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1.
Gene ; 764: 145099, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-32861879

RESUMO

Down syndrome (DS, trisomy 21) is the most common major chromosomal aneuploidy compatible with life. The additional whole or partial copy of chromosome 21 results in genome-wide imbalances that drive the complex pathobiology of DS. Differential DNA methylation in the context of trisomy 21 may contribute to the variable architecture of the DS phenotype. The goal of this study was to examine the genomic DNA methylation landscape in myocardial tissue from non-fetal individuals with DS. >480,000 unique CpG sites were interrogated in myocardial DNA samples from individuals with (n = 12) and without DS (n = 12) using DNA methylation arrays. A total of 93 highly differentially methylated CpG sites and 16 differentially methylated regions were identified in myocardial DNA from subjects with DS. There were 18 differentially methylated CpG sites in chromosome 21, including 5 highly differentially methylated sites. A CpG site in the RUNX1 locus was differentially methylated in DS myocardium, and linear regression suggests that donors' age, gender, DS status, and RUNX1 methylation may contribute up to ~51% of the variability in RUNX1 mRNA expression. In DS myocardium, only 58% of the genes overlapping with differentially methylated regions codify for proteins with known functions and 24% are non-coding RNAs. This study provides an initial snapshot on the extent of genome-wide differential methylation in myocardial tissue from persons with DS.


Assuntos
Ilhas de CpG/genética , Metilação de DNA , Síndrome de Down/genética , Epigênese Genética , Miocárdio/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Cromossomos Humanos Par 21/genética , Subunidade alfa 2 de Fator de Ligação ao Core/genética , Epigenômica , Feminino , Loci Gênicos/genética , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , RNA Mensageiro/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de DNA , Adulto Jovem
2.
Int J Mol Sci ; 21(21)2020 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-33114322

RESUMO

Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.


Assuntos
Uso do Códon , Evolução Molecular , Vírus da Gastroenterite Transmissível/genética , Ilhas de CpG , Genoma Viral , Seleção Genética
3.
PLoS One ; 15(10): e0236612, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33104714

RESUMO

A precisely balanced activity of canonical Wnt signaling is essential for a number of biological processes and its perturbation leads to developmental defects or diseases. Here, we demonstrate that alternative isoforms of the KDM2A and KDM2B lysine demethylases have the ability to negatively regulate canonical Wnt signaling. These KDM2A and KDM2B isoforms (KDM2A-SF and KDM2B-SF) lack the N-terminal demethylase domain, but they still have the ability to bind to CpG islands in promoters and to interact with their protein partners via their other functional domains. We have observed that KDM2A-SF and KDM2B-SF bind to the promoters of axin 2 and cyclin D1, two canonical Wnt signaling target genes, and repress their activity. Moreover, KDM2A-SF and KDM2B-SF are both able to strongly repress a Wnt-responsive luciferase reporter. The transcriptional repression mediated by KDM2A-SF and KDM2B-SF, but also by KDM2A-LF, is dependent on their DNA binding domain, while the N-terminal demethylase domain is dispensable for this process. Surprisingly, KDM2B-LF is unable to repress both the endogenous promoters and the luciferase reporter. Finally, we show that both KDM2A-SF and KDM2B-SF are able to interact with TCF7L1, one of the transcriptional mediators of canonical Wnt signaling. KDM2A-SF and KDM2B-SF are thus likely to negatively affect the transcription of canonical Wnt signaling target genes by binding to their promoters and by interacting with TCF7L1 and other co-repressors.


