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A simple ATAC-seq protocol for population epigenetics 5
De Carvalho Augusto, Ronaldo; Rey, Oliver; Cosseau, Céline; Chaparro, Cristian; Vidal-dupiol, Jeremie; Allienne, Jean-françois; Duval, David; Pinaud, Silvain; Tönges, Sina; Andriantsoa, Ranja; Luquet, Emilien; Aubret, Fabien; Dia Sow, Mamadou; David, Patrice; Thomson, Vicki; Joly, Dominique; Gomes Lima, Mariana; Federico, Déborah; Danchin, Etienne; Minoda, Aki; Grunau, Christoph.
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
Tipo: Text Palavras-chave: Epigenetics; Epigenomics; ATAC-seq; Daphnia pulex; Schistosoma mansoni.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00681/79353/81859.pdf
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Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird 5
Soulsbury, Carl D.; Lipponen, Anssi; Wood, Kristie; Mein, Charles A.; Hoffman, Joseph I.; Lebigre, Christophe.
Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) as well as by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti-related neuropeptide: AgRP) in...
Tipo: Text Palavras-chave: AgRP; Coloration; Epigenetics; Heterozygosity; Melanin; Sexual ornament.
Ano: 2018 URL: http://archimer.ifremer.fr/doc/00452/56391/58029.pdf
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Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon 5
Christensen, Kris A; Le Luyer, Jeremy; Chan, Michelle T T; Rondeau, Eric B; Koop, Ben F; Bernatchez, Louis; Devlin, Robert H.
Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to...
Tipo: Text Palavras-chave: Epigenetics; Transcriptome; GxE; Transgenic; Growth hormone; Salmonid.
Ano: 2021 URL: https://archimer.ifremer.fr/doc/00677/78890/81188.pdf
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Assessment of changes in the brca2 and p53 genes in breast invasive ductal carcinoma in northeast Brazil 48
Ramalho,Eduardo AVF; Silva-Filho,João LQ; Cartaxo,Marina FS; Cavalcanti,Carmelita BL; Rêgo,Moacyr JBM; Oliveira,Maria BM; Beltrão,Eduardo IC.
BACKGROUND: BRCA protein interacts with at least 13 different proteins that have been implicated with cancer susceptibility and loss of BRCA function is correlated to sensitivity to DNA crosslinking agents in preclinical models. RESULTS: BRCA2 methylation frequency was 44%, p53 Pro22 allele frequency was 32% and heterozygous frequency of Arg/Pro72 genotype was 60% which could be associated as risk factor for metastasis (p = 0.046 OR = 4.190). Regarding to polymorphism of codon 249 the frequency of Arg249 allele presented 82% which was considered not statistically significant. CONCLUSIONS: There was not statistical significance to BRCA2 promoter methylation with any parameters chosen. However, our findings suggest that patients who present heterozygous...
Tipo: Journal article Palavras-chave: Breast cancer; Epigenetics; Metastasis; Methylation; Polymorphism.
Ano: 2014 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602014000100003
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BjussuLAAO-II induces cytotoxicity and alters DNA methylation of cell-cycle genes in monocultured/co-cultured HepG2 cells 80
Machado,Ana Rita Thomazela; Aissa,Alexandre Ferro; Ribeiro,Diego Luis; Ferreira Jr.,Rui Seabra; Sampaio,Suely Vilela; Antunes,Lusânia Maria Greggi.
Abstract Background: The use of animal venoms and their toxins as material sources for biotechnological applications has received much attention from the pharmaceutical industry. L-amino acid oxidases from snake venoms (SV-LAAOs) have demonstrated innumerous biological effects and pharmacological potential against different cancer types. Hepatocellular carcinoma has increased worldwide, and the aberrant DNA methylation of liver cells is a common mechanism to promote hepatic tumorigenesis. Moreover, tumor microenvironment plays a major role in neoplastic transformation. To elucidate the molecular mechanisms responsible for the cytotoxic effects of SV-LAAO in human cancer cells, this study aimed to evaluate the cytotoxicity and the alterations in DNA...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Snake venom; Epigenetics; GADD45A; CCND1; CDKN1A.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992019000100305
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Cardio-respiratory development in bird embryos: new insights from a venerable animal model 96
Burggren,Warren W.; Santin,Josele Flores; Antich,Maria Rojas.
