Genomic imprinting in marsupial placentation

Genomic imprinting is a widespread epigenetic phenomenon in eutherian mammals, which regulates many aspects of growth and development. Parental conflict over the degree of maternal nutrient transfer is the favoured hypothesis for the evolution of imprinting. Marsupials, like eutherian mammals, are viviparous but deliver an altricial young after a short gestation supported by a fully functional placenta, so can shed light on the evolution and time of acquisition of genomic imprinting. All orthologues of eutherian imprinted genes examined have a conserved expression in the marsupial placenta regardless of their imprint status. Differentially methylated regions (DMRs) are the most common mechanism controlling genomic imprinting in eutherian mammals, but none were found in the marsupial imprinted orthologues of IGF2 receptor (IGF2R), INS or mesoderm-specific transcript (MEST). Instead, histone modification appears to be the mechanism used to silence these genes. At least three genes in marsupials have DMRs: H19, IGF2 and PEG10. PEG10 is particularly interesting as it is derived from a retrotransposon, providing the first direct evidence that retrotransposon insertion can drive the evolution of an imprinted region and of a DMR in mammals. The insertion occurred after the prototherian–therian mammal divergence, suggesting that there may have been strong selection for the retention of imprinted regions that arose during the evolution of placentation. There is currently no evidence for genomic imprinting in the egg-laying monotreme mammals. However, since these mammals do have a short-lived placenta, imprinting appears to be correlated with viviparity but not placentation.

Download Full-text

Canonical and Non-canonical Genomic Imprinting in Rodents

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.713878 ◽

2021 ◽

Vol 9 ◽

Author(s):

Hisato Kobayashi

Keyword(s):

Dna Methylation ◽

Genomic Imprinting ◽

Mouse Genome ◽

Genetic Regulation ◽

Imprinted Genes ◽

Evolutionary Divergence ◽

Chromatin Modifications ◽

Allele Specific ◽

Epigenetic Phenomenon ◽

Parent Of Origin

Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process is initiated in the germline, and the parental epigenetic memories can be maintained following fertilization and induce further allele-specific transcription and chromatin modifications of single or multiple neighboring genes, known as imprinted genes. To date, more than 260 imprinted genes have been identified in the mouse genome, most of which are controlled by imprinted germline differentially methylated regions (gDMRs) that exhibit parent-of-origin specific DNA methylation, which is considered primary imprint. Recent studies provide evidence that a subset of gDMR-less, placenta-specific imprinted genes is controlled by maternal-derived histone modifications. To further understand DNA methylation-dependent (canonical) and -independent (non-canonical) imprints, this review summarizes the loci under the control of each type of imprinting in the mouse and compares them with the respective homologs in other rodents. Understanding epigenetic systems that differ among loci or species may provide new models for exploring genetic regulation and evolutionary divergence.

Download Full-text

Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice

International Journal of Molecular Sciences ◽

10.3390/ijms21249618 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9618

Author(s):

Lin Yang ◽

Feng Xing ◽

Qin He ◽

Muhammad Tahir ul Qamar ◽

Ling-Ling Chen ◽

...

Keyword(s):

Energy Metabolism ◽

Seed Development ◽

Genomic Imprinting ◽

Gene Editing ◽

Grain Filling ◽

Imprinted Genes ◽

Rt Pcr ◽

Reciprocal Crosses ◽

Reciprocal Hybrids ◽

Epigenetic Phenomenon

Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5–7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, japonica intra-subspecies, and indica intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in japonica intra-subspecies hybrids, and 286 in indica intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (Os01g0151700, Os07g0103100, Os10g0340600, Os11g0679700, and Os12g0632800) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.

Download Full-text

Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

eLife ◽

10.7554/elife.10074 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 53

Author(s):

Philip Wolff ◽

Hua Jiang ◽

Guifeng Wang ◽

Juan Santos-González ◽

Claudia Köhler

Keyword(s):

Arabidopsis Thaliana ◽

Differential Expression ◽

Seed Development ◽

Genomic Imprinting ◽

Imprinted Genes ◽

Functional Requirement ◽

Functional Roles ◽

Epigenetic Phenomenon ◽

Parent Of Origin

Genomic imprinting is an epigenetic phenomenon causing parent-of-origin specific differential expression of maternally and paternally inherited alleles. While many imprinted genes have been identified in plants, the functional roles of most of them are unknown. In this study, we systematically examine the functional requirement of paternally expressed imprinted genes (PEGs) during seed development in Arabidopsis thaliana. While none of the 15 analyzed peg mutants has qualitative or quantitative abnormalities of seed development, we identify three PEGs that establish postzygotic hybridization barriers in the endosperm, revealing that PEGs have a major role as speciation genes in plants. Our work reveals that a subset of PEGs maintains functional roles in the inbreeding plant Arabidopsis that become evident upon deregulated expression.

