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1.
Orv Hetil ; 161(2): 43-49, 2020 Jan.
Artigo em Húngaro | MEDLINE | ID: mdl-31902235

RESUMO

Hormonal imprinting is a physiological process, which is a part of the receptor-hormone complex development. It determines the binding capacity of the receptors across the lifespan. It takes place perinatally in the critical period of hormone receptor development, when the developmental window for imprinting is open and permits the binding of hormone-like molecules (related or synthetic hormones, endocrine disruptors etc.) causing disturbances of the endocrine system, and the systems- influenced organs by it, for life. This is the faulty hormonal imprinting. However, studying the medical database, PubMed, a lot of data can be found on the harmful late (adult age) effects of medication in the critical period of development with non-hormonal molecules, which are manifested later in functional alterations or diseases. This could mean that in the process of faulty imprinting, the openness of the developmental window could be more important than the structural similarity of a molecule to hormones. As developmentally critical period for faulty imprinting by hormone-like molecules is not exclusively the perinatal one (this is justified in the case of faulty hormonal imprinting), the pubertal period was also studied from this aspect and similarities to the impact of perinatal use have been found (this could be called "Pubertal Origin of Health and Disease = POHaD). While in the case of hormonal faulty imprinting, the mechanism seems to be clear (considering the role of receptors), the mechanism of drug-provoked imprinting is presently uncleared (considering the variety of medications which cause late-manifested alterations). The medicaments-caused faulty imprinting conception calls attention to the dangers of medication in the perinatal as well as the pubertal periods. Orv Hetil. 2020; 161(2): 43-49.


Assuntos
Disruptores Endócrinos/efeitos adversos , Impressão Genômica/efeitos dos fármacos , Hormônios/metabolismo , Sistema Endócrino , Feminino , Fertilização , Humanos , Gravidez , Efeitos Tardios da Exposição Pré-Natal/fisiopatologia
2.
Hum Genet ; 138(11-12): 1301-1311, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31686214

RESUMO

Haploinsufficiency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. In one case, the deletion of the maternal allele of the FOXF1 enhancer caused pulmonary hypertension and histopathologically diagnosed MPV without the typical ACD features. In the second case, the deletion of the paternal enhancer resulted in ACDMPV rather than the expected neonatal lethality. In both cases, FOXF1 expression in lung tissue was higher than usually seen or expected in patients with similar deletions, suggesting an increased activity of the remaining allele of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Moreover, in a family with three histopathologically-diagnosed ACDMPV siblings whose missense FOXF1 mutation was inherited from the healthy non-mosaic carrier mother, we have identified a rare SNV rs28571077-A within 2-kb of the above-mentioned non-coding SNVs in the FOXF1 enhancer in the mother, that was absent in the affected newborns and 13 unrelated ACDMPV patients with CNV deletions of this genomic region. Based on the low population frequencies of these three variants, their absence in ACDMPV patients, the results of reporter assay, RNAi and EMSA experiments, and in silico predictions, we propose that the described SNVs might have acted on FOXF1 enhancer as hypermorphs.


Assuntos
Elementos Facilitadores Genéticos , Fatores de Transcrição Forkhead/genética , Mutação de Sentido Incorreto , Síndrome da Persistência do Padrão de Circulação Fetal/prevenção & controle , Polimorfismo de Nucleotídeo Único , Deleção de Sequência , Adulto , Criança , Feminino , Impressão Genômica , Humanos , Recém-Nascido , Síndrome da Persistência do Padrão de Circulação Fetal/genética , Síndrome da Persistência do Padrão de Circulação Fetal/patologia , Fenótipo , Prognóstico
3.
Nature ; 574(7776): 99-102, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31578486

