50 mg), prostaglandin (PG) with last FSH injection, and GnRH 37 h post-PG. Total RNA was extracted from individual MII oocytes in all 3 groups, and expression profiles of putatively imprinted genes (Igf2r, Peg3, and Snrpn) were assayed by real-time PCR (Roche Applied Biosciences, Indianapolis, IN, USA), relative to the housekeeping gene GAPDH. Statistical analysis of expression profiles was performed using REST software. Expression of the Igf2r and Peg3 putatively imprinted genes was significantly up-regulated in individual in vitro-matured MII oocytes (groups A and B, n = 5 replicates per group) when compared with control, individual in vivo-matured MII oocytes (group C, n = 5 replicates; P < 0.05). Gene expression did not differ between in vitro- and in vivo-matured MII oocytes for the putatively imprinted gene, Snrpn. In conclusion, following in vitro maturation of bovine oocytes, the putatively imprinted genes Igf2r and Peg3 were aberrantly expressed in individual oocytes relative to in vivo controls. Both of these putatively imprinted genes have been implicated in the regulation of growth and apoptotic pathways during mammalian development. Analysis of such putatively imprinted genes will facilitate the development of more suitable oocyte maturation conditions. This research was supported by the Serono Research Institute.

Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells

Development ◽  
2002 ◽  
Vol 129 (8) ◽  
pp. 1807-1817 ◽  
Author(s):  
Jiyoung Lee ◽  
Kimiko Inoue ◽  
Ryuichi Ono ◽  
Narumi Ogonuki ◽  
Takashi Kohda ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Nuclear Transfer ◽  
Monoallelic Expression ◽  
Parental Origin ◽  
Imprinted Genes ◽  
Specific Expression ◽  
Male And Female ◽  
Imprinted Gene ◽  
Methylation Patterns

Genomic imprinting is an epigenetic mechanism that causes functional differences between paternal and maternal genomes, and plays an essential role in mammalian development. Stage-specific changes in the DNA methylation patterns of imprinted genes suggest that their imprints are erased some time during the primordial germ cell (PGC) stage, before their gametic patterns are re-established during gametogenesis according to the sex of individuals. To define the exact timing and pattern of the erasure process, we have analyzed parental-origin-specific expression of imprinted genes and DNA methylation patterns of differentially methylated regions (DMRs) in embryos, each derived from a single day 11.5 to day 13.5 PGC by nuclear transfer. Cloned embryos produced from day 12.5 to day 13.5 PGCs showed growth retardation and early embryonic lethality around day 9.5. Imprinted genes lost their parental-origin-specific expression patterns completely and became biallelic or silenced. We confirmed that clones derived from both male and female PGCs gave the same result, demonstrating the existence of a common default state of genomic imprinting to male and female germlines. When we produced clone embryos from day 11.5 PGCs, their development was significantly improved, allowing them to survive until at least the day 11.5 embryonic stage. Interestingly, several intermediate states of genomic imprinting between somatic cell states and the default states were seen in these embryos. Loss of the monoallelic expression of imprinted genes proceeded in a step-wise manner coordinated specifically for each imprinted gene. DNA demethylation of the DMRs of the imprinted genes in exact accordance with the loss of their imprinted monoallelic expression was also observed. Analysis of DNA methylation in day 10.5 to day 12.5 PGCs demonstrated that PGC clones represented the DNA methylation status of donor PGCs well. These findings provide strong evidence that the erasure process of genomic imprinting memory proceeds in the day 10.5 to day 11.5 PGCs, with the timing precisely controlled for each imprinted gene. The nuclear transfer technique enabled us to analyze the imprinting status of each PGC and clearly demonstrated a close relationship between expression and DNA methylation patterns and the ability of imprinted genes to support development.

