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2.
Gene ; 718: 144049, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31430520

RESUMO

The role of epigenetics in development has garnered attention in recent years due to their ability to modulate the embryonic developmental gene expression in response to the environmental cues. The epigenetic mechanisms - DNA methylation, histone modification, and non-coding RNAs have a unique impact on vertebrate development. Zebrafish, a model vertebrate organism is being used widely in developmental studies due to their high fecundability and rapid organogenesis. With increased studies on various aspects of epigenetics in development, this review gives a glimpse of the major epigenetic modifications and their role in zebrafish development. In this review, the basic mechanism behind each modification followed by their status in zebrafish has been reviewed. Further, recent advancements in the epigenetic aspect of zebrafish development have been discussed.


Assuntos
Metilação de DNA/fisiologia , Embrião não Mamífero/embriologia , Desenvolvimento Embrionário/fisiologia , Epigênese Genética/fisiologia , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Peixe-Zebra/embriologia , Animais , Histonas/genética , Histonas/metabolismo , Processamento de Proteína Pós-Traducional/fisiologia , Peixe-Zebra/genética
3.
Nat Commun ; 10(1): 3053, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311924

RESUMO

The germline is the only cellular lineage capable of transferring genetic information from one generation to the next. Intergenerational transmission of epigenetic memory through the germline, in the form of DNA methylation, has been proposed; however, in mammals this is largely prevented by extensive epigenetic erasure during germline definition. Here we report that, unlike mammals, the continuously-defined 'preformed' germline of zebrafish does not undergo genome-wide erasure of DNA methylation during development. Our analysis also uncovers oocyte-specific germline amplification and demethylation of an 11.5-kb repeat region encoding 45S ribosomal RNA (fem-rDNA). The peak of fem-rDNA amplification coincides with the initial expansion of stage IB oocytes, the poly-nucleolar cell type responsible for zebrafish feminisation. Given that fem-rDNA overlaps with the only zebrafish locus identified thus far as sex-linked, we hypothesise fem-rDNA expansion could be intrinsic to sex determination in this species.


Assuntos
Metilação de DNA/fisiologia , DNA Ribossômico/metabolismo , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Oócitos/metabolismo , Peixe-Zebra/fisiologia , Animais , Desmetilação , Epigênese Genética/fisiologia , Feminino , Masculino , RNA Ribossômico/genética , Caracteres Sexuais
4.
Nat Commun ; 10(1): 2581, 2019 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-31197173

RESUMO

Despite existing reports on differential DNA methylation in type 2 diabetes (T2D) and obesity, our understanding of its functional relevance remains limited. Here we show the effect of differential methylation in the early phases of T2D pathology by a blood-based epigenome-wide association study of 4808 non-diabetic Europeans in the discovery phase and 11,750 individuals in the replication. We identify CpGs in LETM1, RBM20, IRS2, MAN2A2 and the 1q25.3 region associated with fasting insulin, and in FCRL6, SLAMF1, APOBEC3H and the 15q26.1 region with fasting glucose. In silico cross-omics analyses highlight the role of differential methylation in the crosstalk between the adaptive immune system and glucose homeostasis. The differential methylation explains at least 16.9% of the association between obesity and insulin. Our study sheds light on the biological interactions between genetic variants driving differential methylation and gene expression in the early pathogenesis of T2D.


Assuntos
Metilação de DNA/fisiologia , Diabetes Mellitus Tipo 2/genética , Glucose/metabolismo , Insulina/metabolismo , Obesidade/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Simulação por Computador , Ilhas de CpG/genética , Diabetes Mellitus Tipo 2/metabolismo , Epigênese Genética/fisiologia , Epigenômica/métodos , Feminino , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/genética , Estudo de Associação Genômica Ampla/métodos , Homeostase/genética , Humanos , Masculino , Redes e Vias Metabólicas/genética , Pessoa de Meia-Idade , Obesidade/metabolismo , Polimorfismo de Nucleotídeo Único/fisiologia , Adulto Jovem
5.
Nat Commun ; 10(1): 2219, 2019 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-31101825