RESUMO

Sexual imprinting-a phenomenon in which offspring learn parental traits and later use them as a model for their own mate preferences-can generate reproductive barriers between species1. When the target of imprinting is a mating trait that differs among young lineages, imprinted preferences may contribute to behavioural isolation and facilitate speciation1,2. However, in most models of speciation by sexual selection, divergent natural selection is also required; the latter acts to generate and maintain variation in the sexually selected trait or traits, and in the mating preferences that act upon them3. Here we demonstrate that imprinting, in addition to mediating female mate preferences, can shape biases in male-male aggression. These biases can act similarly to natural selection to maintain variation in traits and mate preferences, which facilitates reproductive isolation driven entirely by sexual selection. Using a cross-fostering study, we show that both male and female strawberry poison frogs (Oophaga pumilio) imprint on coloration, which is a mating trait that has diverged recently and rapidly in this species4. Cross-fostered females prefer to court mates of the same colour as their foster mother, and cross-fostered males are more aggressive towards rivals that share the colour of their foster mother. We also use a simple population-genetics model to demonstrate that when both male aggression biases and female mate preferences are formed through parental imprinting, sexual selection alone can (1) stabilize a sympatric polymorphism and (2) strengthen the trait-preference association that leads to behavioural reproductive isolation. Our study provides evidence of imprinting in an amphibian and suggests that this rarely considered combination of rival and sexual imprinting can reduce gene flow between individuals that bear divergent mating traits, which sets the stage for speciation by sexual selection.


Assuntos
Anuros/genética , Anuros/fisiologia , Especiação Genética , Impressão Genômica , Preferência de Acasalamento Animal/fisiologia , Pigmentação da Pele/genética , Agressão , Animais , Anuros/anatomia & histologia , Costa Rica , Feminino , Fluxo Gênico/genética , Masculino , Herança Materna/genética , Nicarágua , Panamá , Herança Paterna/genética , Polimorfismo Genético
4.
Nat Commun ; 10(1): 3922, 2019 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-31477727

RESUMO

More than 7 million individuals have been conceived by Assisted Reproductive Technologies (ART) and there is clear evidence that ART is associated with a range of adverse early life outcomes, including rare imprinting disorders. The periconception period and early embryogenesis are associated with widespread epigenetic remodeling, which can be influenced by ART, with effects on the developmental trajectory in utero, and potentially on health throughout life. Here we profile genome-wide DNA methylation in blood collected in the newborn period and in adulthood (age 22-35 years) from a unique longitudinal cohort of ART-conceived individuals, previously shown to have no differences in health outcomes in early adulthood compared with non-ART-conceived individuals. We show evidence for specific ART-associated variation in methylation around birth, most of which occurred independently of embryo culturing. Importantly, ART-associated epigenetic variation at birth largely resolves by adulthood with no direct evidence that it impacts on development and health.


Assuntos
Metilação de DNA , Epigênese Genética , Epigenômica/métodos , Técnicas de Reprodução Assistida , Adulto , Estudos de Coortes , Feminino , Estudo de Associação Genômica Ampla , Impressão Genômica , Humanos , Recém-Nascido , Estudos Longitudinais , Masculino , Gravidez , Adulto Jovem
5.
Nat Rev Cancer ; 19(9): 522-537, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31413324

RESUMO

Human germ cell tumours (GCTs) are derived from stem cells of the early embryo and the germ line. They occur in the gonads (ovaries and testes) and also in extragonadal sites, where migrating primordial germ cells are located during embryogenesis. This group of heterogeneous neoplasms is unique in that their developmental potential is in effect determined by the latent potency state of their cells of origin, which are reprogrammed to omnipotent, totipotent or pluripotent stem cells. Seven GCT types, defined according to their developmental potential, have been identified, each with distinct epidemiological and (epi)genomic features. Heritable predisposition factors affecting the cells of origin and their niches likely explain bilateral, multiple and familial occurrences of the different types of GCTs. Unlike most other tumour types, GCTs are rarely caused by somatic driver mutations, but arise through failure to control the latent developmental potential of their cells of origin, resulting in their reprogramming. Consistent with their non-mutational origin, even the malignant tumours of the group are characterized by wild-type TP53 and high sensitivity for DNA damage. However, tumour progression and the rare occurrence of treatment resistance are driven by embryonic epigenetic state, specific (sub)chromosomal imbalances and somatic mutations. Thus, recent progress in understanding GCT biology supports a comprehensive developmental pathogenetic model for the origin of all GCTs, and provides new biomarkers, as well as potential targets for treatment of resistant disease.