Assuntos
Ciclina D1/metabolismo , Proteínas F-Box/metabolismo , Regulação da Expressão Gênica , Histona Desmetilases com o Domínio Jumonji/metabolismo , Regiões Promotoras Genéticas , Proteína 1 Semelhante ao Fator 7 de Transcrição/metabolismo , Via de Sinalização Wnt , Ilhas de CpG , Ciclina D1/genética , Proteínas F-Box/genética , Células HEK293 , Humanos , Histona Desmetilases com o Domínio Jumonji/genética , Lisina/genética , Lisina/metabolismo , Isoformas de Proteínas , Proteína 1 Semelhante ao Fator 7 de Transcrição/genética
4.
mBio ; 11(5)2020 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-33067384

RESUMO

Recent evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is sensitive to interferons (IFNs). However, the most effective types of IFNs and the underlying antiviral effectors remain to be defined. Here, we show that zinc finger antiviral protein (ZAP), which preferentially targets CpG dinucleotides in viral RNA sequences, restricts SARS-CoV-2. We further demonstrate that ZAP and its cofactors KHNYN and TRIM25 are expressed in human lung cells. Type I, II, and III IFNs all strongly inhibited SARS-CoV-2 and further induced ZAP expression. Comprehensive sequence analyses revealed that SARS-CoV-2 and its closest relatives from horseshoe bats showed the strongest CpG suppression among all known human and bat coronaviruses, respectively. Nevertheless, endogenous ZAP expression restricted SARS-CoV-2 replication in human lung cells, particularly upon treatment with IFN-α or IFN-γ. Both the long and the short isoforms of human ZAP reduced SARS-CoV-2 RNA expression levels, but the former did so with greater efficiency. Finally, we show that the ability to restrict SARS-CoV-2 is conserved in ZAP orthologues of the reservoir bat and potential intermediate pangolin hosts of human coronaviruses. Altogether, our results show that ZAP is an important effector of the innate response against SARS-CoV-2, although this pandemic pathogen emerged from zoonosis of a coronavirus that was preadapted to the low-CpG environment in humans.IMPORTANCE Although interferons inhibit SARS-CoV-2 and have been evaluated for treatment of coronavirus disease 2019 (COVID-19), the most effective types and antiviral effectors remain to be defined. Here, we show that IFN-γ is particularly potent in restricting SARS-CoV-2 and in inducing expression of the antiviral factor ZAP in human lung cells. Knockdown experiments revealed that endogenous ZAP significantly restricts SARS-CoV-2. We further show that CpG dinucleotides which are specifically targeted by ZAP are strongly suppressed in the SARS-CoV-2 genome and that the two closest horseshoe bat relatives of SARS-CoV-2 show the lowest genomic CpG content of all coronavirus sequences available from this reservoir host. Nonetheless, both the short and long isoforms of human ZAP reduced SARS-CoV-2 RNA levels, and this activity was conserved in horseshoe bat and pangolin ZAP orthologues. Our findings indicating that type II interferon is particularly efficient against SARS-CoV-2 and that ZAP restricts this pandemic viral pathogen might promote the development of effective immune therapies against COVID-19.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/virologia , Ilhas de CpG , Pneumonia Viral/virologia , Proteínas de Ligação a RNA/metabolismo , Animais , Betacoronavirus/classificação , Betacoronavirus/genética , Betacoronavirus/metabolismo , Linhagem Celular , Coronavirus/classificação , Coronavirus/genética , Coronavirus/fisiologia , Expressão Gênica/efeitos dos fármacos , Genoma Viral , Humanos , Interferons/farmacologia , Pandemias , Filogenia , Isoformas de Proteínas , RNA Viral/genética , RNA Viral/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Replicação Viral/efeitos dos fármacos
5.
BMC Bioinformatics ; 21(1): 437, 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028199

RESUMO

BACKGROUND: In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations. Besides analyzing them locally for individual genomic locations or globally using correlations between different cells types, intermediate level analyses of these changes are of interest. More specifically, the different distributions of these combinations for different cell types, respectively, are compared to gain new insights. RESULTS AND DISCUSSION: We propose a new tool called 'Masakari' that allows segmenting genomes based on lists of ranges having a certain property, e.g., peaks describing histone modifications. It provides a graphical user interface allowing to select all data sets and setting all parameters needed for the segmentation process. Moreover, the graphical user interface provides statistical graphics allowing to assess the quality and suitability of the segmentation and the selected data. CONCLUSION: Masakari provides statistics based visualizations and thus fosters insights into the combination of histone modification marks on genome ranges, and the differences of the distribution of these combinations between different cell types.