ABSTRACT The avian embryo is a time-honored animal model for understanding vertebrate development. A key area of extensive study using bird embryos centers on developmental phenotypic plasticity of the cardio-respiratory system and how its normal development can be affected by abiotic factors such as temperature and oxygen availability. Through the investigation of the plasticity of development, we gain a better understanding of both the regulation of the developmental process and the embryo's capacity for self-repair. Additionally, experiments with abiotic and biotic stressors during development have helped delineate not just critical windows for avian cardio-respiratory development, but the general characteristics (e.g., timing and dose-dependence) of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bird embryos; Cardiovascular; Epigenetics; Fetal programing; Respiratory plasticity; Toxicants.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982016001100709
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Challenges and perspectives to enhance cattle production via in vitro techniques: focus on epigenetics and cell-secreted vesicles 65
Bressan,Fabiana Fernandes; Fantinato-Neto,Paulo; Andrade,Gabriella Mamede; Sangalli,Juliano Rodrigues; Sampaio,Rafael Vilar; Silveira,Juliano Coelho da; Perecin,Felipe; Meirelles,Flávio Vieira.
This review aim to present some clinical problems found in IVP-derived animals focusing on NT procedures and to discuss the possible role of epigenetics in such process. Also, as cell-secreted vesicles have been reported as possible regulators of important physiological reproductive processes such as folliculogenesis and fertilization, it is also presented herein a new perspective of manipulating the pre-implantation period trough effector molecules contained in such vesicles.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Embryo development; Nuclear transfer; Epigenetics; Extra-cellular vesicles..
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782015001001879
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ChIP-seq analysis of histone H3K9 trimethylation in peripheral blood mononuclear cells of membranous nephropathy patients 56
Sui,W.G.; He,H.Y.; Yan,Q.; Chen,J.J.; Zhang,R.H.; Dai,Y..
Membranous nephropathy (MN), characterized by the presence of diffuse thickening of the glomerular basement membrane and subepithelial in situimmune complex disposition, is the most common cause of idiopathic nephrotic syndrome in adults, with an incidence of 5-10 per million per year. A number of studies have confirmed the relevance of several experimental insights to the pathogenesis of human MN, but the specific biomarkers of MN have not been fully elucidated. As a result, our knowledge of the alterations in histone methylation in MN is unclear. We used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to analyze the variations in a methylated histone (H3K9me3) in peripheral blood mononuclear cells from 10 MN patients and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: ChIP-seq; Epigenetics; H3K9me3; Membranous nephropathy.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2014000100042
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Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme 5
Cheray, Mathilde; Etcheverry, Amandine; Jacques, Camille; Pacaud, Romain; Bougras-cartron, Gwenola; Aubry, Marc; Denoual, Florent; Peterlongo, Pierre; Nadaradjane, Arulraj; Briand, Josephine; Akcha, Farida; Heymann, Dominique; Vallette, François M.; Mosser, Jean; Ory, Benjamin; Cartron, Pierre-françois.
Background Literature reports that mature microRNA (miRNA) can be methylated at adenosine, guanosine and cytosine. However, the molecular mechanisms involved in cytosine methylation of miRNAs have not yet been fully elucidated. Here we investigated the biological role and underlying mechanism of cytosine methylation in miRNAs in glioblastoma multiforme (GBM). Methods RNA immunoprecipitation with the anti-5methylcytosine (5mC) antibody followed by Array, ELISA, dot blot, incorporation of a radio-labelled methyl group in miRNA, and miRNA bisulfite sequencing were perfomred to detect the cytosine methylation in mature miRNA. Cross-Linking immunoprecipiation qPCR, transfection with methylation/unmethylated mimic miRNA, luciferase promoter reporter plasmid,...