RESUMO

A long-standing question in the field of embryogenesis is how the zygotic genome is precisely activated by maternal factors, allowing normal early embryonic development. We have previously shown that N6-methyladenine (6mA) DNA modification is highly dynamic in early Drosophila embryos and forms an epigenetic mark. However, little is known about how 6mA-formed epigenetic information is decoded. Here we report that the Fox-family protein Jumu binds 6mA-marked DNA and acts as a maternal factor to regulate the maternal-to-zygotic transition. We find that zelda encoding the pioneer factor Zelda is marked by 6mA. Our genetic assays suggest that Jumu controls the proper zygotic genome activation (ZGA) in early embryos, at least in part, by regulating zelda expression. Thus, our findings not only support that the 6mA-formed epigenetic marks can be read by specific transcription factors, but also uncover a mechanism by which the Jumu regulates ZGA partially through Zelda in early embryos.


Assuntos
DNA/metabolismo , Proteínas de Drosophila/metabolismo , Desenvolvimento Embrionário/fisiologia , Fatores de Transcrição/metabolismo , Zigoto/metabolismo , Adenina/análogos & derivados , Adenina/metabolismo , Animais , Animais Geneticamente Modificados , Proteínas de Drosophila/genética , Drosophila melanogaster/fisiologia , Embrião não Mamífero , Epigênese Genética/fisiologia , Feminino , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Técnicas de Silenciamento de Genes , Genoma de Inseto , Masculino , Fatores de Transcrição/genética
6.
Nat Commun ; 10(1): 2063, 2019 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-31048693

RESUMO

RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Metilação de DNA/fisiologia , Histonas/metabolismo , Histona Desmetilases com o Domínio Jumonji/metabolismo , Fatores de Transcrição/metabolismo , 5-Metilcitosina/metabolismo , Epigênese Genética/fisiologia , Eucromatina/metabolismo , Heterocromatina/metabolismo , Mutação , Plantas Geneticamente Modificadas , Dedos de Zinco/fisiologia
7.
Nat Commun ; 10(1): 2133, 2019 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-31086177

RESUMO

Polycomb (PcG) and Trithorax (TrxG) group proteins give stable epigenetic memory of silent and active gene expression states, but also allow poised states in pluripotent cells. Here we systematically address the relationship between poised, active and silent chromatin, by integrating 73 publications on PcG/TrxG biochemistry into a mathematical model comprising 144 nucleosome modification states and 8 enzymatic reactions. Our model predicts that poised chromatin is bistable and not bivalent. Bivalent chromatin, containing opposing active and silent modifications, is present as an unstable background population in all system states, and different subtypes co-occur with active and silent chromatin. In contrast, bistability, in which the system switches frequently between stable active and silent states, occurs under a wide range of conditions at the transition between monostable active and silent system states. By proposing that bistability and not bivalency is associated with poised chromatin, this work has implications for understanding the molecular nature of pluripotency.


Assuntos
Cromatina/metabolismo , Epigênese Genética/fisiologia , Modelos Biológicos , Proteínas do Grupo Polycomb/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Proteínas de Drosophila/metabolismo , Enzimas/metabolismo , Código das Histonas/fisiologia , Histona-Lisina N-Metiltransferase/metabolismo , Histonas/metabolismo , Proteína de Leucina Linfoide-Mieloide/metabolismo , Nucleossomos/metabolismo
8.
Nat Commun ; 10(1): 1786, 2019 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-30992430