Assuntos
Genoma , Interface Usuário-Computador , Animais , Cromatina/metabolismo , Ilhas de CpG , Código das Histonas , Histonas/metabolismo , Humanos
6.
BMC Med Genet ; 21(1): 201, 2020 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-33046033

RESUMO

BACKGROUND: CDKN2A hypermethylation is among the major events associated with carcinogenesis and is also observed in non-neoplastic colonic mucosa in patients with ulcerative colitis (UC). Macrophage migration inhibitory factor (MIF) plays a crucial role in promoting gastrointestinal inflammation characteristic of UC. The aim of this study is to explore associations between CDKN2A methylation status and MIF polymorphisms (rs755622 and rs5844572). METHODS: One hundred and fifty-nine patients diagnosed with UC were enrolled in this study. The methylation status of p14ARF and p16INK4a was determined by MSP; MIF genotypes were identified by PCR-SSCP. RESULTS: We found no differences with respect to mean age, gender, clinical type (chronic continuous or relapse/remitting), or extent of disease among the patients with methylated and unmethylated p14ARF or p16INK4a. Carrying the rs755622 C allele indicated a significantly higher risk for p14ARF methylation (odds ratio (OR), 2.16; 95% confidence interval (CI), 1.08-4.32; p = 0.030); similarly, carrying the rs5844572 7-repeat allele indicated a significantly higher risk for p16INK4a methylation (OR, 2.57; 95% CI, 1.26-5.24; p = 0.0094) after an adjusted regression analysis. The carriers of the rs755662 C allele or the rs5844572 7-repeat allele were both at a significantly higher risk for methylation of both p14ARF and p16INK4a when compared to the cohort in which neither of the genes were methylated (OR, 2.70; 95% CI, 1.22-6.01; p = 0.015 and OR, 2.87; 95% CI, 1.25-6.62; p = 0.013, respectively). Additionally, carrying rs755622 C allele was significantly associated with CIHM in chronic continuous of clinical type and total colitis (OR, 25.9; 95% CI, 2.55-262.6; p = 0.0059 and OR, 4.38; 95% CI, 1.12-17.2; p = 0.034, respectively), and carrying 7-repeat allele of rs5844572 was significantly associated in chronic continuous type (OR, 14.5; 95%CI, 1.46-144.3; p = 0.022). CONCLUSIONS: Taken together, our findings suggest that MIF genotypes associated with inflammation may also be involved in promoting carcinogenesis via CDKN2A hypermethylation in patients diagnosed with UC.


Assuntos
Colite Ulcerativa/genética , Ilhas de CpG/genética , Inibidor p16 de Quinase Dependente de Ciclina/genética , Metilação de DNA , Oxirredutases Intramoleculares/genética , Fatores Inibidores da Migração de Macrófagos/genética , Polimorfismo de Nucleotídeo Único , Adulto , Alelos , Colite Ulcerativa/diagnóstico , Feminino , Frequência do Gene , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Fatores de Risco
7.
BMC Med Genet ; 21(1): 205, 2020 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-33066747