Assuntos
Biomarcadores Tumorais/genética , Epigênese Genética , Neoplasias Embrionárias de Células Germinativas/genética , Alelos , Animais , Biomarcadores Tumorais/metabolismo , Movimento Celular , Progressão da Doença , Desenvolvimento Embrionário , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Regulação Neoplásica da Expressão Gênica , Impressão Genômica , Genômica , Humanos , Cariotipagem , Masculino , Mutação , Neoplasias Embrionárias de Células Germinativas/metabolismo , Células-Tronco/metabolismo
6.
EBioMedicine ; 46: 368-380, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31383551

RESUMO

BACKGROUND: The imprinted gene Delta like non-canonical Notch ligand 1 (Dlk1) is considered an inhibitor of adipogenesis, but its in vivo impact on fat mass indeed remains elusive and controversial. METHODS: Fat deposits were assessed by MRI and DXA scanning in two cohorts of non-diabetic men, whereas glucose disposal rate (GDR) was determined during euglycemic hyperinsulinemic clamp. Blood analyte measurements were used for correlation and mediation analysis to investigate how age, BMI, and fat percentage affect the relation between DLK1 and GDR. Confirmatory animal studies performed in normal (NC) and high fat diet (HFD) fed Dlk1+/+ and Dlk1-/- mice included DXA scanning, glucose tolerance tests (GTTs), blood measurements, and skeletal muscle glucose uptake studies by positron emission tomography (PET), histology, qRT-PCR, and in vitro cell studies. FINDINGS: Overall, DLK1 is positively correlated with fat amounts, which is consistent with a negative linear relationship between DLK1 and GDR. This relationship is not mediated by age, BMI, or fat percentage. In support, DLK1 also correlates positively with HOMA-IR and ADIPO-IR in these humans, but has no linear relationship with the early diabetic inflammation marker MCP-1. In Dlk1-/- mice, the increase in fat percentage and adipocyte size induced by HFD is attenuated, and these animals are protected against insulin resistance. These Dlk1 effects seem independent of gluconeogenesis, but at least partly relies on increased in vivo glucose uptake in skeletal muscles by Dlk1 regulating the major glucose transporter Glut4 in vivo as well as in two independent cell lines. INTERPRETATION: Thus, instead of an adipogenic inhibitor, Dlk1 should be regarded as a factor causally linked to obesity and insulin resistance, and may be used to predict development of type 2 diabetes. FUND: The Danish Diabetes Academy supported by the Novo Nordisk Foundation, The Danish National Research Council (#09-073648), The Lundbeck Foundation, University of Southern Denmark, and Dep. Of Clinical Biochemistry and Pharmacology/Odense University Hospital, the Swedish Research Council, the Swedish Diabetes Foundation, the Strategic Research Program in Diabetes at Karolinska Institute and an EFSD/Lilly grant.


Assuntos
Proteínas de Ligação ao Cálcio/genética , Impressão Genômica , Glucose/metabolismo , Resistência à Insulina , Músculo Esquelético/metabolismo , Obesidade/genética , Obesidade/metabolismo , Tecido Adiposo/metabolismo , Adiposidade , Adulto , Animais , Proteínas de Ligação ao Cálcio/metabolismo , Linhagem Celular , Modelos Animais de Doenças , Feminino , Humanos , Masculino , Camundongos , Camundongos Knockout , Pessoa de Meia-Idade , Obesidade/diagnóstico por imagem , Tomografia Computadorizada com Tomografia por Emissão de Pósitrons , Adulto Jovem
7.
Int J Mol Sci ; 20(16)2019 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-31409051

RESUMO

It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. We also observed that the ASM of the CpG island was associated with allele-specific expression in heterozygous embryos. These results suggest that a long polymorphic GT microsatellite within a gene promoter mediates non-imprinted ASM of the local CpG island in a goldfish inter-strain hybrid.