RESUMO

Acquisition of pluripotency by somatic cells is a striking process that enables multicellular organisms to regenerate organs. This process includes silencing of genes to erase original tissue memory and priming of additional cell type specification genes, which are then poised for activation by external signal inputs. Here, through analysis of genome-wide histone modifications and gene expression profiles, we show that a gene priming mechanism involving LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3) specifically eliminates H3K4me2 during formation of the intermediate pluripotent cell mass known as callus derived from Arabidopsis root cells. While LDL3-mediated H3K4me2 removal does not immediately affect gene expression, it does facilitate the later activation of genes that act to form shoot progenitors when external cues lead to shoot induction. These results give insights into the role of H3K4 methylation in plants, and into the primed state that provides plant cells with high regenerative competency.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Código das Histonas/fisiologia , Histona Desmetilases/metabolismo , Brotos de Planta/fisiologia , Regeneração , Proteínas de Arabidopsis/genética , Desmetilação , Epigênese Genética/fisiologia , Regulação da Expressão Gênica de Plantas/fisiologia , Histona Desmetilases/genética , Histonas/metabolismo , Células Vegetais/fisiologia , Brotos de Planta/citologia , Plantas Geneticamente Modificadas , Processamento de Proteína Pós-Traducional/fisiologia
9.
Nat Commun ; 10(1): 1605, 2019 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-30962428

RESUMO

Colonies of the bumblebee Bombus terrestris are characterized by wide phenotypic variability among genetically similar full-sister workers, suggesting a major role for epigenetic processes. Here, we report a high level of ADAR-mediated RNA editing in the bumblebee, despite the lack of an ADAR1-homolog. We identify 1.15 million unique genomic sites, and 164 recoding sites residing in 100 protein coding genes, including ion channels, transporters, and receptors predicted to affect brain function and behavior. Some edited sites are similarly edited in other insects, cephalopods and even mammals. The global editing level of protein coding and non-coding transcripts weakly correlates with task performance (brood care vs. foraging), but not affected by dominance rank or juvenile hormone known to influence physiology and behavior. Taken together, our findings show that brain editing levels are high in naturally behaving bees, and may be regulated by relatively short-term effects associated with brood care or foraging activities.


Assuntos
Abelhas/fisiologia , Comportamento Animal/fisiologia , Edição de RNA/fisiologia , RNA/genética , Comportamento Social , Adenosina Desaminase/genética , Adenosina Desaminase/metabolismo , Animais , Encéfalo/metabolismo , Epigênese Genética/fisiologia , Feminino , Variação Genética/genética , Variação Genética/fisiologia , Masculino , RNA/isolamento & purificação , RNA/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Análise de Sequência de RNA
10.
Gene ; 704: 134-141, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-30981839

RESUMO

To maintain normal function of cartilage tissue normally, the presence of a sufficient amount of type II collagen and aggrecan is essential, and their synthesis is tightly regulated. Therefore, understanding the mechanisms that control the expression of type II collagen and aggrecan would be useful for understanding gene expression changes in diseases such as osteoarthritis. Recently, we have identified two pairs of enhancer elements, termed E1 and E2 in the type II collagen gene and Ea and Eb in the aggrecan gene. However, their different mechanisms of action remained unclear. Thus, the central aim of this study was to clarify the different transcriptional regulation mediated through each enhancer element. To this end, we established different stable reporter cell lines that express a reporter gene under the control of different enhancer elements using a silent reporter system we previously constructed. Using these cell lines, we found that dexamethasone, forskolin, and trichostatin A affect the gene expression of type II collagen and aggrecan via different enhancer elements. Moreover, we clarified that E1 and E2 enhancer activities are regulated through distinct epigenetic modifications by histone deacetylase 10 and sirtuin 6.


Assuntos
Agrecanas/genética , Colágeno Tipo II/genética , Elementos Facilitadores Genéticos/genética , Epigênese Genética/fisiologia , Agrecanas/metabolismo , Animais , Condrócitos/metabolismo , Condrócitos/patologia , Colágeno Tipo II/metabolismo , Regulação da Expressão Gênica , Histona Desacetilases do Grupo III/metabolismo , Regiões Promotoras Genéticas , Ratos , Sirtuínas/metabolismo , Células Tumorais Cultivadas
11.
Nat Commun ; 10(1): 1251, 2019 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-30890697

RESUMO

Male gametes are generated through a specialised differentiation pathway involving a series of developmental transitions that are poorly characterised at the molecular level. Here, we use droplet-based single-cell RNA-Sequencing to profile spermatogenesis in adult animals and at multiple stages during juvenile development. By exploiting the first wave of spermatogenesis, we both precisely stage germ cell development and enrich for rare somatic cell-types and spermatogonia. To capture the full complexity of spermatogenesis including cells that have low transcriptional activity, we apply a statistical tool that identifies previously uncharacterised populations of leptotene and zygotene spermatocytes. Focusing on post-meiotic events, we characterise the temporal dynamics of X chromosome re-activation and profile the associated chromatin state using CUT&RUN. This identifies a set of genes strongly repressed by H3K9me3 in spermatocytes, which then undergo extensive chromatin remodelling post-meiosis, thus acquiring an active chromatin state and spermatid-specific expression.


