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Efeito das concentrações das vitaminas (séricas e da dieta) e do polimorfismo MTHFR C677T na taxa de metilação global do DNA durante o período gestacional; Effect of serum vitamin, vitamin intake and MTHFR C677T gene polymorphism on global DNA methylation during pregnancy

Kubota, Ananka Midori
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 14/11/2008 PT
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66.37%
A cobalamina (vitamina B12) e o ácido fólico são nutrientes essenciais para síntese de DNA, metionina e S-adenosilmetionina (SAM). A SAM é uma potente doadora de grupo metil necessário nas reações de metilação do DNA. Deficiências dessas vitaminas podem comprometer as concentrações da SAM e, indiretamente, a metilação do DNA. O objetivo deste estudo foi avaliar o efeito das concentrações de vitaminas (no sangue e na dieta), metabólitos (no soro) e do polimorfismo MTHFR C677T na taxa de metilação global do DNA. Participaram do estudo 103 gestantes, das quais foram colhidas amostras de sangue nas idades gestacionais de 16, 28 e 36 semanas. Foram realizadas as determinações dos valores de folato eritrocitário, e das concentrações séricas de folato, cobalamina, vitamina B6, homocisteína (tHcy), metionina, ácido metilmalônico (MMA), SAM e S-adenosilhomocisteína (SAH), além genotipagem para o polimorfismo MTHFR C677T por PCR-RFLP. A taxa de metilação global do DNA foi avaliada indiretamente por reação de extensão usando [3H]dCTP. Para avaliação nutricional foi aplicado um inquérito recordatório de 24 horas no dia de cada coleta. Devido ao uso de suplementação com ácido fólico e/ou polivitamínicos...

Avaliação da taxa de metilação do DNA de leucócitos na região promotora dos genes IFNγ, Serpin B5 e Stratifin durante o período gestacional e sua relação com o metabolismo das vitaminas e metabólitos; Assessment of leukocyte DNA methylation index in the promoter region of IFNγ, Serpin B5 and Stratifin genes in women with different gestational ages and their relationship to the metabolism of vitamins and metabolites

Silva, Thaiomara Alves
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 15/10/2010 PT
Relevância na Pesquisa
66.43%
A metilação do DNA é uma alteração epigenética que atua na regulação da expressão gênica. A deficiência de vitaminas (cobalamina, B6 e folato) pode interferir na taxa de metilação. O efeito da deficiência destas vitaminas foi determinado em estudos com cultura de células e em animais. No entanto, são raros os estudos realizados com seres humanos. Os objetivos deste trabalho foram: avaliar a taxa de metilação do DNA de leucócitos na região promotora dos genes Interferon gama (IFNγ), Serpin B5 e Stratifin; verificar se existe associação entre as concentrações das vitaminas e dos metabólitos com a taxa de metilação do DNA dos 3 genes; e analisar quais são os fatores de predição para a taxa de metilação do DNA (variável dependente) considerando como variáveis independentes os valores séricos das vitaminas e metabólitos, em mulheres com idades gestacionais de 16, 28 e 36 semanas. Cento e oitenta e três mulheres foram convidadas a participar desse estudo, porém apenas 96 completaram o estudo prospectivo. Foram determinadas as concentrações séricas da cobalamina (Cbl), folato, vitamina B6, S-adenosilmetionina (SAM), S-adenosilhomocisteína (SAH), ácido metilmalônico (MMA), homocisteína total (tHcy) e folato eritrocitário. A taxa de metilação nos 3 genes foi determinada por qMSP (Quantitative Methylation Specific - Polimerase Chain Reaction). Várias mulheres estavam fazendo uso de suplementação com ácido fólico e/ou polivitamínicos. Diante deste fato foram formados 4 subgrupos: Grupo 1 (constituído por mulheres que não usaram suplementação)...

Avaliação da taxa de metilação do DNA em região promotora e de vitaminas e citocinas em mulheres com história de abortos recorrentes; Investigation of DNA methylation rate in promoter region and vitamins and cytokines in women with a history of recurrent miscarriage.