RESUMO

BACKGROUND: CpG methylation of tumor suppressor genes occurs in the early stage of carcinogenesis. Detecting risk factors for aberrant CpG methylation is clinically important for predicting cancer development. DNA methyltransferase (DNMT) 3a is considered to play critical roles in the DNA methylation process during pathogenesis. In this study, we evaluated the association between DNMT3A polymorphisms (rs6733868 and rs13428812) and CpG methylation status in non-cancerous gastric mucosa. METHODS: We determined the DNMT3A genotype and CpG methylation status of 4 genes (p14ARF, p16INK4a, DAPK, and CDH1) in 510 subjects without gastric cancer. Helicobacter pylori (HP) infection status was determined by the rapid urease test, urea breath test, speculum examination, or serum antibody test. We determined the DNMT3A genotype using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP). CpG methylation status was determined by methylation-specific polymerase chain reaction (MSP). When the methylated band was stronger than 10 ng/µL according to the DNA marker, we judged CpG island hypermethylation (CIHM) to be present. Associations between genotypes and susceptibilities were assessed by logistic regression analysis. RESULTS: The minor allele frequencies of both polymorphisms (rs6733868 and rs13428812) were lower in the CpG methylated groups of each of the 4 genes (p14ARF, p16INK4a, DAPK, and CDH1). Using a dominant genetic model, rs6733868 was significantly associated with the hypermethylation of each gene, whereas rs13428812 was associated with the methylation of 3 genes (all except p14ARF). When low-CIHM was defined as 1 or 2 CpG islands methylated and high-CIHM was defined as 3 or more CpG islands methylated, carrying the minor allele of rs6733868 was associated with both decreased low- and high-CIHM, and that of rs13428812 also was associated with a decrease. Comparing low-CIHM with high-CIHM, carrying the minor alleles of rs6733868 or rs13428812 was related to decreased susceptibility to high-CIHM. In HP-infected subjects, carrying the minor alleles of rs6733868 or rs13428812 had a significantly greater association with decreased susceptibility to high-CIHM. CONCLUSIONS: Our study indicates that polymorphisms of DNMT3A are associated with the accumulation of gene methylation in gastric mucosa. Carrying the minor alleles of rs6733868 or rs13428812 inhibits aberrant gene methylations, which are typically enhanced by HP infection.


Assuntos
Ilhas de CpG/genética , DNA (Citosina-5-)-Metiltransferases/genética , Metilação de DNA , Mucosa Gástrica/metabolismo , Polimorfismo de Nucleotídeo Único , Idoso , Alelos , Antígenos CD/genética , Caderinas/genética , Inibidor p16 de Quinase Dependente de Ciclina/genética , Proteínas Quinases Associadas com Morte Celular/genética , Feminino , Mucosa Gástrica/microbiologia , Frequência do Gene , Genótipo , Infecções por Helicobacter/diagnóstico , Infecções por Helicobacter/microbiologia , Helicobacter pylori/fisiologia , Humanos , Masculino , Pessoa de Meia-Idade
9.
Nat Commun ; 11(1): 5238, 2020 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-33067439

RESUMO

In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.


Assuntos
Metilação de DNA , Doença/genética , Alelos , Ilhas de CpG , Haplótipos , Humanos , Polimorfismo de Nucleotídeo Único , Especificidade da Espécie , Sequenciamento Completo do Genoma
10.
Nat Commun ; 11(1): 5417, 2020 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-33110091

RESUMO

De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.


Assuntos
Blastocisto/metabolismo , DNA (Citosina-5-)-Metiltransferases/metabolismo , Genoma , Herança Materna , Herança Paterna , Alelos , Animais , Ilhas de CpG , DNA (Citosina-5-)-Metiltransferases/genética , Metilação de DNA , Epigenômica , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Camundongos Endogâmicos DBA , Oócitos/metabolismo , Espermatozoides/metabolismo
11.
PLoS One ; 15(9): e0239196, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32991610

RESUMO

The aim of the present study was to (1) investigate the relationship between late-onset Alzheimer's disease (AD) and DNA methylation levels in six of the top seven AD-associated genes identified through a meta-analysis of recent genome wide association studies, APOE, BIN1, PICALM, CR1, CLU, and ABCA7, in blood, and (2) examine its applicability to the diagnosis of AD. We examined methylation differences at CpG island shores in the six genes using Sanger sequencing, and one of two groups of 48 AD patients and 48 elderly controls was used for a test or replication analysis. We found that methylation levels in three out of the six genes, CR1, CLU, and PICALM, were significantly lower in AD subjects. The combination of CLU methylation levels and the APOE genotype classified AD patients with AUC = 0.84 and 0.80 in the test and replication analyses, respectively. Our study implicates methylation differences at the CpG island shores of AD-associated genes in the onset of AD and suggests their diagnostic value.