Assuntos
Metilação de DNA , Carpa Dourada/genética , Repetições de Microssatélites , Alelos , Animais , Quimera/genética , Ilhas de CpG , Cruzamentos Genéticos , Feminino , Impressão Genômica , Carpa Dourada/embriologia , Masculino , Polimorfismo Genético , Regiões Promotoras Genéticas
8.
Int J Mol Sci ; 20(17)2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31466347

RESUMO

Silver-Russell and Beckwith-Wiedemann syndromes (SRS, BWS) are rare congenital human disorders characterized by opposite growth disturbances. With the increasing knowledge on the molecular basis of SRS and BWS, it has become obvious that the disorders mirror opposite alterations at the same genomic loci in 11p15.5. In fact, these changes directly or indirectly affect the expression of IGF2 and CDKN1C and their associated pathways, and thereby, cause growth disturbances as key features of both diseases. The increase of knowledge has become possible with the development and implementation of new and comprehensive assays. Whereas, in the beginning molecular testing was restricted to single chromosomal loci, many tests now address numerous loci in the same run, and the diagnostic implementation of (epi)genome wide assays is only a question of time. These high-throughput approaches will be complemented by the analysis of other omic datasets (e.g., transcriptome, metabolome, proteome), and it can be expected that the integration of these data will massively improve the understanding of the pathobiology of imprinting disorders and their diagnostics. Especially long-read sequencing methods, e.g., nanopore sequencing, allowing direct detection of native DNA modification, will strongly contribute to a better understanding of genomic imprinting in the near future. Thereby, new genomic loci and types of pathogenic variants will be identified, resulting in more precise discrimination into different molecular subgroups. These subgroups serve as the basis for (epi)genotype-phenotype correlations, allowing a more directed prognosis, counseling, and therapy. By deciphering the pathophysiological consequences of SRS and BWS and their molecular disturbances, future therapies will be available targeting the basic cause of the disease and respective pathomechanisms and will complement conventional therapeutic strategies.


Assuntos
Síndrome de Beckwith-Wiedemann/genética , Serviços em Genética/normas , Impressão Genômica , Síndrome de Silver-Russell/genética , Síndrome de Beckwith-Wiedemann/diagnóstico , Síndrome de Beckwith-Wiedemann/terapia , Cromossomos Humanos Par 11/genética , Gerenciamento Clínico , Humanos , Síndrome de Silver-Russell/diagnóstico , Síndrome de Silver-Russell/terapia
9.
Nucleic Acids Res ; 47(18): 9524-9541, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31392315

RESUMO

Co-transcriptional imprinting of mRNA by Rpb4 and Rpb7 subunits of RNA polymerase II (RNAPII) and by the Ccr4-Not complex conditions its post-transcriptional fate. In turn, mRNA degradation factors like Xrn1 are able to influence RNAPII-dependent transcription, making a feedback loop that contributes to mRNA homeostasis. In this work, we have used repressible yeast GAL genes to perform accurate measurements of transcription and mRNA degradation in a set of mutants. This genetic analysis uncovered a link from mRNA decay to transcription elongation. We combined this experimental approach with computational multi-agent modelling and tested different possibilities of Xrn1 and Ccr4 action in gene transcription. This double strategy brought us to conclude that both Xrn1-decaysome and Ccr4-Not regulate RNAPII elongation, and that they do it in parallel. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII. We found that xrn1Δ and ccr4Δ exhibited very different patterns of TFIIS versus RNAPII occupancy, which confirmed their distinct role in controlling transcription elongation. We also found that the relative influence of Xrn1 and Ccr4 is different in the genes encoding ribosomal proteins as compared to the rest of the genome.


Assuntos
Exorribonucleases/genética , RNA Polimerase II/genética , Estabilidade de RNA/genética , Ribonucleases/genética , Proteínas de Saccharomyces cerevisiae/genética , Regulação Fúngica da Expressão Gênica , Genoma Fúngico/genética , Impressão Genômica , Proteínas Ribossômicas/genética , Saccharomyces cerevisiae/genética , Fatores de Elongação da Transcrição/genética
10.
BMC Plant Biol ; 19(1): 307, 2019 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-31299897

RESUMO

BACKGROUND: DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway. RESULTS: In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories. CONCLUSIONS: The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.