Tipo: Text Palavras-chave: MiRNA; Cytosine-methylation; Epigenetics; DNMT3A; AGO4; Glioblastoma; Epitranscriptomics.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00610/72196/70980.pdf
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Detection of differentially methylated regions of irradiated fig tree selections 63
Rodrigues,Maria Gabriela Fontanetti; Soares,Murilo Racy; Gimenez,Daniele Fernanda Jovino; Fonseca,Larissa Fernanda Simielli; Torrieri,Erico; Ramos,Ester Silveira; Giuliatti,Silvana.
ABSTRACT Fig tree (Ficus carica L.) breeding programs using conventional methods, such as directed crosses, to obtain new cultivars, are unworkable in many countries, including Brazil. Consequently, genetic breeding through mutagenesis has emerged as an important line of research that can improve this crop, and be a significant source of information about this species and assist in the implementation of propagation projects and appropriate management. The aim of this study was to verify the existence of epigenetic variability attributable to DNA methylation in irradiated fig selections when compared both to each other and to the main commercial cultivar, “Roxo-de-Valinhos”, which had previously used methylation-sensitive amplified polymorphism (MSAP) and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ficus carica; DMRs; Methylation; Plant breeding; Epigenetics.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162017000400285
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Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation 5
Dugé De Bernonville, Thomas; Maury, Stéphane; Delaunay, Alain; Daviaud, Christian; Chaparro, Cristian; Tost, Jörg; O’connor, Sarah Ellen; Courdavault, Vincent.
Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples...
Tipo: Text Palavras-chave: Alkaloids; DNA methylation; Epigenetics; Folivory; Organs; Plant specialized metabolism.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00652/76453/77543.pdf
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Dynamics in global DNA methylation and endogenous polyamine levels during protocorm-like bodies induction of Cattleya tigrina A. Richard 3
Almeida, Vivian; Fraga, Hugo Pacheco de Freitas; Navarro, Bruno Bachiega; Guerra, Miguel Pedro; Pescador, Rosete.
Cattleya tigrina is endemic to the Atlantic forest biome and classified as vulnerable in the Red Book of Brazilian Flora. In vitro techniques comprise valuable tools for the conservation of endangered plant species. The aim of the present study was to evaluate the morphological features, global DNA methylation levels and free polyamines during protocorm-like bodies (PLBs) induction of C. tigrina. Along with that, an efficient protocol for in vitro propagation of this species is proposed. The first evidences of PLBs induction in C. tigrina occurred at seven days in culture, starting from the basal portion of the leaf abaxial surface. A hypomethylation marked the beginning of cell differentiation, followed by an increased global DNA methylation at 35 days in...
Tipo: Info:eu-repo/semantics/article Palavras-chave: 2.03.00.00-0; 2.03.03.00-9; 2.03.06.00-8 orchids; Micropropagation; In vitro culture; Epigenetics; PLBs. Botânica.
Ano: 2017 URL: http://periodicos.uem.br/ojs/index.php/ActaSciBiolSci/article/view/36656
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Efficacy of the dietary histone deacetylase inhibitor butyrate alone or in combination with vitamin A against proliferation of MCF-7 human breast cancer cells 56
Andrade,F.O.; Nagamine,M.K.; Conti,A. De; Chaible,L.M.; Fontelles,C.C.; Jordão Junior,A.A.; Vannucchi,H.; Dagli,M.L.Z.; Bassoli,B.K.; Moreno,F.S.; Ong,T.P..