Putative imprinted gene expression in uniparental bovine embryo models

2008 ◽  
Vol 20 (5) ◽  
pp. 589 ◽  
Author(s):  
Nancy T. D' Cruz ◽  
Katrina J. Wilson ◽  
Melissa A. Cooney ◽  
R. Tayfur Tecirlioglu ◽  
Irina Lagutina ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Monoallelic Expression ◽  
Cell Physiology ◽  
Imprinted Genes ◽  
Bovine Embryo ◽  
Dependent Manner ◽  
Abnormal Growth

Altered patterns of gene expression and the imprinted status of genes have a profound effect on cell physiology and can markedly alter embryonic and fetal development. Failure to maintain correct imprinting patterns can lead to abnormal growth and behavioural problems, or to early pregnancy loss. Recently, it has been reported that the Igf2R and Grb10 genes are biallelically expressed in sheep blastocysts, but monoallelically expressed at Day 21 of development. The present study investigated the imprinting status of 17 genes in in vivo, parthenogenetic and androgenetic bovine blastocysts in order to determine the prevalence of this unique phenomenon. Specifically, the putatively imprinted genes Ata3, Impact, L3Mbtl, Magel2, Mkrn3, Peg3, Snrpn, Ube3a and Zac1 were investigated for the first time in bovine in vitro fertilised embryos. Ata3 was the only gene not detected. The results of the present study revealed that all genes, except Xist, failed to display monoallelic expression patterns in bovine embryos and support recent results reported for ovine embryos. Collectively, the data suggest that monoallelic expression may not be required for most imprinted genes during preimplantation development, especially in ruminants. The research also suggests that monoallelic expression of genes may develop in a gene- and time-dependent manner.

scholarly journals Genomic imprinting and cancer: Remembering the parental origin

2010 ◽  
Vol 32 (5) ◽  
pp. 26-29
Author(s):  
Adele Murrell ◽  
Santiago Uribe-Lewis
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Histone Modifications ◽  
Germ Cells ◽  
Parental Origin ◽  
Imprinted Genes ◽  
Parental Allele ◽  
Paternal Line ◽  
Specific Manner ◽  
Parental Copy

Genomic imprinting results in only one copy of a diploid pair of alleles being expressed in a parentof-origin-specific manner. The ‘imprint’ encodes a memory of whether a gene came through the maternal or paternal line and contains the information that decides which parental copy will be active or silent. Imprints are established in the developing gametes, passed on to the next generation after fertilization where they are read and maintained in the somatic cells or erased and reset in the germ cells. The components of the ‘memory’ are a combination of epigenetic features such as DNA methylation, post-translational histone modifications and protein/RNA factors that can bind to DNA and label the genes such that a cell's transcription machinery can distinguish between maternal and paternal alleles. Most imprinted genes are associated with sequences that are methylated on only one parental allele, known as differentially methylated regions (DMRs).

scholarly journals A Comprehensive Overview of Genomic Imprinting in Breast & Its Deregulation in Cancer

2018 ◽  
Author(s):  
Tine Goovaerts ◽  
Sandra Steyaert ◽  
Chari A Vandenbussche ◽  
Jeroen Galle ◽  
Olivier Thas ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genomic Imprinting ◽  
Significant Loss ◽  
Dna Demethylation ◽  
Distribution Model ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Comprehensive Overview ◽  
Loss Of Imprinting ◽  
A Genome

ABSTRACTGenomic imprinting, the parent-of-origin specific monoallelic expression of genes, plays an important role in growth and development. Loss of imprinting of individual genes has been found in varying cancers, yet data-analytical challenges have impeded systematic studies so far. We developed a mixture distribution model to detect monoallelically expressed loci in a genome-wide manner without the need for genotyping data, and applied the methodology on TCGA breast tissue RNA-seq data. We identified 35 putatively imprinted genes in healthy breast. In breast cancer however, HM13 was featured by significant loss of imprinting and expression upregulation, which could be linked to DNA demethylation. Other imprinted genes (25 out of 35) demonstrated consistent expression downregulation in breast cancer, which often correlated with loss of imprinting. A breast imprinted gene network, deregulated in cancer, might hence be present. In summary, our novel methodology highlights the massive deregulation of imprinting in breast cancer.

scholarly journals Smchd1 is a maternal effect gene required for genomic imprinting

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Iromi Wanigasuriya ◽  
Quentin Gouil ◽  
Sarah A Kinkel ◽  
Andrés Tapia del Fierro ◽  
Tamara Beck ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Maternal Effect ◽  
Imprinted Genes ◽  
Parental Allele ◽  
Maternal Effect Gene ◽  
Parent Of Origin ◽  
Mammalian Genes ◽  
Dose Dependent ◽  
Dose Dependent Effect ◽  
Effect Gene

Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor Smchd1 as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice. We also found zygotic SMCHD1 had a dose-dependent effect on the imprinted expression of seven genes. Together, zygotic and maternal SMCHD1 regulate three classic imprinted clusters and eight other genes, including non-canonical imprinted genes. Interestingly, the loss of maternal SMCHD1 does not alter germline DNA methylation imprints pre-implantation or later in gestation. Instead, what appears to unite most imprinted genes sensitive to SMCHD1 is their reliance on polycomb-mediated methylation as germline or secondary imprints, therefore we propose that SMCHD1 acts downstream of polycomb imprints to mediate its function.

scholarly journals Evolution of viviparity in mammals: what genomic imprinting tells us about mammalian placental evolution

2019 ◽  
Vol 31 (7) ◽  
pp. 1219 ◽  
Author(s):  
Tomoko Kaneko-Ishino ◽  
Fumitoshi Ishino
Keyword(s):  
Oxygen Concentration ◽  
Genomic Imprinting ◽  
Atmospheric Oxygen ◽  
Epigenetic Mechanism ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Low Oxygen ◽  
Exogenous Dna ◽  
A Genome ◽  
Key Factor

Genomic imprinting is an epigenetic mechanism of regulating parent-of-origin-specific monoallelic expression of imprinted genes in viviparous therian mammals such as eutherians and marsupials. In this review we discuss several issues concerning the relationship between mammalian viviparity and genomic imprinting, as well as the domestication of essential placental genes: why has the genomic imprinting mechanism been so widely conserved despite the evident developmental disadvantages originating from monoallelic expression? How have genomic imprinted regions been established in the course of mammalian evolution? What drove the evolution of mammalian viviparity and how have genomic imprinting and domesticated genes contributed to this process? In considering the regulatory mechanism of imprinted genes, reciprocal expression of paternally and maternally expressed genes (PEGs and MEGs respectively) and the presence of several essential imprinted genes for placental formation and maintenance, it is likely that complementary, thereby monoallelic, expression of PEGs and MEGs is an evolutionary trade-off for survival. The innovation in novel imprinted regions was associated with the emergence of imprinting control regions, suggesting that genomic imprinting arose as a genome defence mechanism against the insertion of exogenous DNA. Mammalian viviparity emerged in the period when the atmospheric oxygen concentration was the lowest (~12%) during the last 550 million years (the Phanerozoic eon), implying this low oxygen concentration was a key factor in promoting mammalian viviparity as a response to a major evolutionary pressure. Because genomic imprinting and gene domestication from retrotransposons or retroviruses are effective measures of changing genomic function in therian mammals, they are likely to play critical roles in the emergence of viviparity for longer gestation periods.

scholarly journals Leaf-derived ABA regulates rice seed development via a transporter-mediated and temperature-sensitive mechanism

2021 ◽  
Vol 7 (3) ◽  
pp. eabc8873
Author(s):  
Peng Qin ◽  
Guohua Zhang ◽  
Binhua Hu ◽  
Jie Wu ◽  
Weilan Chen ◽  
...  
Keyword(s):  
Seed Development ◽  
Starch Synthesis ◽  
Biological Significance ◽  
Grain Filling ◽  
Temperature Sensitive ◽  
Rice Seed ◽  
Dependent Manner ◽  
Long Distance ◽  
Long Distance Transport ◽  
Mechanistic Basis

Long-distance transport of the phytohormone abscisic acid (ABA) has been studied for ~50 years, yet its mechanistic basis and biological significance remain very poorly understood. Here, we show that leaf-derived ABA controls rice seed development in a temperature-dependent manner and is regulated by defective grain-filling 1 (DG1), a multidrug and toxic compound extrusion transporter that effluxes ABA at nodes and rachilla. Specifically, ABA is biosynthesized in both WT and dg1 leaves, but only WT caryopses accumulate leaf-derived ABA. Our demonstration that leaf-derived ABA activates starch synthesis genes explains the incompletely filled and floury seed phenotypes in dg1. Both the DG1-mediated long-distance ABA transport efficiency and grain-filling phenotypes are temperature sensitive. Moreover, we extended these mechanistic insights to other cereals by observing similar grain-filling defects in a maize DG1 ortholog mutant. Our study demonstrates that rice uses a leaf-to-caryopsis ABA transport–based mechanism to ensure normal seed development in response to variable temperatures.

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