Assuntos
Histonas/metabolismo , Espermatócitos/crescimento & desenvolvimento , Espermatogênese/fisiologia , Transcrição Genética/fisiologia , Cromossomo X/metabolismo , Animais , Separação Celular/métodos , Cromatina/metabolismo , Mapeamento Cromossômico/métodos , Cromossomos Humanos Par 21/genética , Epigênese Genética/fisiologia , Feminino , Citometria de Fluxo/métodos , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Histonas/genética , Humanos , Masculino , Prófase Meiótica I/fisiologia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Análise de Sequência de RNA , Análise de Célula Única , Espermatócitos/metabolismo , Testículo/citologia
12.
Glia ; 67(4): 718-728, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30793389

RESUMO

During development or after brain injury, oligodendrocyte precursor cells (OPCs) differentiate into oligodendrocytes to supplement the number of oligodendrocytes. Although mechanisms of OPC differentiation have been extensively examined, the role of epigenetic regulators, such as histone deacetylases (HDACs) and DNA methyltransferase enzymes (DNMTs), in this process is still mostly unknown. Here, we report the differential roles of epigenetic regulators in OPC differentiation. We prepared primary OPC cultures from neonatal rat cortex. Our cultured OPCs expressed substantial amounts of mRNA for HDAC1, HDAC2, DNMT1, and DNMT3a. mRNA levels of HDAC1 and HDAC2 were both decreased by the time OPCs differentiated into myelin-basic-protein expressing oligodendrocytes. However, DNMT1 or DNMT3a mRNA level gradually decreased or increased during the differentiation step, respectively. We then knocked down those regulators in cultured OPCs with siRNA technique before starting OPC differentiation. While HDAC1 knockdown suppressed OPC differentiation, HDAC2 knockdown promoted OPC differentiation. DNMT1 knockdown also suppressed OPC differentiation, but unlike HDAC1/2, DNMT1-deficient cells showed cell damage during the later phase of OPC differentiation. On the other hand, when OPCs were transfected with siRNA for DNMT3a, the number of OPCs was decreased, indicating that DNMT3a may participate in OPC survival/proliferation. Taken together, these data demonstrate that each epigenetic regulator has different phase-specific roles in OPC survival and differentiation.


Assuntos
Epigênese Genética/fisiologia , Células Precursoras de Oligodendrócitos/fisiologia , Animais , Animais Recém-Nascidos , Diferenciação Celular , Córtex Cerebral/citologia , DNA (Citosina-5-)-Metiltransferases/genética , DNA (Citosina-5-)-Metiltransferases/metabolismo , Metilação de DNA/efeitos dos fármacos , Metilação de DNA/genética , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Histona Desacetilases/genética , Histona Desacetilases/metabolismo , Proteína Básica da Mielina/genética , Proteína Básica da Mielina/metabolismo , RNA Mensageiro/metabolismo , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Ratos , Ratos Sprague-Dawley , Receptor alfa de Fator de Crescimento Derivado de Plaquetas/genética , Receptor alfa de Fator de Crescimento Derivado de Plaquetas/metabolismo , Transfecção
13.
Arch Pharm Res ; 42(2): 159-170, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30806885