Assuntos
Doença de Alzheimer/genética , Clusterina , Ilhas de CpG , Metilação de DNA , Proteínas Monoméricas de Montagem de Clatrina , Receptores de Complemento 3b , Idoso , Doença de Alzheimer/diagnóstico , Biomarcadores/sangue , Clusterina/sangue , Clusterina/genética , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Humanos , Japão , Masculino , Pessoa de Meia-Idade , Proteínas Monoméricas de Montagem de Clatrina/sangue , Proteínas Monoméricas de Montagem de Clatrina/genética , Receptores de Complemento 3b/sangue , Receptores de Complemento 3b/genética
12.
Mol Biol Evol ; 37(9): 2463-2464, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32893295

RESUMO

Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. Although Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their genetic dissimilarity to SARS-CoV-2 is so high that they are highly unlikely to be its direct ancestors. Thus, an intermediary host is suspected to link bat to human coronaviruses. Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastrointestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. Therefore, reduced genomic CpG alone is not a highly predictive biomarker, suggesting a need for additional biomarkers to reveal intermediate hosts or tissues. The hunt for the zoonotic origin of SARS-CoV-2 continues.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Genoma Viral , Pandemias , Pneumonia Viral/epidemiologia , Proteínas Virais/genética , Zoonoses/epidemiologia , Animais , Betacoronavirus/classificação , Betacoronavirus/patogenicidade , Quirópteros/virologia , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Ilhas de CpG , Eutérios/virologia , Evolução Molecular , Expressão Gênica , Mutação , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Vírus Reordenados/classificação , Vírus Reordenados/genética , Vírus Reordenados/patogenicidade , Recombinação Genética , Proteínas Virais/metabolismo , Zoonoses/transmissão , Zoonoses/virologia
13.
PLoS Pathog ; 16(9): e1008844, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32886716

RESUMO

The genomes of RNA and small DNA viruses of vertebrates display significant suppression of CpG dinucleotide frequencies. Artificially increasing dinucleotide frequencies results in substantial attenuation of virus replication, suggesting that these compositional changes may facilitate recognition of non-self RNA sequences. Recently, the interferon inducible protein ZAP, was identified as the host factor responsible for sensing CpG in viral RNA, through direct binding and possibly downstream targeting for degradation. Using an arrayed interferon stimulated gene expression library screen, we identified ZAPS, and its associated factor TRIM25, as inhibitors of human cytomegalovirus (HCMV) replication. Exogenous expression of ZAPS and TRIM25 significantly reduced virus replication while knockdown resulted in increased virus replication. HCMV displays a strikingly heterogeneous pattern of CpG representation with specific suppression of CpG motifs within the IE1 major immediate early transcript which is absent in subsequently expressed genes. We demonstrated that suppression of CpG dinucleotides in the IE1 gene allows evasion of inhibitory effects of ZAP. We show that acute virus replication is mutually exclusive with high levels of cellular ZAP, potentially explaining the higher levels of CpG in viral genes expressed subsequent to IE1 due to the loss of pressure from ZAP in infected cells. Finally, we show that TRIM25 regulates alternative splicing between the ZAP short and long isoforms during HCMV infection and interferon induction, with knockdown of TRIM25 resulting in decreased ZAPS and corresponding increased ZAPL expression. These results demonstrate for the first time that ZAP is a potent host restriction factor against large DNA viruses and that HCMV evades ZAP detection through suppression of CpG dinucleotides within the major immediate early 1 transcript. Furthermore, TRIM25 is required for efficient upregulation of the interferon inducible short isoform of ZAP through regulation of alternative splicing.