The combined treatment with histone deacetylase inhibitors (HDACi) and retinoids has been suggested as a potential epigenetic strategy for the control of cancer. In the present study, we investigated the effects of treatment with butyrate, a dietary HDACi, combined with vitamin A on MCF-7 human breast cancer cells. Cell proliferation was evaluated by the crystal violet staining method. MCF-7 cells were plated at 5 x 10(4) cells/mL and treated with butyrate (1 mM) alone or combined with vitamin A (10 µM) for 24 to 120 h. Cell proliferation inhibition was 34, 10 and 46% following treatment with butyrate, vitamin A and their combination, respectively, suggesting that vitamin A potentiated the inhibitory activities of butyrate. Furthermore, exposure to this...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Breast cancer; MCF-7 cells; Butyric acid; Vitamin A; Epigenetics.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012000900008
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Epigenetic alterations in human brain tumors in a Brazilian population 74
Anselmo,Nilson Praia; Bello,Maria Josefa; Gonzalez-Gomez,Pilar; Dias,Luis Antonio Araújo; Almeida,José Reinaldo Walter de; Santos,Marcelo José dos; Rey,Juan A.; Casartelli,Cacilda.
Aberrant methylation of CpG islands located in promoter regions represents one of the major mechanisms for silencing cancer-related genes in tumor cells. We determined the frequency of aberrant CpG island methylation for several tumor-associated genes: DAPK, MGMT, p14ARF, p16INK4a, TP73, RB1 and TIMP-3 in 55 brain tumors, consisting of 26 neuroepithelial tumors, 6 peripheral nerve tumors, 13 meningeal tumors and 10 metastatic brain tumors. Aberrant methylation of at least one of the seven genes studied was detected in 83.6% of the cases. The frequencies of aberrant methylation were: 40% for p14ARF, 38.2% for MGMT, 30.9% for, p16INK4a, 14.6% for TP73 and for TIMP-3, 12.7% for DAPK and 1.8% for RB1. These data suggest that the hypermethylation observed in...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Brain tumors; Epigenetics; Methylation.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000300001
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Epigenetic origin of adaptive phenotypic variants in the human blood fluke Schistosoma mansoni 5
Fneich, Sara; Theron, Andre; Cosseau, Celine; Rognon, Anne; Aliaga, Benoit; Buard, Jerome; Duval, David; Arancibia, Nathalie; Boissier, Jerome; Roquis, David; Mitta, Guillaume; Grunau, Christoph.
Background: Adaptive evolution is not possible without the generation of phenotypic variants. The origin of these variations has been a central topic in evolutionary biology. Up to now, it was commonly accepted that standing genetic variation is the only cause of phenotypic variants. However, epigenetic information is emerging as a complementary source of heritable phenotypic variation that contributes to evolution. The relative importance of genetics and epigenetics in generating heritable phenotypic variation is nevertheless a matter of debate. Results: We used a host-parasite system to address this question. The human blood fluke Schistosoma mansoni can adapt rapidly to new intermediate snail hosts. The interaction between parasite and mollusk is...
Tipo: Text Palavras-chave: Epigenetics; Adaptive evolution; Compatibility polymorphism; Schistosoma mansoni.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00615/72708/71730.pdf
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Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis 5
Danchin, Etienne; Pocheville, Arnaud; Rey, Olivier; Pujol, Benoit; Blanchet, Simon.
After decades of debate about the existence of non-genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non-genetic and genetic inheritance, may help build the long-sought inclusive vision of evolution. After briefly reviewing the wealth of evidence documenting the existence and ubiquity of non-genetic inheritance in a table, we review the categories of mechanisms of parent-offspring resemblance that underlie inheritance. We then review several lines of argument for the existence of interactions between non-genetic and genetic components of inheritance, leading to a discussion of the contrasting timescales of action of non-genetic and genetic inheritance....