Monteiro, Nathalia Sierra
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 20/03/2014 PT
Relevância na Pesquisa
66.4%
O aborto espontâneo recorrente (AER) caracteriza-se pela ocorrência de três ou mais abortos consecutivos espontâneos até a 20ª semana de gestação. É uma condição patológica multifatorial, em que alterações morfológicas uterinas, distúrbios endócrinos, alterações no cariótipo, polimorfismos genéticos relacionados aos genes envolvidos no metabolismo da homocisteína, hemostasia, infecções, autoanticorpos e o processo inflamatório podem contribuir para a ocorrência de AER. O estado fisiológico do endométrio é essencial para a implantação do embrião no útero durante a gestação. Na interface materno-fetal, há uma modulação de citocinas, necessária para o estabelecimento da angiogênese e desenvolvimento da placenta. Um desequilíbrio entre as citocinas pode diminuir a tolerância ao feto e ocasionar rejeição fetal. A concentração de citocinas pode ser modificada por conta de uma diminuição na expressão de alguns genes, e esta pode ser regulada pelo seu estado de metilação sítio-específica. A metilação do DNA é um mecanismo epigenético de regulação gênica, e que corresponde à incorporação de grupos metila em ilhas CpG localizadas próximas às regiões promotoras de genes humanos...

Dynamics of DNA Methylation during Early Development of the Preimplantation Bovine Embryo

Dobbs, Kyle B.; Rodriguez, Marlon; Sudano, Mateus J.; Ortega, M. Sofia; Hansen, Peter J.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
66.36%
There is species divergence in control of DNA methylation during preimplantation development. The exact pattern of methylation in the bovine embryo has not been established nor has its regulation by gender or maternal signals that regulate development such as colony stimulating factor 2 (CSF2). Using immunofluorescent labeling with anti-5-methylcytosine and embryos produced with X-chromosome sorted sperm, it was demonstrated that methylation decreased from the 2-cell stage to the 6-8 cell stage and then increased thereafter up to the blastocyst stage. In a second experiment, embryos of specific genders were produced by fertilization with X- or Y-sorted sperm. The developmental pattern was similar to the first experiment, but there was stage × gender interaction. Methylation was greater for females at the 8-cell stage but greater for males at the blastocyst stage. Treatment with CSF2 had no effect on labeling for DNA methylation in blastocysts. Methylation was lower for inner cell mass cells (i.e., cells that did not label with anti-CDX2) than for trophectoderm (CDX2-positive). The possible role for DNMT3B in developmental changes in methylation was evaluated by determining gene expression and degree of methylation. Steady-state mRNA for DNMT3B decreased from the 2-cell stage to a nadir for D 5 embryos >16 cells and then increased at the blastocyst stage. High resolution melting analysis was used to assess methylation of a CpG rich region in an intronic region of DNMT3B. Methylation percent decreased between the 6-8 cell and the blastocyst stage but there was no difference in methylation between ICM and TE. Results indicate that DNA methylation undergoes dynamic changes during the preimplantation period in a manner that is dependent upon gender and cell lineage. Developmental changes in expression of DNMT3B are indicative of a possible role in changes in methylation. Moreover...

A survey of DNA methylation across social insect species, life stages, and castes reveals abundant and caste-associated methylation in a primitively social wasp

Weiner, Susan A.; Galbraith, David A.; Adams, Dean C.; Valenzuela, Nicole; Noll, Fernando B.; Grozinger, Christina M.; Toth, Amy L.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 795-799
ENG
Relevância na Pesquisa
66.35%
DNA methylation plays an important role in the epigenetic control of developmental and behavioral plasticity, with connections to the generation of striking phenotypic differences between castes (larger, reproductive queens and smaller, non-reproductive workers) in honeybees and ants. Here, we provide the first comparative investigation of caste- and life stage-associated DNA methylation in several species of bees and vespid wasps displaying different levels of social organization. Our results reveal moderate levels of DNA methylation in most bees and wasps, with no clear relationship to the level of sociality. Strikingly, primitively social Polistes dominula paper wasps show unusually high overall DNA methylation and caste-related differences in site-specific methylation. These results suggest DNA methylation may play a role in the regulation of behavioral and physiological differences in primitively social species with more flexible caste differences. © 2013 Springer-Verlag Berlin Heidelberg.