Download Full-text

Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm

BMC Plant Biology ◽

10.1186/s12870-021-03344-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhichao Zhang ◽

Shuai Yu ◽

Jing Li ◽

Yanbin Zhu ◽

Siqi Jiang ◽

...

Keyword(s):

Genomic Imprinting ◽

Noncoding Rnas ◽

Methylation Pattern ◽

Flowering Plants ◽

Imprinted Genes ◽

Genome Wide ◽

Allelic Gene ◽

Potential Basis ◽

Epigenetic Phenomenon ◽

Global Patterns

Abstract Background Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. Results Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. Conclusion Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

Download Full-text

Genome-wide screen of genomic imprinting in endosperm and population-level analysis reveal allelic variation for imprinting in flax

10.1101/2020.11.20.390799 ◽

2020 ◽

Author(s):

Haixia Jiang ◽

Dongliang Guo ◽

Jiali Ye ◽

Yanfang Gao ◽

Huiqing Liu ◽

...

Keyword(s):

Positive Selection ◽

Genomic Imprinting ◽

Allelic Variation ◽

Population Level ◽

Vital Role ◽

Genomic Variation ◽

Imprinted Genes ◽

Fiber Flax ◽

Genome Wide ◽

Epigenetic Phenomenon

AbstractGenomic imprinting is an epigenetic phenomenon caused by the biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in triploid endosperm and plays a vital role in seed development. In this study, we identified 241 candidate imprinted genes including 143 maternally expressed imprinted genes (MEGs) and 98 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. The conservation of imprinting in plants is very limited and imprinting clustering is not a general feature. MEGs tends to be endosperm expression specific, while PEGs are non-tissue specific. Imprinted SNPs differentiated 200 flax cultivars into oil flax, oil-fiber dual purpose flax (OF) and fiber flax subgroups, suggesting that genomic imprinting contributes to intraspecific variation in flax. The nucleotide diversity (π) of imprinted genes in oil flax subgroup is significantly higher than that in fiber flax subgroup, indicating that some imprinted genes undergo positive selection during flax domestication from oil flax to fiber flax. Imprinted genes undergo positive selection is related to the functions. Eleven imprinted genes related to seed size and weight were identified using the candidate gene-based association study. Our study provides information for further exploring the function and genomic variation of imprinted genes in flax population.

Download Full-text

Genomic imprinting in germ cells: imprints are under control

Reproduction ◽

10.1530/rep-10-0173 ◽

2010 ◽

Vol 140 (3) ◽

pp. 411-423 ◽

Cited By ~ 57

Author(s):

Philippe Arnaud

Keyword(s):

Dna Methylation ◽

Genomic Imprinting ◽

Germ Cells ◽

Imprinted Genes ◽

Regulatory Sequences ◽

Sequence Specificity ◽

Maternal Allele ◽

Primary Sequence ◽

Chromatin Configuration

The cis-acting regulatory sequences of imprinted gene loci, called imprinting control regions (ICRs), acquire specific imprint marks in germ cells, including DNA methylation. These epigenetic imprints ensure that imprinted genes are expressed exclusively from either the paternal or the maternal allele in offspring. The last few years have witnessed a rapid increase in studies on how and when ICRs become marked by and subsequently maintain such epigenetic modifications. These novel findings are summarised in this review, which focuses on the germline acquisition of DNA methylation imprints and particularly on the combined role of primary sequence specificity, chromatin configuration, non-histone proteins and transcriptional events.

Download Full-text

Genomic Imprinting of Dopa decarboxylase in Heart and Reciprocal Allelic Expression with Neighboring Grb10

Molecular and Cellular Biology ◽

10.1128/mcb.00862-07 ◽

2007 ◽

Vol 28 (1) ◽

pp. 386-396 ◽

Cited By ~ 28

Author(s):

Trevelyan R. Menheniott ◽

Kathryn Woodfine ◽

Reiner Schulz ◽

Andrew J. Wood ◽

David Monk ◽

...