Assuntos
Metilação de DNA , Epigênese Genética , Impressão Genômica , Plantas/genética , Evolução Molecular , Éxons/genética , Íntrons/genética , Filogenia
11.
Anim Genet ; 50(5): 417-422, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31268171

RESUMO

IPW (imprinted gene in the Prader-Willi syndrome region), a long non-coding RNA, is a paternally expressed gene in the PWS/AS imprinted domain on human chromosome 15 and mouse chromosome 7. Disruption of the PWS/AS region is associated with three neurogenic disorders in humans. In this study, we identified the bovine homolog of the IPW gene; multiple transcripts obtained by RT-PCR and RACE showed a complex and tissue-specific expression pattern of IPW in the brain, heart, kidney, liver, lung, spleen and skeletal muscle. An informative single nucleotide polymorphism (rs133341090) in the long exon H was identified by sequencing the genomic DNA, and mono-allelic expression of IPW was confirmed by sequencing the cDNAs of heterozygous individuals, indicating that IPW may be imprinted in cattle. The protein-coding potential of IPW transcripts was assessed using coding potential calculator (cpc) software, which showed a negative score. In addition, sequencing analysis also indicated multiple small open reading frames in the bovine IPW transcript, but none of the ATGs was consistent with Kozak consensus. Taken together, the IPW transcripts are most likely long non-coding RNAs.


Assuntos
Bovinos/genética , Cromossomos de Mamíferos , RNA Longo não Codificante/genética , Animais , Clonagem Molecular , Feminino , Expressão Gênica , Impressão Genômica , Masculino , Estrutura Molecular , Especificidade de Órgãos , Síndrome de Prader-Willi/genética , Homologia de Sequência do Ácido Nucleico
12.
Cell Mol Life Sci ; 76(20): 4009-4021, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31270580

RESUMO

Imprinted genes display parent-of-origin-specific expression with this epigenetic system of regulation found exclusively in therian mammals. Historically, defined imprinted gene functions were almost solely focused on pregnancy and the influence on the growth parameters of the developing embryo and placenta. More recently, a number of postnatal functions have been identified which converge on resource allocation, both for animals in the nest and in adults. While many of the prenatal functions of imprinted genes that have so far been described adhere to the "parental conflict" hypothesis, no clear picture has yet emerged on the functional role of imprints on postnatal metabolism. As these roles are uncovered, interest in the potential for these genes to influence postnatal metabolism and associated adult-onset disease outcomes when dysregulated has gathered pace. Here, we review the published data on imprinted genes and their influence on postnatal metabolism, starting in the nest, and then progressing through to adulthood. When observing the functional effects of these genes on adult metabolism, we must always be careful to acknowledge the influence both of direct expression in the relevant metabolic tissue, but also indirect metabolic programming effects caused by their modulation of both in utero and postnatal growth trajectories.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Regulação da Expressão Gênica no Desenvolvimento , Impressão Genômica , Herança Materna , Herança Paterna , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Adulto , Animais , Comportamento Animal , Regulação da Temperatura Corporal/genética , Embrião de Mamíferos , Desenvolvimento Embrionário , Feminino , Humanos , Masculino , Obesidade/genética , Obesidade/metabolismo , Obesidade/patologia , Placenta/metabolismo , Gravidez
13.
Mol Cell ; 75(3): 523-537.e10, 2019 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-31256989

RESUMO

Long noncoding RNAs (lncRNAs) cause Polycomb repressive complexes (PRCs) to spread over broad regions of the mammalian genome. We report that in mouse trophoblast stem cells, the Airn and Kcnq1ot1 lncRNAs induce PRC-dependent chromatin modifications over multi-megabase domains. Throughout the Airn-targeted domain, the extent of PRC-dependent modification correlated with intra-nuclear distance to the Airn locus, preexisting genome architecture, and the abundance of Airn itself. Specific CpG islands (CGIs) displayed characteristics indicating that they nucleate the spread of PRCs upon exposure to Airn. Chromatin environments surrounding Xist, Airn, and Kcnq1ot1 suggest common mechanisms of PRC engagement and spreading. Our data indicate that lncRNA potency can be tightly linked to lncRNA abundance and that within lncRNA-targeted domains, PRCs are recruited to CGIs via lncRNA-independent mechanisms. We propose that CGIs that autonomously recruit PRCs interact with lncRNAs and their associated proteins through three-dimensional space to nucleate the spread of PRCs in lncRNA-targeted domains.