DNA methylation as a potential biomarker for Alzheimer disease; Metilação de DNA como potencial biomarcador da doença de Alzheimer

Almeida, João Carlos Moutinho de
Fonte: Universidade de Aveiro Publicador: Universidade de Aveiro
Tipo: Dissertação de Mestrado
ENG
Relevância na Pesquisa
66.39%
DNA methylation is the major studied epigenetic mechanism and consists in the addiction of a methyl group to 5’ carbon position of the cytosine ring. Methylation of promoter gene regions are directly correlated with gene silencing, which can allow the development of certain diseases since relevant genes may be inhibited due to its promoter methylation; being that the opposite can also occur. This epigenetic mechanism has been linked to cancer and recently it is also being pointed to have an important role in neurological disorders, such as Alzheimer’s Disease (AD). Furthermore, aging is the major risk factor for AD, and also the process underlying many of the epigenetic alterations. As AD etiology and pathological development is not complete understood, alterations in epigenetic mechanisms like DNA methylation may underlie the basis of gene expression alterations. Hence, in this study, possible AD patients and age- and sex-matched controls were used. Genomic DNA was extracted from blood samples and the global methylation levels were determined using an ELISA-type assay, The possible AD patients exhibit lower methylation levels (0,75%±0,29) than age- and sex-matched controls (0,86%±0,29). Gene specific methylation profiles of AD related genes...

Predicting the progress of colon cancer by DNA methylation markers of the p16 gene in feces - Evidence from an animal model

Wu,Wen-Chih; Hsu,Chih-Hsiung; Kuan,Jen-Chun; Hsieh,Jih-Fu; Sun,Chien-An; Yang,Tsan; Wu,Chang-Chieh; Chou,Yu-Ching
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2013 EN
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66.35%
A new noninvasive screening tool for colorectal neoplasia detects epigenetic alterations exhibited by gastrointestinal tumor cells shed into stool. There is insufficient existing data to determine temporal associations between colorectal cancer (CRC) progression and aberrant DNA methylation. To evaluate the feasibility of using fecal DNA methylation status to determine CRC progression, we collected stool samples from 14 male SD rats aged six weeks, and administered subcutaneous injections of either 1,2-dimethylhydrazine or saline weekly. p16 DNA methylation statuses in tumorous and normal colon tissue, and from stool samples were determined using methylation-specific PCR. Additionally, p16 methylation was detected in stool DNA from 85.7% of the CRC rats. The earliest change in p16 methylation status in the DMH-treated group stool samples occurred during week nine; repeatabilities were 57.1% in week 19 (p = 0.070) and 85.7% in week 34 (p = 0.005). A temporal correlation was evidenced between progression of CRC and p16 methylation status, as evidenced by DMH-induced rat feces. Using fecal DNA methylation status to determine colorectal tissue methylation status can reveal CRC progression. Our data suggests that p16 promoter methylation is a feasible epigenetic marker for the detection and may be useful for CRC screening.

Effects of Particulate Matter on Genomic DNA Methylation Content and iNOS Promoter Methylation

Tarantini, Letizia; Bonzini, Matteo; Apostoli, Pietro; Pegoraro, Valeria; Bollati, Valentina; Marinelli, Barbara; Cantone, Laura; Rizzo, Giovanna; Hou, Lifang; Bertazzi, Pier Alberto; Schwartz, Joel David; Baccarelli, Andrea
Fonte: National Institute of Environmental Health Sciences Publicador: National Institute of Environmental Health Sciences
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.37%
Background: Altered patterns of gene expression mediate the effects of particulate matter (PM) on human health, but mechanisms through which PM modifies gene expression are largely undetermined.Objectives We aimed at identifying short- and long-term effects of PM exposure on DNA methylation, a major genomic mechanism of gene expression control, in workers in an electric furnace steel plant with well-characterized exposure to PM with aerodynamic diameters < 10 μm (PM10). Methods: We measured global genomic DNA methylation content estimated in Alu and long interspersed nuclear element-1 (LINE-1) repeated elements, and promoter DNA methylation of iNOS (inducible nitric oxide synthase), a gene suppressed by DNA methylation and induced by PM exposure in blood leukocytes. Quantitative DNA methylation analysis was performed through bisulfite PCR pyrosequencing on blood DNA obtained from 63 workers on the first day of a work week (baseline, after 2 days off work) and after 3 days of work (postexposure). Individual PM10 exposure was between 73.4 and 1,220 μg/m3. Results: Global methylation content estimated in Alu and LINE-1 repeated elements did not show changes in postexposure measures compared with baseline. PM10 exposure levels were negatively associated with methylation in both Alu [β = −0.19 %5-methylcytosine (%5mC); p = 0.04] and LINE-1 [β = −0.34 %5mC; p = 0.04]...

