scholarly journals DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana

2018 ◽  
Vol 115 (42) ◽  
pp. E9962-E9970 ◽  
Author(s):  
Haifeng Zhu ◽  
Wenxiang Xie ◽  
Dachao Xu ◽  
Daisuke Miki ◽  
Kai Tang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Seed Dormancy ◽  
Genomic Imprinting ◽  
Dna Demethylation ◽  
Paternal Allele ◽  
Maternal Allele ◽  
Imprinted Gene ◽  
Differential Gene ◽  
Parent Of Origin ◽  
Dna Demethylase

Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4. DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4. Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.

scholarly journals Genomic imprinting and its role in ethiology of human hereditary diseases

2004 ◽  
Vol 3 (3) ◽  
pp. 8-17
Author(s):  
S. A. Nazarenko
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Special Class ◽  
Growth And Development ◽  
Epigenetic Inheritance ◽  
Hereditary Diseases ◽  
Parental Origin ◽  
Imprinted Genes ◽  
Methylation Of Dna ◽  
Differential Gene

Genomic imprinting is a form of non-Mendelian epigenetic inheritance that is defined by differential gene expression depending on its parental origin — maternal or paternal. It is known about 60 imprinted genes many of which effect significantly on the fetus growth and development. Methylation of DNA cytosine bases that defines the interaction of DNA and proteins identifying the modified bases and controls the gene expression through chromatin compacting-decompacting mechanism, is a main epigenetic genom modifier. Disturbances in monoallelic gene expression lead to the development of a special class of human hereditary diseases — genomic imprinting diseases.

scholarly journals The discovery and importance of genomic imprinting

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Anne C Ferguson-Smith ◽  
Deborah Bourchis
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Genetic Disorders ◽  
Epigenetic Inheritance ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Epigenetic Control ◽  
International Award ◽  
Parent Of Origin ◽  
Shed Light

The discovery of genomic imprinting by Davor Solter, Azim Surani and co-workers in the mid-1980s has provided a foundation for the study of epigenetic inheritance and the epigenetic control of gene activity and repression, especially during development. It also has shed light on a range of diseases, including both rare genetic disorders and common diseases. This article is being published to celebrate Solter and Surani receiving a 2018 Canada Gairdner International Award "for the discovery of mammalian genomic imprinting that causes parent-of-origin specific gene expression and its consequences for development and disease".

scholarly journals Parent-of-origin effects, allele-specific expression, genomic imprinting and paternal manipulation in social insects

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Benjamin P. Oldroyd ◽  
Boris Yagound
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Social Insects ◽  
Social Insect ◽  
Specific Gene ◽  
Specific Expression ◽  
Rna Molecules ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Gene Expression Studies

Haplo-diploidy and the relatedness asymmetries it generates mean that social insects are prime candidates for the evolution of genomic imprinting. In single-mating social insect species, some genes may be selected to evolve genomic mechanisms that enhance reproduction by workers when they are inherited from a female. This situation reverses in multiple mating species, where genes inherited from fathers can be under selection to enhance the reproductive success of daughters. Reciprocal crosses between subspecies of honeybees have shown strong parent-of-origin effects on worker reproductive phenotypes, and this could be evidence of such genomic imprinting affecting genes related to worker reproduction. It is also possible that social insect fathers directly affect gene expression in their daughters, for example, by placing small interfering RNA molecules in semen. Gene expression studies have repeatedly found evidence of parent-specific gene expression in social insects, but it is unclear at this time whether this arises from genomic imprinting, paternal manipulation, an artefact of cyto-nuclear interactions, or all of these. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

scholarly journals Chasing the Apomictic Factors in the Ranunculus auricomus Complex: Exploring Gene Expression Patterns in Microdissected Sexual and Apomictic Ovules

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 728 ◽  
Author(s):  
Marco Pellino ◽  
Diego Hojsgaard ◽  
Elvira Hörandl ◽  
Timothy F. Sharbel
Keyword(s):  
Gene Expression ◽  
Asexual Reproduction ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Dominant Factor ◽  
Gene Expression Patterns ◽  
Future Studies ◽  
Dosage Effects ◽  
Differential Gene ◽  
Parent Of Origin