Assuntos
Processamento Alternativo , Ilhas de CpG , Infecções por Citomegalovirus/metabolismo , Citomegalovirus/fisiologia , Regulação Viral da Expressão Gênica , Proteínas de Ligação a RNA/metabolismo , Proteínas Repressoras/metabolismo , Replicação Viral , Linhagem Celular , Infecções por Citomegalovirus/genética , Infecções por Citomegalovirus/patologia , Humanos , Proteínas Imediatamente Precoces , Proteínas de Ligação a RNA/genética , Proteínas Repressoras/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Proteínas com Motivo Tripartido/genética , Proteínas com Motivo Tripartido/metabolismo , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo
14.
Nat Commun ; 11(1): 4779, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32963246

RESUMO

Highly reproducible smoking-associated DNA methylation changes in whole blood have been reported by many Epigenome-Wide-Association Studies (EWAS). These epigenetic alterations could have important implications for understanding and predicting the risk of smoking-related diseases. To this end, it is important to establish if these DNA methylation changes happen in all blood cell subtypes or if they are cell-type specific. Here, we apply a cell-type deconvolution algorithm to identify cell-type specific DNA methylation signals in seven large EWAS. We find that most of the highly reproducible smoking-associated hypomethylation signatures are more prominent in the myeloid lineage. A meta-analysis further identifies a myeloid-specific smoking-associated hypermethylation signature enriched for DNase Hypersensitive Sites in acute myeloid leukemia. These results may guide the design of future smoking EWAS and have important implications for our understanding of how smoking affects immune-cell subtypes and how this may influence the risk of smoking related diseases.


Assuntos
Metilação de DNA/efeitos dos fármacos , Epigenoma , Fumar/efeitos adversos , Algoritmos , Grupo com Ancestrais do Continente Asiático , Sangue , Ilhas de CpG , Epigenômica/métodos , Grupos Étnicos , Feminino , Humanos , Linfócitos , Masculino , Pessoa de Meia-Idade , Modelos Estatísticos , Células Mieloides
15.
Adv Exp Med Biol ; 1255: 123-132, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949395

RESUMO

Hypermethylation can downregulate many tumor suppressor gene expressions. Aplasia Ras homologue member I (ARHI, DIRAS3) is one of the maternally imprinted tumor suppressors in the RAS superfamily. This chapter overviewed the importance of ARHI methylation and expression phenomes in various types of cancers, although the exact mechanisms remain unclear. As an imprinted gene, aberrant DNA methylation of the paternal allele of ARHI was identified as a primary inhibitor of ARHI expression. The role of methylation in the CpG islands of the ARHI promoter region vary among ovarian cancers, breast cancers, hepatocellular carcinoma, colon cancers, pancreatic cancer osteosarcoma, glial tumors, follicular thyroid carcinoma, or lung cancers. The methylation of ARHI provides a new insight to understand molecular mechanisms of tumorigenesis and progression of cancers.


Assuntos
Ilhas de CpG/genética , Metilação de DNA , Neoplasias/genética , Regiões Promotoras Genéticas , Proteínas rho de Ligação ao GTP/genética , Regulação Neoplásica da Expressão Gênica/genética , Genes Supressores de Tumor , Humanos
16.
Nat Commun ; 11(1): 4529, 2020 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-32913184

RESUMO

Although Huntington's disease (HD) is a well studied Mendelian genetic disorder, less is known about its associated epigenetic changes. Here, we characterize DNA methylation levels in six different tissues from 3 species: a mouse huntingtin (Htt) gene knock-in model, a transgenic HTT sheep model, and humans. Our epigenome-wide association study (EWAS) of human blood reveals that HD mutation status is significantly (p < 10-7) associated with 33 CpG sites, including the HTT gene (p = 6.5 × 10-26). These Htt/HTT associations were replicated in the Q175 Htt knock-in mouse model (p = 6.0 × 10-8) and in the transgenic sheep model (p = 2.4 × 10-88). We define a measure of HD motor score progression among manifest HD cases based on multiple clinical assessments. EWAS of motor progression in manifest HD cases exhibits significant (p < 10-7) associations with methylation levels at three loci: near PEX14 (p = 9.3 × 10-9), GRIK4 (p = 3.0 × 10-8), and COX4I2 (p = 6.5 × 10-8). We conclude that HD is accompanied by profound changes of DNA methylation levels in three mammalian species.