RESUMO

Cancer can be identified as a chaotic cell state, which breaks the rules that govern growth and reproduction, with main characteristics such as uncontrolled division, invading other tissues, usurping resources, and eventually killing its host. It was once believed that cancer is caused by a progressive series of genetic aberrations, and certain mutations of genes, including oncogenes and tumor suppressor genes, have been identified as the cause of cancer. However, piling evidence suggests that epigenetic modifications working in concert with genetic mechanisms to regulate transcriptional activity are dysregulated in many diseases, including cancer. Cancer epigenetics explain a wide range of heritable changes in gene expression, which do not come from any alteration in DNA sequences. Aberrant DNA methylation, histone modifications, and expression of long non-coding RNAs (lncRNAs) are key epigenetic mechanisms associated with tumor initiation, cancer progression, and metastasis. Within the past decade, cancer epigenetics have enabled us to develop novel biomarkers and therapeutic target for many types of cancers. In this review, we will summarize the major epigenetic changes involved in cancer biology along with clinical and preclinical results developed as novel cancer therapeutics.


Assuntos
Epigênese Genética/fisiologia , Terapia Genética/métodos , Neoplasias/genética , Neoplasias/terapia , Animais , Metilação de DNA/efeitos dos fármacos , Metilação de DNA/fisiologia , Epigênese Genética/efeitos dos fármacos , Terapia Genética/tendências , Histonas/antagonistas & inibidores , Histonas/metabolismo , Humanos , Neoplasias/metabolismo
14.
J Cutan Pathol ; 46(5): 327-334, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30719726

RESUMO

BACKGROUND: Hair follicle (HF) cycling is dependent upon activation and differentiation of an epithelial subpopulation of cells with stem-like characteristics. These cells express cytokeratin 15 (CK15) and are sequestered within a specialized niche termed the follicular bulge. The pathways that mediate bulge activation are poorly understood, although growing evidence suggests a role for epigenetic events. METHODS: Here we investigated murine and human HFs to determine whether a recently described epigenetic hydroxymethylation marker, 5-hmC, known to mediate cell growth and differentiation, may play a role in bulge activation. RESULTS: We found the bulge region of murine HFs to show variable 5-hmC distribution within the nuclei of CK15-positive stem cells during early anagen, a pattern that was not associated with resting stem cells of telogen follicles, which did not express 5-hmC. Moreover, during phases of early anagen that were induced in an organ culture model, spatial alterations in bulge stem cell 5-hmC reactivity, as assessed by dual labeling, were noted. CONCLUSIONS: These preliminary findings suggest that 5-hmC may play a dynamic role in bulge activation during anagen growth, and provide a foundation for further experimental inquiry into epigenomic regulation of HF stem cells.


Assuntos
5-Metilcitosina/análogos & derivados , Diferenciação Celular , Proliferação de Células , Epigênese Genética/fisiologia , Folículo Piloso/metabolismo , Células-Tronco/metabolismo , 5-Metilcitosina/metabolismo , Animais , Biomarcadores/metabolismo , Folículo Piloso/citologia , Humanos , Queratina-15/metabolismo , Camundongos , Células-Tronco/citologia
15.
J Reprod Dev ; 65(1): 83-90, 2019 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-30606958

RESUMO

Parthenogenesis is an activation process of oocytes that occur without the participation of sperm. Evidence suggests that normal development of embryos requires proper expression of several imprinted genes inherited from both the paternal and maternal genomes. Compared to gene expression, histone modifications and chromatin remodeling are not well-documented. In this research, by using immunofluorescence staining for several developmental-associated histone modifications, we investigated whether epigenetic impairments in parthenogenetic embryos act as constraints for proper development. At early stages, fertilized embryos exhibited high methylation of histone H3 at lysine 9 (Me-H3-K9) and Heterochromatin Protein 1 (HP1) present in the maternal chromatin, while paternal chromatin showed weaker HP1 signals. We found that at the two-cell stage in fertilized embryos, HP1, initially detected around the nucleolus, colocalized with chromocenters at one pole of the blastomere, while parthenotes showed a diffused distribution pattern of HP1 throughout the entire nucleoplasm. At the four-cell stage, methylation of histone H3 at arginine 26 (Me-H3-R26) increased at nascent RNA repression sites in fertilized embryos, while parthenotes recorded weaker signals throughout the nucleoplasm, suggesting differences in pluripotency of the ICM cells between the two types of embryos. Moreover, at the blastocyst stage, we observed that the acetylation level of histone H4 at lysine 12 (Ac-H4-K12) was significantly decreased in parthenogenetic ICM compared to that in its fertilized counterpart. To summarize, differences in epigenetic modifications correlating with paternal chromatin's capacity to regulate nascent RNA repression may contribute to aberrant development and lineage allocation in mouse parthenogenetic embryos.