Biomarkers of Lead Exposure and DNA Methylation within Retrotransposons

Bollati, Valentina; Tarantini, Letizia; Hu, Howard; Schwartz, Joel David; Wright, Rosalind Jo; Park, Sung Kyun; Sparrow, David; Vokonas, Pantel S; Baccarelli, Andrea; Wright, Robert O.
Fonte: National Institute of Environmental Health Sciences Publicador: National Institute of Environmental Health Sciences
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.39%
Background: DNA methylation is an epigenetic mark that regulates gene expression. Changes in DNA methylation within white blood cells may result from cumulative exposure to environmental metals such as lead. Bone lead, a marker of cumulative exposure, may therefore better predict DNA methylation than does blood lead. Objective: In this study we compared associations between lead biomarkers and DNA methylation. Methods: We measured global methylation in participants of the Normative Aging Study (all men) who had archived DNA samples. We measured patella and tibia lead levels by K-X-Ray fluorescence and blood lead by atomic absorption spectrophotometry. DNA samples from blood were used to determine global methylation averages within CpG islands of long interspersed nuclear elements-1 (LINE-1) and Alu retrotransposons. A mixed-effects model using repeated measures of Alu or LINE-1 as the dependent variable and blood/bone lead (tibia or patella in separate models) as the primary exposure marker was fit to the data. Results: Overall mean global methylation (± SD) was 26.3 ± 1.0 as measured by Alu and 76.8 ± 1.9 as measured by LINE-1. In the mixed-effects model, patella lead levels were inversely associated with LINE-1 (β = −0.25; p less than 0.01) but not Alu (β = −0.03; p = 0.4). Tibia lead and blood lead did not predict global methylation for either Alu or LINE-1. Conclusion: Patella lead levels predicted reduced global DNA methylation within LINE-1 elements. The association between lead exposure and LINE-1 DNA methylation may have implications for the mechanisms of action of lead on health outcomes...

Particulate Matter, DNA Methylation in Nitric Oxide Synthase, and Childhood Respiratory Disease

Breton, Carrie V.; Salam, Muhammad T.; Siegmund, Kimberly D.; Gilliland, Frank D.; Wang, Xinhui; Byun, Hyang-Min
Fonte: National Institute of Environmental Health Sciences Publicador: National Institute of Environmental Health Sciences
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.37%
Background: Air pollutants have been associated with childhood asthma and wheeze. Epigenetic regulation of nitric oxide synthase—the gene responsible for nitric oxide production—may be affected by air pollutants and contribute to the pathogenesis of asthma and wheeze. Objective: Our goal was to investigate the association between air pollutants, DNA methylation, and respiratory outcomes in children. Methods: Given residential address and buccal sample collection date, we estimated 7-day, 1-month, 6-month, and 1-year cumulative average (PM_{2.5}) and (PM_{10}) (particulate matter ≤ 2.5 and ≤ 10 µm aerodynamic diameter, respectively) exposures for 940 participants in the Children’s Health Study. Methylation of 12 CpG sites in three NOS (nitric oxide synthase) genes was measured using a bisulfite-polymerase chain reaction Pyrosequencing assay. Beta regression models were used to estimate associations between air pollutants, percent DNA methylation, and respiratory outcomes. Results: A 5-µg/(m^3) increase in (PM_{2.5}) was associated with a 0.20% [95% confidence interval (CI): –0.32, –0.07] to 1.0% (95% CI: –1.61, –0.56) lower DNA methylation at NOS2A position 1, 0.06% (95% CI: –0.18, 0.06) to 0.58% (95% CI: –1.13...