Assuntos
RNA Longo não Codificante/genética , Animais , Cromatina/genética , Montagem e Desmontagem da Cromatina , Ilhas de CpG/genética , Genoma/genética , Impressão Genômica/genética , Humanos , Camundongos , Complexo Repressor Polycomb 1/genética , Regiões Promotoras Genéticas , Células-Tronco/metabolismo , Trofoblastos/metabolismo
14.
PLoS Genet ; 15(7): e1008268, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31329595

RESUMO

Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.


Assuntos
Elementos Facilitadores Genéticos , Inativação Gênica , Proteínas de Transporte de Cátions Orgânicos/genética , RNA Longo não Codificante/genética , Animais , Feminino , Impressão Genômica , Histonas/metabolismo , Masculino , Camundongos , Transportador 2 de Cátion Orgânico/genética , Diester Fosfórico Hidrolases/genética , Regiões Promotoras Genéticas , Receptor IGF Tipo 2/genética , Deleção de Sequência
15.
Artigo em Inglês | MEDLINE | ID: mdl-31336636

RESUMO

Human exposure to polycyclic aromatic hydrocarbons (PAHs) results in adverse health implications. However, the specific impact of paternal preconception PAHs exposure has not been fully studied. In this study, a total of 219 men aged 24-53 were recruited and an investigation was conducted using a questionnaire requesting information about age, occupation, education, family history, lifestyle, and dietary preferences. Urine and semen samples were examined for the levels of the hydroxyl metabolites of PAHs (OH-PAHs) using ultra-high-performance liquid chromatography-tandem mass spectrometry and sperm DNA methylation by pyrosequencing. The results from the correlation analysis using seven OH-PAHs and the average methylation levels of the imprinting genes H19, PEG3, and MEG3 indicated that 1-OHPH is positively correlated with H19/PEG3 methylation levels. We further examined the correlation between each OH-PAH and the methylation levels at the individual CpGs. The results showed 1-OHPH is specifically correlated with CpG4 and CpG6 of the imprinted gene H19, CpG1 and CpG2 of PEG3, and CpG2 of MEG3; whereas 1-OHP is positively correlated with PEG3 at CpG1. Multivariate regression model analysis confirmed that 1-OHPH and 1-OHP are independent risk factors for the methylation of H19. These data show that sperm DNA imprinting genes are sensitive to adverse environmental perturbations.


Assuntos
Metilação de DNA , DNA/metabolismo , Poluentes Ambientais/análise , Hidrocarbonetos Policíclicos Aromáticos/análise , Espermatozoides , Adulto , Ilhas de CpG , Impressão Genômica , Humanos , Hidroxilação , Masculino , Pessoa de Meia-Idade , Exposição Paterna , Sêmen/química , Adulto Jovem
16.
BMC Biol ; 17(1): 50, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31234833