Apomixis, the asexual reproduction via seeds, is associated to polyploidy and hybridization. To identify possible signatures of apomixis, and possible candidate genes underlying the shift from sex to apomixis, microarray-based gene expression patterns of live microdissected ovules at four different developmental stages were compared between apomictic and sexual individuals of the Ranunculus auricomus complex. Following predictions from previous work on mechanisms underlying apomixis penetrance and expressivity in the genus, gene expression patterns were classified into three categories based on their relative expression in apomicts compared to their sexual parental ancestors. We found evidence of misregulation and differential gene expression between apomicts and sexuals, with the highest number of differences detected during meiosis progression and emergence of aposporous initial (AI) cells, a key developmental stage in the ovule of apomicts where a decision between divergent reproductive pathways takes place. While most of the differentially expressed genes (DEGs) could not be annotated, gene expression was classified into transgressive, parent of origin and ploidy effects. Genes related to gametogenesis and meiosis demonstrated patterns reflective of transgressive and genome dosage effects, which support the hypothesis of a dominant factor controlling apomixis in Ranunculus and modulated by secondary modifiers. Three genes with probable functions in sporogenesis and gametogenesis development are identified and characterized for future studies.

20 NUCLEAR TRANSFER ALTERS EXPRESSION AND HISTONE MODIFICATIONS OF THE IMPRINTED GENE PHLDA2 IN THE BOVINE PLACENTA

2015 ◽  
Vol 27 (1) ◽  
pp. 102
Author(s):  
J. C. T. Penteado ◽  
D. R. Arnold ◽  
R. C. Gaspar ◽  
C. V. da Rocha ◽  
J. R. Sangalli ◽  
...  
Keyword(s):  
Gene Expression ◽  
In Vitro Fertilization ◽  
Promoter Region ◽  
Nuclear Transfer ◽  
Proximal Promoter ◽  
Paternal Allele ◽  
Vitro Fertilization ◽  
Histone Marks ◽  
Imprinted Gene

Proper implantation and placental formation are crucial for the continuity of mammalian species. Embryonic and placental developments are under intense genetic and epigenetic control, such as the regulation of differentiation of pluripotent cells into highly specialised fetal and placental cells. In the present study the objectives were to evaluate expression and epigenetic control of the imprinted gene PHLDA2, a maternally expressed gene that appears to be a regulator of placental growth, in cotyledonary and inter-cotyledonary tissues of bovine placentas on Day 60 of pregnancies produced by embryo transfer (ET; n = 3), in vitro fertilization (IVF; n = 5), and nuclear transfer (NT; n = 6), by real time PCR (qPCR). In vitro culture of IVF and NT embryos was performed in SOF medium supplemented with 2.5% fetal bovine serum, at 39°C in a humidified atmosphere of 5% CO2 and 5% O2 for 7 days. For evaluation of gene expression, gene-specific standard curves were used, and results were analysed as a ratio to 2 separate housekeeping controls (GAPDH and β-actin). Chromatin immunoprecipitation followed by qPCR (ChIP-qPCR; precipitated/total input DNA) was also performed on the proximal promoter region of PHLDA2, with antibodies against H3K4me2 (permissive histone modification) and H3K9me2 (inhibitory histone modification) in these samples. Products of the ChIP-qPCR for PHLDA2 were digested with a restriction enzyme (AciI) that recognises a specific sequence of the maternal allele (Bos indicus), separating it visually on a gel, from the paternal allele (Bos taurus). Digestion products were separated on a 3% agarose gel, and ethidium bromide was used for visualisation. ImageJ (NIH, Bethesda, MD, USA) was used to analyse band intensity. Gene expression, ChIP, and digestion data were analysed using the least-squares ANOVA and the general linear model procedures (SAS Institute Inc., Cary, NC, USA). Further comparison of means was performed using Duncan's multiple range test (P < 0.05 was considered significant). Expression of the imprinted gene PHLDA2 was 11 times higher in samples produced by NT and, interestingly, also in samples produced by IVF (P < 0.05) compared with the samples produced by ET. ChIP-qPCR for the histone marks, followed by allelic analysis, showed a significant increase of the permissive mark H3K4me2, especially in the silenced paternal allele (P < 0.05), and a reduction of the inhibitory H3K9me2 mark, in the promoter region of the PHLDA2 gene, in clones. The differences observed for these 2 histone marks corroborated with the pattern of gene expression for these samples (elevated in TN placentas). In conclusion, the reproductive biotechnologies of nuclear transfer and in vitro fertilization induce changes in placental expression of the imprinted gene PHLDA2, and nuclear transfer also affects the pattern of histone marks on the proximal promoter region of the imprinted gene PHLDA2.