Effects of airborne pollutants on mitochondrial DNA Methylation

Byun, Hyang-Min; Panni, Tommaso; Motta, Valeria; Hou, Lifang; Nordio, Francesco; Apostoli, Pietro; Bertazzi, Pier Alberto; Baccarelli, Andrea
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.36%
Background: Mitochondria have small mitochondrial DNA (mtDNA) molecules independent from the nuclear DNA, a separate epigenetic machinery that generates mtDNA methylation, and are primary sources of oxidative-stress generation in response to exogenous environments. However, no study has yet investigated whether mitochondrial DNA methylation is sensitive to pro-oxidant environmental exposures. Methods: We sampled 40 male participants (20 high-, 20 low-exposure) from each of three studies on airborne pollutants, including investigations of steel workers exposed to metal-rich particulate matter (measured as PM1) in Brescia, Italy (Study 1); gas-station attendants exposed to air benzene in Milan, Italy (Study 2); and truck drivers exposed to traffic-derived Elemental Carbon (EC) in Beijing, China (Study 3). We have measured DNA methylation from buffy coats of the participants. We measured methylation by bisulfite-Pyrosequencing in three mtDNA regions, i.e., the transfer RNA phenylalanine (MT-TF), 12S ribosomal RNA (MT-RNR1) gene and “D-loop” control region. All analyses were adjusted for age and smoking. Results: In Study 1, participants with high metal-rich PM1 exposure showed higher MT-TF and MT-RNR1 methylation than low-exposed controls (difference = 1.41...

A panel study of occupational exposure to fine particulate matter and changes in DNA methylation over a single workday and years worked in boilermaker welders

Kile, Molly L; Fang, Shona; Baccarelli, Andrea A; Tarantini, Letizia; Cavallari, Jennifer; Christiani, David C
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.34%
Background: Exposure to pollutants including metals and particulate air pollution can alter DNA methylation. Yet little is known about intra-individual changes in DNA methylation over time in relationship to environmental exposures. Therefore, we evaluated the effects of acute- and chronic metal-rich PM2.5 exposures on DNA methylation. Methods: Thirty-eight male boilermaker welders participated in a panel study for a total of 54 person days. Whole blood was collected prior to any welding activities (pre-shift) and immediately after the exposure period (post-shift). The percentage of methylated cytosines (%mC) in LINE-1, Alu, and inducible nitric oxide synthase gene (iNOS) were quantified using pyrosequencing. Personal PM2.5 (particulate matter with an aerodynamic diameter ≤ 2.5 μm) was measured over the work-shift. A questionnaire assessed job history and years worked as a boilermaker. Linear mixed models with repeated measures evaluated associations between DNA methylation, PM2.5 concentration (acute exposure), and years worked as a boilermaker (chronic exposure). Results: PM2.5 exposure was associated with increased methylation in the promoter region of the iNOS gene (β = 0.25, SE: 0.11, p-value = 0.04). Additionally, the number of years worked as a boilermaker was associated with increased iNOS methylation (β = 0.03...

Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants

Byun, Hyang-Min; Motta, Valeria; Panni, Tommaso; Bertazzi, Pier Alberto; Apostoli, Pietro; Hou, Lifang; Baccarelli, Andrea A
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
66.37%
Background: Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods: We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies. Results: High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study...

Obesity alone or with type 2 diabetes is associated with tissue specific alterations in DNA methylation and gene expression of PPARGC1A and IGF2

Chen, M.; Macpherson, A.; Owens, J.; Wittert, G.; Heilbronn, L.
Fonte: Herbert Publications Ltd Publicador: Herbert Publications Ltd
Tipo: Artigo de Revista Científica
Publicado em //2012 EN
Relevância na Pesquisa
66.38%
BACKGROUND: Epigenetic modifications of key genes have been linked to the development of aging related diseases, such as type 2 diabetes, with increased DNA methylation of the transcriptional co-activator, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) in islets and skeletal muscle of patients with type 2 diabetes. Here, we examined DNA methylation and gene expression of PPARGC1A and insulin like growth factor-2 (IGF2) in adipose tissue and skeletal muscle of lean and morbidly obese individuals with or without type 2 diabetes. METHODS: Adipose tissue and skeletal muscle biopsies were collected from 24 lean, obese, and obese patients with type 2 diabetes (n=8/group). DNA methylation and gene expression of PPARGC1A and IGF2 were measured using pyrosequencing and quantitative real-time PCR respectively. RESULTS: DNA methylation and expression of both genes varied in a tissue specific manner (P<0.05). The highest levels of PPARGC1A methylation were observed in subcutaneous adipose tissue and lowest in muscle (P≤0.001), whereas IGF2 methylation was lowest in subcutaneous adipose tissue as compared with visceral adipose tissue and muscle (P≤0.04). Expression of PPARGC1A and IGF2 was highest in muscle and lowest in subcutaneous adipose tissue (P≤0.001) and PPARGC1A expression was conversely correlated with DNA methylation in skeletal muscle (r=-0.54...