RESUMO

BACKGROUND: Identification of imprinted genes, demonstrating a consistent preference towards the paternal or maternal allelic expression, is important for the understanding of gene expression regulation during embryonic development and of the molecular basis of developmental disorders with a parent-of-origin effect. Combining allelic analysis of RNA-Seq data with phased genotypes in family trios provides a powerful method to detect parent-of-origin biases in gene expression. RESULTS: We report findings in 296 family trios from two large studies: 165 lymphoblastoid cell lines from the 1000 Genomes Project and 131 blood samples from the Genome of the Netherlands (GoNL) participants. Based on parental haplotypes, we identified > 2.8 million transcribed heterozygous SNVs phased for parental origin and developed a robust statistical framework for measuring allelic expression. We identified a total of 45 imprinted genes and one imprinted unannotated transcript, including multiple imprinted transcripts showing incomplete parental expression bias that was located adjacent to strongly imprinted genes. For example, PXDC1, a gene which lies adjacent to the paternally expressed gene FAM50B, shows a 2:1 paternal expression bias. Other imprinted genes had promoter regions that coincide with sites of parentally biased DNA methylation identified in the blood from uniparental disomy (UPD) samples, thus providing independent validation of our results. Using the stranded nature of the RNA-Seq data in lymphoblastoid cell lines, we identified multiple loci with overlapping sense/antisense transcripts, of which one is expressed paternally and the other maternally. Using a sliding window approach, we searched for imprinted expression across the entire genome, identifying a novel imprinted putative lncRNA in 13q21.2. Overall, we identified 7 transcripts showing parental bias in gene expression which were not reported in 4 other recent RNA-Seq studies of imprinting. CONCLUSIONS: Our methods and data provide a robust and high-resolution map of imprinted gene expression in the human genome.


Assuntos
Alelos , Expressão Gênica/genética , Impressão Genômica/genética , Haplótipos/genética , Análise Química do Sangue , Linhagem Celular , Humanos , Análise de Sequência de RNA
17.
PLoS Genet ; 15(6): e1008151, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31220079

RESUMO

Genomic imprinting in mammals was discovered over 30 years ago through elegant embryological and genetic experiments in mice. Imprinted genes show a monoallelic and parent of origin-specific expression pattern; the development of techniques that can distinguish between expression from maternal and paternal chromosomes in mice, combined with high-throughput strategies, has allowed for identification of many more imprinted genes, most of which are conserved in humans. Undoubtedly, technical progress has greatly promoted progress in the field of genomic imprinting. Here, we summarize the techniques used to discover imprinted genes, identify new imprinted genes, define imprinting regulation mechanisms, and study imprinting functions.


Assuntos
Desenvolvimento Embrionário/genética , Impressão Genômica/genética , Genômica/métodos , Biologia Molecular/métodos , Animais , Metilação de DNA/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Genoma/genética , Humanos , Camundongos , Oócitos/crescimento & desenvolvimento
18.
Sheng Wu Gong Cheng Xue Bao ; 35(5): 910-918, 2019 May 25.
Artigo em Chinês | MEDLINE | ID: mdl-31223009

RESUMO

Parthenogenetic embryonic stem cells (pESCs) derived from bi-maternal genomes do not have competency of tetraploid complementation, due to lacking of paternal imprinting genes. To make pESCs possess fully development potentials and similar pluripotency to zygote-derived ESCs, we knocked out one allelic gene of the two essential maternal imprinting genes (H19 and IG) in their differentially methylated regions (DMR) via CRISPR/Cas9 system and obtained double knock out (DKO) pESCs. Maternal pESCs had similar morphology, expression levels of pluripotent makers and in vitro neural differentiation potentials to zygotes-derived ESCs. Besides that, DKO pESCs could contribute to full-term fetuses through tetraploid complementation, proving that they held fully development potentials. Derivation of DKO pESCs provided a type of major histocompatibility complex (MHC) matched pluripotent stem cells, which would benefit research in regenerative medicine.


Assuntos
Células-Tronco Embrionárias , Partenogênese , Células-Tronco Pluripotentes , Tetraploidia , Animais , Técnicas de Inativação de Genes , Impressão Genômica , Camundongos , Medicina Regenerativa
19.
Mol Med Rep ; 20(1): 95-102, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31115529