Assuntos
Blastocisto/fisiologia , Epigênese Genética/fisiologia , Partenogênese/genética , Acetilação , Animais , Arginina/química , Cromatina/química , Cromatina/genética , Montagem e Desmontagem da Cromatina , Proteínas Cromossômicas não Histona/análise , Proteínas Cromossômicas não Histona/química , Desenvolvimento Embrionário/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Histonas/química , Histonas/metabolismo , Lisina/química , Masculino , Metilação , Camundongos , Camundongos Endogâmicos ICR , Injeções de Esperma Intracitoplásmicas
16.
Oncogene ; 38(18): 3387-3401, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30643192

RESUMO

Blood circulating cell-free DNA (ccfDNA) is a suggested biosource of valuable clinical information for cancer, meeting the need for a minimally-invasive advancement in the route of precision medicine. In this paper, we evaluated the prognostic and predictive potential of ccfDNA parameters in early and advanced breast cancer. Groups consisted of 150 and 16 breast cancer patients under adjuvant and neoadjuvant therapy respectively, 34 patients with metastatic disease and 35 healthy volunteers. Direct quantification of ccfDNA in plasma revealed elevated concentrations correlated to the incidence of death, shorter PFS, and non-response to pharmacotherapy in the metastatic but not in the other groups. The methylation status of a panel of cancer-related genes chosen based on previous expression and epigenetic data (KLK10, SOX17, WNT5A, MSH2, GATA3) was assessed by quantitative methylation-specific PCR. All but the GATA3 gene was more frequently methylated in all the patient groups than in healthy individuals (all p < 0.05). The methylation of WNT5A was statistically significantly correlated to greater tumor size and poor prognosis characteristics and in advanced stage disease with shorter OS. In the metastatic group, also SOX17 methylation was significantly correlated to the incidence of death, shorter PFS, and OS. KLK10 methylation was significantly correlated to unfavorable clinicopathological characteristics and relapse, whereas in the adjuvant group to shorter DFI. Methylation of at least 3 or 4 genes was significantly correlated to shorter OS and no pharmacotherapy response, respectively. Classification analysis by a fully automated, machine learning software produced a single-parametric linear model using ccfDNA plasma concentration values, with great discriminating power to predict response to chemotherapy (AUC 0.803, 95% CI [0.606, 1.000]) in the metastatic group. Two more multi-parametric signatures were produced for the metastatic group, predicting survival and disease outcome. Finally, a multiple logistic regression model was constructed, discriminating between patient groups and healthy individuals. Overall, ccfDNA emerged as a highly potent predictive classifier in metastatic breast cancer. Upon prospective clinical evaluation, all the signatures produced could aid accurate prognosis.


Assuntos
Neoplasias da Mama/sangue , Neoplasias da Mama/patologia , Ácidos Nucleicos Livres/sangue , Metilação de DNA/fisiologia , DNA de Neoplasias/sangue , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/sangue , Mama/metabolismo , Mama/patologia , Neoplasias da Mama/metabolismo , Epigênese Genética/fisiologia , Feminino , Humanos , Calicreínas/metabolismo , Pessoa de Meia-Idade , Prognóstico
18.
Nat Commun ; 10(1): 416, 2019 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-30679435

RESUMO

DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.