DNA methylation in the rectal mucosa is associated with crypt proliferation and fecal short-chain fatty acids

Worthley, D.; Whitehall, V.; Le Leu, R.; Irahara, N.; Buttenshaw, R.; Mallitt, K.A.; Greco, S.; Ramsnes, I.; Winter, J.; Hu, Y.; Ogino, S.; Young, G.; Leggett, B.
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
Relevância na Pesquisa
66.38%
BACKGROUND DNA methylation varies throughout the normal colorectal mucosa and DNA methylation in normal appearing mucosa is associated with serrated and adenomatous neoplasia elsewhere within the colorectum. AIMS The purpose of this study was to measure luminal chemistry, rectal proliferation and mucosal DNA methylation and thus determine whether regional and pathological patterns of DNA methylation could be explained by luminal and epithelial factors. METHODS Twenty healthy subjects had normal rectal mucosal biopsies and a 24-h fecal collection. Rectal biopsies were analyzed for epithelial proliferation (Ki67 immunohistochemistry) and DNA methylation at 17 different markers, including “type A” markers (ESR1, GATA5, HIC1, HPP1, SFRP1), “type C” markers (MGMT, MLH1, CDKN2A, MINT1, MINT2, MINT31, IGF2, CACNA1G, NEUROG1, SOCS1, RUNX3), and LINE-1. Fecal analysis included short-chain fatty acids (SCFA), pH and ammonia. Mean “type A” and CIMP panel methylation Z-scores were calculated. RESULTS Rectal proliferation was significantly correlated with methylation at ESR1 (ρ = 0.81, P = 0.003) and GATA5 (ρ = 0.78, P = 0.012). LINE-1 methylation was 71.7 vs. 74.1%, in patients with “low” and “high” fecal total SCFA concentration (defined by the median value)...

Genomic distribution of H3K9me2 and DNA methylation in a maize genome

West, Patrick T.; Li, Qing; Ji, Lexiang; Eichten, Steven R.; Song, Jawon; Vaughn, Matthew W.; Schmitz, Robert J.; Springer, Nathan M.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica Formato: 10 pages
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66.35%
DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.; The research was supported by a grant from the National Science Foundation (IOS-1237931) to MWV and NMS. This work also used resources or cyberinfrastructure provided by iPlant Collaborative. The iPlant Collaborative is funded by a grant from the National Science Foundation (DBI-0735191; www. iplantcollaborative.org). Start-up funds from the University of Georgia and a research grant from the National Science Foundation (IOS-1339194) to RJS supported aspects of this study.

Quantitation of DNA methylation by melt curve analysis

Smith, E.; Jones, M.; Drew, P.
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em //2009 EN
Relevância na Pesquisa
66.39%
Background: Methylation of DNA is a common mechanism for silencing genes, and aberrant methylation is increasingly being implicated in many diseases such as cancer. There is a need for robust, inexpensive methods to quantitate methylation across a region containing a number of CpGs. We describe and validate a rapid, in-tube method to quantitate DNA methylation using the melt data obtained following amplification of bisulfite modified DNA in a real-time thermocycler. Methods: We first describe a mathematical method to normalise the raw fluorescence data generated by heating the amplified bisulfite modified DNA. From this normalised data the temperatures at which melting begins and finishes can be calculated, which reflect the less and more methylated template molecules present respectively. Also the T50, the temperature at which half the amplicons are melted, which represents the summative methylation of all the CpGs in the template mixture, can be calculated. These parameters describe the methylation characteristics of the region amplified in the original sample. Results: For validation we used synthesized oligonucleotides and DNA from fresh cells and formalin fixed paraffin embedded tissue, each with known methylation. Using our quantitation we could distinguish between unmethylated...