scholarly journals Angelman syndrome imprinting center encodes a transcriptional promoter

2014 ◽  
Vol 112 (22) ◽  
pp. 6871-6875 ◽  
Author(s):  
Michael W. Lewis ◽  
Jason O. Brant ◽  
Joseph M. Kramer ◽  
James I. Moss ◽  
Thomas P. Yang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Angelman Syndrome ◽  
Paternal Allele ◽  
Specific Gene ◽  
Prader Willi Syndrome ◽  
Maternal Allele ◽  
Expression Of Genes ◽  
Imprinting Center ◽  
Maternal Contribution ◽  
Parent Of Origin

Clusters of imprinted genes are often controlled by an imprinting center that is necessary for allele-specific gene expression and to reprogram parent-of-origin information between generations. An imprinted domain at 15q11–q13 is responsible for both Angelman syndrome (AS) and Prader–Willi syndrome (PWS), two clinically distinct neurodevelopmental disorders. Angelman syndrome arises from the lack of maternal contribution from the locus, whereas Prader–Willi syndrome results from the absence of paternally expressed genes. In some rare cases of PWS and AS, small deletions may lead to incorrect parent-of-origin allele identity. DNA sequences common to these deletions define a bipartite imprinting center for the AS–PWS locus. The PWS–smallest region of deletion overlap (SRO) element of the imprinting center activates expression of genes from the paternal allele. The AS–SRO element generates maternal allele identity by epigenetically inactivating the PWS–SRO in oocytes so that paternal genes are silenced on the future maternal allele. Here we have investigated functional activities of the AS–SRO, the element necessary for maternal allele identity. We find that, in humans, the AS–SRO is an oocyte-specific promoter that generates transcripts that transit the PWS–SRO. Similar upstream promoters were detected in bovine oocytes. This result is consistent with a model in which imprinting centers become DNA methylated and acquire maternal allele identity in oocytes in response to transiting transcription.

scholarly journals Mouse U2af1-rs1 is a neomorphic imprinted gene.

1997 ◽  
Vol 17 (2) ◽  
pp. 789-798 ◽  
Author(s):  
A Nabetani ◽  
I Hatada ◽  
H Morisaki ◽  
M Oshimura ◽  
T Mukai
Keyword(s):  
Genomic Imprinting ◽  
Genome Structure ◽  
Proximal Region ◽  
Paternal Allele ◽  
Chromosome 2 ◽  
Chromosome 11 ◽  
Imprinted Gene ◽  
Genome Region ◽  
Allele Specific ◽  
Allele Specific Methylation

The mouse U2af1-rs1 gene is an endogenous imprinted gene on the proximal region of chromosome 11. This gene is transcribed exclusively from the unmethylated paternal allele, while the methylated maternal allele is silent. An analysis of genome structure of this gene revealed that the whole gene is located in an intron of the Murr1 gene. Although none of the three human U2af1-related genes have been mapped to chromosome 2, the human homolog of Murr1 is assigned to chromosome 2. The mouse Murr1 gene is transcribed biallelically, and therefore it is not imprinted in neonatal mice. Allele-specific methylation is limited to a region around U2af1-rs1 in an intron of Murr1. These results suggest that in chromosomal homology and genomic imprinting, the U2af1-rs1 gene is distinct from the genome region surrounding it. We have proposed the neomorphic origin of the U2af1-rs1 gene by retrotransposition and the particular mechanism of genomic imprinting of ectopic genes.