Keyword(s):

Genomic Imprinting ◽

Promoter Region ◽

Germ Line ◽

Differential Methylation ◽

Dopa Decarboxylase ◽

Imprinted Genes ◽

Chromosome 11 ◽

Imprinted Gene ◽

Line Methylation ◽

Intron 1

ABSTRACT By combining a tissue-specific microarray screen with mouse uniparental duplications, we have identified a novel imprinted gene, Dopa decarboxylase (Ddc), on chromosome 11. Ddc_exon1a is a 2-kb transcript variant that initiates from an alternative first exon in intron 1 of the canonical Ddc transcript and is paternally expressed in trabecular cardiomyocytes of the embryonic and neonatal heart. Ddc displays tight conserved linkage with the maternally expressed and methylated Grb10 gene, suggesting that these reciprocally imprinted genes may be coordinately regulated. In Dnmt3L mutant embryos that lack maternal germ line methylation imprints, we show that Ddc is overexpressed and Grb10 is silenced. Their imprinting is therefore dependent on maternal germ line methylation, but the mechanism at Ddc does not appear to involve differential methylation of the Ddc_exon1a promoter region and may instead be provided by the oocyte mark at Grb10. Our analysis of Ddc redefines the imprinted Grb10 domain on mouse proximal chromosome 11 and identifies Ddc_exon1a as the first example of a heart-specific imprinted gene.

Download Full-text

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome

mBio ◽

10.1128/mbio.00395-17 ◽

2017 ◽

Vol 8 (3) ◽

Cited By ~ 14

Author(s):

Matthew J. Belousoff ◽

Zohar Eyal ◽

Mazdak Radjainia ◽

Tofayel Ahmed ◽

Rebecca S. Bamert ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Structural Information ◽

Structural Basis ◽

Common Mechanism ◽

Resistance Mutations ◽

Antimicrobial Drugs ◽

Linezolid Resistance ◽

Drug Modification ◽

Antibiotic Resistance Mutations ◽

Shed Light

ABSTRACT An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus. This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821–832, 2015, https://doi.org/10.1038/nrd4675 ). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821–832, 2015, https://doi.org/10.1038/nrd4675 ). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.

Download Full-text

Social modulation of oogenesis and egg-laying in Drosophila melanogaster

10.1101/2021.09.13.460109 ◽

2021 ◽

Author(s):

Bailly Tiphaine ◽

Philip Kohlmeier ◽

Rampal Etienne ◽

Bregje Wertheim ◽

Jean-Christophe Billeter

Keyword(s):

Drosophila Melanogaster ◽

Social Context ◽

Social Systems ◽

Fruit Fly ◽

Egg Laying ◽

Physiological Adaptation ◽

Group Members ◽

Selection For ◽

Underlying Mechanisms ◽

Gravid Females

Being part of a group facilitates cooperation between group members, but also creates competition for limited resources. This conundrum is problematic for gravid females who benefit from being in a group, but whose future offspring may struggle for access to nutrition in larger groups. Females should thus modulate their reproductive output depending on their social context. Although social-context dependent modulation of reproduction is documented in a broad range of species, its underlying mechanisms and functions are poorly understood. In the fruit fly Drosophila melanogaster, females actively attract conspecifics to lay eggs on the same resources, generating groups in which individuals may cooperate or compete. The tractability of the genetics of this species allows dissecting the mechanisms underlying physiological adaptation to their social context. Here, we show that females produce eggs increasingly faster as group size increases. By laying eggs faster in group than alone, females appear to reduce competition between offspring and increase their likelihood of survival. In addition, females in a group lay their eggs during the light phase of the day, while isolated females lay them during the night. We show that responses to the presence of others are determined by vision through the motion detection pathway and that flies from any sex, mating status or species can trigger these responses. The mechanisms of this modulation of egg-laying by group is connected to a lifting of the inhibition of light on oogenesis and egg-laying by stimulating hormonal pathways involving juvenile hormone. Because modulation of reproduction by social context is a hallmark of animals with higher levels of sociality, our findings represent a protosocial mechanism in a species considered solitary that may have been the target of selection for the evolution of more complex social systems.

Download Full-text

Genomic imprinting and its role in ethiology of human hereditary diseases

Bulletin of Siberian Medicine ◽

10.20538/1682-0363-2004-3-8-17 ◽

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.

Download Full-text