24-Hour Rhythms of DNA Methylation and Their Relation with Rhythms of RNA Expression in the Human Dorsolateral Prefrontal Cortex

Lim, Andrew S. P.; Srivastava, Gyan P.; Yu, Lei; Chibnik, Lori B.; Xu, Jishu; Buchman, Aron S.; Schneider, Julie A.; Myers, Amanda J.; Bennett, David A.; De Jager, Philip L.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
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66.4%
Circadian rhythms modulate the biology of many human tissues, including brain tissues, and are driven by a near 24-hour transcriptional feedback loop. These rhythms are paralleled by 24-hour rhythms of large portions of the transcriptome. The role of dynamic DNA methylation in influencing these rhythms is uncertain. While recent work in Neurospora suggests that dynamic site-specific circadian rhythms of DNA methylation may play a role in modulating the fungal molecular clock, such rhythms and their relationship to RNA expression have not, to our knowledge, been elucidated in mammalian tissues, including human brain tissues. We hypothesized that 24-hour rhythms of DNA methylation exist in the human brain, and play a role in driving 24-hour rhythms of RNA expression. We analyzed DNA methylation levels in post-mortem human dorsolateral prefrontal cortex samples from 738 subjects. We assessed for 24-hour rhythmicity of 420,132 DNA methylation sites throughout the genome by considering methylation levels as a function of clock time of death and parameterizing these data using cosine functions. We determined global statistical significance by permutation. We then related rhythms of DNA methylation with rhythms of RNA expression determined by RNA sequencing. We found evidence of significant 24-hour rhythmicity of DNA methylation. Regions near transcription start sites were enriched for high-amplitude rhythmic DNA methylation sites...

Assessing DNA methylation in the developing human intestinal epithelium - potential link to Inflammatory Bowel Disease

Kraiczy, Judith; Nayak, Komal; Ross, Alexander; Raine, Tim; Mak, Tim Nam; Gasparetto, Marco; Cario, Elke; Rakyan, Vardhman; Heuschkel, Robert; Zilbauer, Matthias
Fonte: Department of Paediatrics, University of Cambridge Publicador: Department of Paediatrics, University of Cambridge
Tipo: Article; published version
EN
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This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/mi.2015.88; DNA methylation is one of the major epigenetic mechanisms implicated in regulating cellular development and cell-type specific gene expression. Here, we performed simultaneous genome-wide DNA methylation and gene expression analysis on purified intestinal epithelial cells derived from human foetal gut, healthy paediatric biopsies and children newly diagnosed with IBD. Results were validated using pyrosequencing, real-time PCR and immunostaining. The functional impact of DNA methylation changes on gene expression was assessed by employing in-vitro assays in intestinal cell lines. DNA methylation analyses allowed identification of 214 genes, for which expression is regulated via DNA methylation, i.e. regulatory differentially methylated regions (rDMRs). Pathway and functional analysis of rDMRs suggested a critical role for DNA methylation in regulating gene expression and functional development of the human intestinal epithelium. Moreover, analysis performed on intestinal epithelium of children newly diagnosed with IBD revealed alterations in DNA methylation within genomic loci, which were found to overlap significantly with those undergoing methylation changes during intestinal development. Our study provides novel insights into the physiological role of DNA methylation in regulating functional maturation of the human intestinal epithelium. Moreover...

Predicting Genome-wide DNA Methylation in Humans

Zhang, Weiwei
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Tese de Doutorado
Publicado em //2014
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66.37%

DNA methylation is one of the most studied and important epigenetic modifications in cells, playing a role in DNA transcription, splicing, and imprinting. Recently, advanced genome-wide DNA methylation profiling technologies have been developed, making it possible to conduct methylome-wide association studies. One of the problems with large scale DNA methylation studies is that the current technologies are either targeting only a limited number of CpG sites in the genome or whole genome sequencing is expensive and time consuming for most laboratories. Computational prediction of CpG site-specific methylation levels is the cost-saving and time-saving alternative.

In this work, we found striking patterns of DNA methylation across the genome. We show that correlation among CpG sites decays rapidly within several hundreds base pairs in contrast to the LD structure of genotypes which holds for up to several KB. Using genomic features including, neighbor CpG site methylation and genomic distance, genomic context such as CpG island regions, and genomic regulatory elements, we built random forest classifiers to predict CpG site methylation levels. Our approach achieves 92% prediction accuracy at single CpG sites in different genome-wide methylation datasets. We achieves the highest accuracy as 98% for prediction within CpG island regions. What's more...