Loss of genomic imprinting in Drosophila clones

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1043-1046 ◽  
Author(s):  
Andrew J Haigh ◽  
Vett K Lloyd
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Imprinting ◽  
X Chromosome ◽  
Chromatin Structure ◽  
Nuclear Transfer ◽  
Paternal Allele ◽  
Monoallelic Expression ◽  
C Elegans ◽  
Human Cancers ◽  
Parent Of Origin

Genomic imprinting is a process that genetically distinguishes maternal and paternal genomes, and can result in parent-of-origin-dependent monoallelic expression of a gene that is dependent on the parent of origin. As such, an otherwise functional maternally inherited allele may be silenced so that the gene is expressed exclusively from the paternal allele, or vice versa. Once thought to be restricted to mammals, genomic imprinting has been documented in angiosperm plants (J.L. Kermicle. 1970. Genetics, 66: 69–85), zebrafish (C.C. Martin and R. McGowan. 1995. Genet. Res. 65: 21–28), insects, and C. elegans (C.J. Bean, C.E. Schaner, and W.G. Kelly. 2004. Nat. Genet. 36: 100–105.). In each case, it appears to rely on differential chromatin structure. Aberrant imprinting has been implicated in various human cancers and has been detected in a number of cloned mammals, potentially limiting the usefulness of somatic nuclear transfer. Here we show that genomic imprinting associated with a mini-X chromosome is lost in Drosophila melanogaster clones.Key words: cloning, Drosophila, genomic imprinting, nuclear transfer.

scholarly journals A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

2017 ◽  
Vol 7 (7) ◽  
pp. 2227-2234 ◽  
Author(s):  
Yasuaki Takada ◽  
Ryutaro Miyagi ◽  
Aya Takahashi ◽  
Toshinori Endo ◽  
Naoki Osada
Keyword(s):  
Gene Expression ◽  
Maternal Effects ◽  
Genomic Imprinting ◽  
Whole Body ◽  
Specific Gene ◽  
Rna Seq ◽  
Simple Method ◽  
Specific Gene Expression ◽  
Allele Specific ◽  
Parent Of Origin

Abstract Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.

scholarly journals Intrafamily and intragenomic conflicts in human warfare

2017 ◽  
Vol 284 (1849) ◽  
pp. 20162699 ◽  
Author(s):  
Alberto J. C. Micheletti ◽  
Graeme D. Ruxton ◽  
Andy Gardner
Keyword(s):  
Gene Expression ◽  
Mathematical Model ◽  
Genomic Imprinting ◽  
Social Group ◽  
Ecological Study ◽  
Conflicts Of Interest ◽  
Ecological Perspective ◽  
Evolution Of Sex ◽  
Intragenomic Conflict ◽  
Parent Of Origin

Recent years have seen an explosion of multidisciplinary interest in ancient human warfare. Theory has emphasized a key role for kin-selected cooperation, modulated by sex-specific demography, in explaining intergroup violence. However, conflicts of interest remain a relatively underexplored factor in the evolutionary-ecological study of warfare, with little consideration given to which parties influence the decision to go to war and how their motivations may differ. We develop a mathematical model to investigate the interplay between sex-specific demography and human warfare, showing that: the ecology of warfare drives the evolution of sex-biased dispersal; sex-biased dispersal modulates intrafamily and intragenomic conflicts in relation to warfare; intragenomic conflict drives parent-of-origin-specific patterns of gene expression—i.e. ‘genomic imprinting’—in relation to warfare phenotypes; and an ecological perspective of conflicts at the levels of the gene, individual, and social group yields novel predictions as to pathologies associated with mutations and epimutations at loci underpinning human violence.

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