Assuntos
Metilação de DNA , Epigênese Genética , Proteína Huntingtina/genética , Doença de Huntington/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Animais Geneticamente Modificados , Comportamento Animal , Ilhas de CpG/genética , Estudos Transversais , Modelos Animais de Doenças , Progressão da Doença , Feminino , Seguimentos , Técnicas de Introdução de Genes , Loci Gênicos , Estudo de Associação Genômica Ampla , Carga Global da Doença , Humanos , Doença de Huntington/sangue , Doença de Huntington/diagnóstico , Doença de Huntington/epidemiologia , Estudos Longitudinais , Masculino , Camundongos , Pessoa de Meia-Idade , Mutação , Estudos Prospectivos , Proteínas Recombinantes/genética , Sistema de Registros/estatística & dados numéricos , Índice de Gravidade de Doença , Ovinos , Adulto Jovem
17.
PLoS Comput Biol ; 16(9): e1008270, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32966276

RESUMO

We present Epiclomal, a probabilistic clustering method arising from a hierarchical mixture model to simultaneously cluster sparse single-cell DNA methylation data and impute missing values. Using synthetic and published single-cell CpG datasets, we show that Epiclomal outperforms non-probabilistic methods and can handle the inherent missing data characteristic that dominates single-cell CpG genome sequences. Using newly generated single-cell 5mCpG sequencing data, we show that Epiclomal discovers sub-clonal methylation patterns in aneuploid tumour genomes, thus defining epiclones that can match or transcend copy number-determined clonal lineages and opening up an important form of clonal analysis in cancer. Epiclomal is written in R and Python and is available at https://github.com/shahcompbio/Epiclomal.


Assuntos
Metilação de DNA , Análise de Célula Única , Análise por Conglomerados , Ilhas de CpG , Humanos , Probabilidade , Análise de Sequência de DNA/métodos
18.
DNA Cell Biol ; 39(11): 2052-2058, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32907377

RESUMO

Aberrant DNA methylation is thought to be an early event in cancer development. Thus, identification of DNA methylation-based markers may provide valuable evidence in clinical decision-making. In this study, a DNA methylation dataset from 514 normal-tumor pairs is used to explore possible shared differentially methylated regions (DMRs) across 12 cancer types. Results showed that DMR in Dopamine receptor D5 (DRD5) promoter may be serviced as a good candidate biomarker across different cancer types. We further validated the extended DMR (292bp) in DRD5 promoter using SEQUENOM MassARRAY platform. Detection of DRD5 promoter dynamic methylation will allow rapid risk assessment at diagnosis, for suspicious tumor with the tissue biopsies.


Assuntos
Biomarcadores Tumorais/genética , Metilação de DNA/genética , Neoplasias/genética , Receptores de Dopamina D5/genética , Ilhas de CpG/genética , Epigênese Genética/genética , Feminino , Humanos , Masculino , Neoplasias/classificação , Neoplasias/patologia , Regiões Promotoras Genéticas/genética
19.
Life Sci ; 261: 118311, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32861793