RESUMO

Prader­Willi syndrome (PWS), a complicated neurodevelopmental disorder arising from errors in genomic imprinting, is characterized by evident hypotonia along with feeding difficulties and the absence of crying in early infancy. Hyperphagia and obesity are not uncommon in patients with PWS, usually accompanied by intellectual disability, cognitive impairment, short stature, small hands and feet, as well as hypogonadism and typical facial features. Due to the severe complications associated with PWS, a thorough understanding of its features and an early diagnosis, preferably in the fetal period, are important for clinical management. According to previous studies, prenatal diagnosis has been confirmed in only a few cases of PWS, using ultrasound, or as an accidental finding by cytogenetic molecular techniques, as no precise fetal phenotype has been defined. In this present study, an infant with PWS arising from maternal heterodisomy of chromosome 15 is described. This is a typical case of missed diagnosis by fetal ultrasound examination, chromosome karyotype analysis and chromosome microarray (CMA) conducted during the pregnancy. To delineate the complex prenatal characteristics of a fetus with PWS, prenatally­diagnosed cases of PWS described in the literature were reviewed. This present study indicated that although prenatal signs are not sufficient for a diagnosis to be confirmed, a comprehensive consideration of these signs is important in leading to a diagnosis of suspected PWS, and thus prompts further prenatal investigations using molecular genetic tools. Furthermore, this present study also suggested that CMA can lead to a missed diagnosis of PWS/Angelman syndrome and other imprinting disorders despite its high value in the detection of copy­number variants in individuals with developmental delay. If clinical signs strongly suggest PWS, other prenatal molecular genetic investigations, including methylation tests and short tandem repeat­based linkage analysis for uniparental disomy, are recommended as an additional tool to aid diagnosis.


Assuntos
Deficiências do Desenvolvimento/genética , Diagnóstico Precoce , Síndrome de Prader-Willi/genética , Diagnóstico Pré-Natal , Adulto , Pré-Escolar , Cromossomos Humanos Par 15/genética , Variações do Número de Cópias de DNA/genética , Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/fisiopatologia , Feminino , Feto , Impressão Genômica/genética , Humanos , Hiperfagia/genética , Hiperfagia/fisiopatologia , Lactente , Recém-Nascido , Cariotipagem , Masculino , Análise em Microsséries , Obesidade/genética , Obesidade/patologia , Obesidade/fisiopatologia , Fenótipo , Síndrome de Prader-Willi/diagnóstico , Síndrome de Prader-Willi/fisiopatologia , Gravidez
20.
Nucleic Acids Res ; 47(14): e81, 2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31049595

RESUMO

Bisulfite amplicon sequencing has become the primary choice for single-base methylation quantification of multiple targets in parallel. The main limitation of this technology is a preferential amplification of an allele and strand in the PCR due to methylation state. This effect, known as 'PCR bias', causes inaccurate estimation of the methylation levels and calibration methods based on standard controls have been proposed to correct for it. Here, we present a Bayesian calibration tool, MethylCal, which can analyse jointly all CpGs within a CpG island (CGI) or a Differentially Methylated Region (DMR), avoiding 'one-at-a-time' CpG calibration. This enables more precise modeling of the methylation levels observed in the standard controls. It also provides accurate predictions of the methylation levels not considered in the controlled experiment, a feature that is paramount in the derivation of the corrected methylation degree. We tested the proposed method on eight independent assays (two CpG islands and six imprinting DMRs) and demonstrated its benefits, including the ability to detect outliers. We also evaluated MethylCal's calibration in two practical cases, a clinical diagnostic test on 18 patients potentially affected by Beckwith-Wiedemann syndrome, and 17 individuals with celiac disease. The calibration of the methylation levels obtained by MethylCal allows a clearer identification of patients undergoing loss or gain of methylation in borderline cases and could influence further clinical or treatment decisions.


Assuntos
Teorema de Bayes , Biologia Computacional/métodos , Ilhas de CpG/genética , Metilação de DNA , Impressão Genômica , Análise de Sequência de DNA/métodos , Algoritmos , Síndrome de Beckwith-Wiedemann/diagnóstico , Síndrome de Beckwith-Wiedemann/genética , Síndrome de Beckwith-Wiedemann/terapia , Calibragem , Doença Celíaca/diagnóstico , Doença Celíaca/genética , Doença Celíaca/terapia , Humanos , Canais de Potássio de Abertura Dependente da Tensão da Membrana/genética , RNA Longo não Codificante/genética , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
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