Tipo: Text Palavras-chave: Non-genetic inheritance; Inclusive heritability; Epigenetics; Central dogma; Genetic assimilation; Mutation randomness; Inclusive evolutionary synthesis.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00479/59037/62430.pdf
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Fantastically plastic: fish larvae equipped for a new world 5
Pittman, Karin; Yufera, Manuel; Pavlidis, Michail; Geffen, Audrey J.; Koven, Willian; Ribeiro, Laura; Zambonino, Jose Luiz; Tandler, Amos.
Teleost fish are more diverse than any other vertebrate group, and yet only a limited number of species are fished and farmed globally. Efforts to expand the quantity and diversity of fish produced are hampered by the extreme diversity of ontogenetic responses of fish, especially during larval development. This review looks at advances in molecular phylogeny, endocrine and nutrient influences and long-term studies of the phenotypes of commercially important fish to put the sources and consequences of this plasticity into context. This nested context of evolutionary forces of the fish-specific genome duplication, epigenetic influences, ontogenetically conserved processes like metamorphosis and cell determination is further presented in relation to how fish...
Tipo: Text Palavras-chave: Development; Epigenetics; Fish-specific genome duplication; Juveniles; Larvae; Metamorphosis; Plasticity.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00144/25509/23655.pdf
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In vitro fertilization (IVF) in mammals: epigenetic and developmental alterations. Scientific and bioethical implications for IVF in humans 48
Ventura-Juncá,Patricio; Irarrázaval,Isabel; Rolle,Augusto J; Gutiérrez,Juan I; Moreno,Ricardo D; Santos,Manuel J.
The advent of in vitro fertilization (IVF) in animals and humans implies an extraordinary change in the environment where the beginning of a new organism takes place. In mammals fertilization occurs in the maternal oviduct, where there are unique conditions for guaranteeing the encounter of the gametes and the first stages of development of the embryo and thus its future. During this period a major epigenetic reprogramming takes place that is crucial for the normal fate of the embryo. This epigenetic reprogramming is very vulnerable to changes in environmental conditions such as the ones implied in IVF, including in vitro culture, nutrition, light, temperature, oxygen tension, embryo-maternal signaling, and the general absence of protection against foreign...
Tipo: Journal article Palavras-chave: In vitro fertilization (IVF) in mammals; Epigenetics; Developmental alterations; Bioethical implications.
Ano: 2015 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100068
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Low-protein diet does not alter reproductive, biochemical, and hematological parameters in pregnant Wistar rats 56
Barros,M.A.V.; Andrade,E.B.; Barros,R.G.N.; Costa,I.K.M.; Costa,I.C.L.; Vitorino,G.F.A.; Andrade,J.J.C.; Paulino-Silva,K.M.; Nogueira,V.O.; de Brito Alves,J.L.; Costa-Silva,J.H..
The aim of this study was to investigate the reproductive, biochemical, and hematological outcomes of pregnant rats exposed to protein restriction. Wistar rat dams were fed a control normal-protein (NP, 17% protein, n=8) or a low-protein (LP, 8% protein, n=14) diet from the 1st to the 20th day of pregnancy. On the 20th day, the clinical signs of toxicity were evaluated. The pregnant rats were then anesthetized and blood samples were collected for biochemical-hematological analyses, and laparotomy was performed to evaluate reproductive parameters. No sign of toxicity, or differences (P>0.05) in body weight gain and biochemical parameters (urea, creatinine, albumin, globulin, and total protein) between NP and LP pregnant dams were observed. Similarly,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Development; Epigenetics; Fertility; Gestation; Intrauterine growth; Nutrition.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2018000600613
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Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types 5
Bulla, Ingo; Aliaga, Benoit; Lacal, Virginia; Bulla, Jan; Grunau, Christoph; Chaparro, Cristian.
Background: DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. Results: Predominantly model-based approaches essentially founded on...
Tipo: Text Palavras-chave: Epigenetics; DNA methylation; Kernel density estimation; CpG o/e ratio; CpN o/e ratio.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00437/54816/71790.pdf
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