Assuntos
Aberrações Cromossômicas , Período de Replicação do DNA/fisiologia , Epigênese Genética/fisiologia , Neoplasias/genética , Neoplasias da Mama , Linhagem Celular Tumoral , Metilação de DNA , Replicação do DNA , Desoxirribonuclease I/análise , Epigenômica , Feminino , Regulação Neoplásica da Expressão Gênica , Genoma , Genômica , Heterocromatina , Humanos , Masculino , Neoplasias da Próstata , Sequenciamento Completo do Genoma
19.
Diabetes Res Clin Pract ; 148: 189-199, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30641161

RESUMO

AIMS: Epigenetic mechanisms regulate gene expression and may influence the pathogenesis of type 2 diabetes through the loss of insulin sensitivity. The aims of this study were to measure variation in DNA methylation at the type 2 diabetes locus KCNQ1 and assess its relationship with metabolic measures and with genotype. METHODS: DNA methylation from whole blood DNA was quantified using pyrosequencing at 5 CpG sites at the KCNQ1 locus in 510 individuals without diabetes from the 'Relationship between Insulin Sensitivity and Cardiovascular disease' (RISC) cohort. Genotype data was analysed at the same locus in 1119 individuals in the same cohort. Insulin sensitivity was assessed by euglycaemic-hyperinsulinaemic clamp. RESULTS: DNA methylation at the KCNQ1 locus was inversely associated with insulin sensitivity and serum adiponectin. This association was driven by a methylation-altering Single Nucleotide Polymorphism (SNP) (rs231840) which ablated a methylation site and reduced methylation levels. A second SNP (rs231357), in weak Linkage Disequilibrium (LD) with rs231840, was also associated with insulin sensitivity and DNA methylation. These SNPs have not been previously reported to be associated with type 2 diabetes risk or insulin sensitivity. CONCLUSION: Evidence indicates that genetic and epigenetic determinants at the KCNQ1 locus influence insulin sensitivity.


Assuntos
Ilhas de CpG/efeitos dos fármacos , Ilhas de CpG/genética , Metilação de DNA , Diabetes Mellitus Tipo 2/genética , Loci Gênicos/genética , Resistência à Insulina/genética , Canal de Potássio KCNQ1/genética , Adulto , Estudos de Coortes , Análise Mutacional de DNA/métodos , Epigênese Genética/fisiologia , Feminino , Estudos de Associação Genética , Genótipo , Humanos , Desequilíbrio de Ligação , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único
20.
PLoS One ; 14(1): e0210217, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30677064

RESUMO

Polycomb group (PcG) proteins are essential regulators of epigenetic gene silencing and development. The PcG protein enhancer of zeste homolog 2 (Ezh2) is a key component of the Polycomb Repressive Complex 2 and is responsible for placing the histone H3 lysine 27 trimethylation (H3K27me3) repressive mark on the genome through its methyltransferase domain. Ezh2 is highly conserved in vertebrates. We studied the role of ezh2 during development of zebrafish with the use of a mutant allele (ezh2(sa1199), R18STOP), which has a stop mutation in the second exon of the ezh2 gene. Two versions of the same line were used during this study. The first and original version of zygotic ezh2(sa1199) mutants unexpectedly retained ezh2 expression in brain, gut, branchial arches, and eyes at 3 days post-fertilization (dpf), as revealed by in-situ hybridization. Moreover, the expression pattern in homozygous mutants was identical to that of wild types, indicating that mutant ezh2 mRNA is not subject to nonsense mediated decay (NMD) as predicted. Both wild type and ezh2 mutant embryos presented edemas at 2 and 3 dpf. The line was renewed by selective breeding to counter select the non-specific phenotypes and survival was assessed. In contrast to earlier studies on ezh2 mutant zebrafish, ezh2(sa1199) mutants survived until adulthood. Interestingly, the ezh2 mRNA and Ezh2 protein were present during adulthood (70 dpf) in both wild type and ezh2(sa1199) mutant zebrafish. We conclude that the ezh2(sa1199) allele does not exhibit an ezh2 loss-of-function phenotype.


Assuntos
Proteína Potenciadora do Homólogo 2 de Zeste/genética , Epigênese Genética/fisiologia , Proteínas de Peixes/genética , Peixe-Zebra/crescimento & desenvolvimento , Animais , Códon sem Sentido , Metilação de DNA/fisiologia , Embrião não Mamífero , Éxons/genética , Histonas/metabolismo , Homozigoto , Fenótipo , RNA Mensageiro/metabolismo , Peixe-Zebra/genética
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