RESUMO

AIM: Bladder cancer (BCa) is one of the most commonly occurring urological malignancy. DNA methylation mediated by DNA methyltransferase 1 (DNMT1) plays a crucial role in the physiological and pathological processes of cancer. However, the role of upstream regulatory factors and downstream target genes of DNA methylation mediated by DNMT1 needs further study in BCa. We aim to discover the upstream regulatory factor and downstream target gene of DNMT1, which form a signaling pathway to regulate the progression of BCa. MAIN METHODS: DNMT1 expression in BCa tissues and cells was detected by qPCR and Western Blot. Balbc/nu/nu mice were used to determine the relationship between DNMT1 expression and tumor growth. CCK8, EdU, and transwell assays were employed to measure cell viability, proliferation, and migration respectively. RNA immunoprecipitation (RIP) assays and dual luciferase reporter assays were applied to determine the relationships among DNMT1, miR-152-3p and PTEN. KEY FINDINGS: A significant up-regulation of DNMT1 in BCa tissues and cells, and silencing of DNMT1 expression inhibited the tumor growth in vivo. Knockdown of DNMT1 inhibited the cell growth and migration of BCa cells. miR-152-3p inhibited the DNMT1 and over-expression of DNMT1 restored the cellular function of miR-152-3p in BCa cells. DNMT1 regulated the phosphatase and tensin homolog (PTEN) expression via modulating the status of DNA methylation in the promoter of PTEN. SIGNIFICANCE: This study confirmed the role and underlying mechanism of DNMT1-mediated DNA methylation and displayed a novel regulatory pathway miR-152/DNMT1/PTEN in BCa, thus, providing a potential diagnostic and therapeutic targets for BCa.


Assuntos
MicroRNAs/genética , PTEN Fosfo-Hidrolase/genética , Proteínas Repressoras/genética , Neoplasias da Bexiga Urinária/genética , Animais , Linhagem Celular Tumoral , Ilhas de CpG/genética , Metilação de DNA , Regulação Neoplásica da Expressão Gênica , Técnicas de Silenciamento de Genes , Inativação Gênica , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Neoplasias da Bexiga Urinária/patologia , Ensaios Antitumorais Modelo de Xenoenxerto
20.
Proc Natl Acad Sci U S A ; 117(34): 20785-20793, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32778592

RESUMO

Transfer RNA (tRNA) activity is tightly regulated to provide a physiological protein translation, and tRNA chemical modifications control its function in a complex with ribosomes and messenger RNAs (mRNAs). In this regard, the correct hypermodification of position G37 of phenylalanine-tRNA, adjacent to the anticodon, is critical to prevent ribosome frameshifting events. Here we report that the tRNA-yW Synthesizing Protein 2 (TYW2) undergoes promoter hypermethylation-associated transcriptional silencing in human cancer, particularly in colorectal tumors. The epigenetic loss of TYW2 induces guanosine hypomodification in phenylalanine-tRNA, an increase in -1 ribosome frameshift events, and down-regulation of transcripts by mRNA decay, such as of the key cancer gene ROBO1. Importantly, TYW2 epigenetic inactivation is linked to poor overall survival in patients with early-stage colorectal cancer, a finding that could be related to the observed acquisition of enhanced migration properties and epithelial-to-mesenchymal features in the colon cancer cells that harbor TYW2 DNA methylation-associated loss. These findings provide an illustrative example of how epigenetic changes can modify the epitranscriptome and further support a role for tRNA modifications in cancer biology.


Assuntos
Neoplasias do Colo/genética , Mudança da Fase de Leitura do Gene Ribossômico , RNA de Transferência/genética , Ribossomos/genética , tRNA Metiltransferases/deficiência , Adulto , Idoso , Anticódon/genética , Anticódon/metabolismo , Linhagem Celular Tumoral , Neoplasias do Colo/enzimologia , Neoplasias do Colo/metabolismo , Ilhas de CpG , Epigênese Genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Conformação de Ácido Nucleico , Fenilalanina/genética , Fenilalanina/metabolismo , Regiões Promotoras Genéticas , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Transferência/metabolismo , Ribossomos/metabolismo , tRNA Metiltransferases/genética , tRNA Metiltransferases/metabolismo
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