共查询到20条相似文献,搜索用时 31 毫秒
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Anneleen Decock Maté Ongenaert Jasmien Hoebeeck Katleen De Preter Gert Van Peer Wim Van Criekinge Ruth Ladenstein Johannes H Schulte Rosa Noguera Raymond L Stallings An Van Damme Geneviève Laureys Jo?lle Vermeulen Tom Van Maerken Frank Speleman Jo Vandesompele 《Genome biology》2012,13(10):R95
Background
Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers.Results
To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2''-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival.Conclusions
This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma. 相似文献3.
Anneleen Decock Maté Ongenaert Jasmien Hoebeeck Katleen De Preter Gert Van Peer Wim Van Criekinge Ruth Ladenstein Johannes H Schulte Rosa Noguera Raymond L Stallings An Van Damme Geneviève Laureys Joëlle Vermeulen Tom Van Maerken Frank Speleman Jo Vandesompele 《Genome biology》2012,13(10):1-15
ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance. 相似文献
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DNA methylation in fungi 总被引:4,自引:0,他引:4
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DNA methylation in eukaryotes 总被引:10,自引:0,他引:10
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Many proteins are modified by posttranslational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g., respiratory Complex I, citrate synthase, and the ATP synthase. In the present review, we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation and present an outlook for this emergent research field. 相似文献
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The epigenome plays a vital role in helping to maintain and regulate cell functions in all organisms. Alleles with differing epigenetic marks in the same nucleus do not function in isolation but can interact in trans to modify the epigenetic state of one or both alleles. This is particularly evident when two divergent epigenomes come together in a hybrid resulting in thousands of alterations to the methylome. These changes mainly involve the methylation patterns at one allele being changed to resemble the methylation patterns of the other allele, in processes we have termed trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). These processes are primarily modulated by siRNAs and the RNA directed DNA methylation pathway. Drawing from other examples of trans-allelic interactions, we describe the process of TCM and TCdM and the effect such changes can have on genome activity. Trans-allelic epigenetic interactions may be a common occurrence in many biological systems. 相似文献
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《Epigenetics》2013,8(8):800-805
The epigenome plays a vital role in helping to maintain and regulate cell functions in all organisms. Alleles with differing epigenetic marks in the same nucleus do not function in isolation but can interact in trans to modify the epigenetic state of one or both alleles. This is particularly evident when two divergent epigenomes come together in a hybrid resulting in thousands of alterations to the methylome. These changes mainly involve the methylation patterns at one allele being changed to resemble the methylation patterns of the other allele, in processes we have termed trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). These processes are primarily modulated by siRNAs and the RNA directed DNA methylation pathway. Drawing from other examples of trans-allelic interactions, we describe the process of TCM and TCdM and the effect such changes can have on genome activity. Trans-allelic epigenetic interactions may be a common occurrence in many biological systems. 相似文献
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Adenine methylation in zein genes 总被引:1,自引:0,他引:1
J A Pintor-Toro 《Biochemical and biophysical research communications》1987,147(3):1082-1087
This paper reports the novel finding of adenine methylation in higher plants. Comparison of restriction patterns of genomic maize DNA digested with enzymes MboI and Sau3A enabled us to detect the existence of adenine methylation in zein genes. Adenine methylation within or around zein genes turned out to be similar in endosperm (where zeins are actively synthesized) and in seedling tissue (where zein genes are not expressed). Furthermore, adenine methylation patterns were found to be similar both in wild-type and opaque-2 mutant plants. These lines of evidence suggest that adenine methylation is unrelated to the regulation of gene expression. 相似文献
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M Saceda P García-Morales J M Mato W J Malaisse I Valverde 《Biochemistry international》1984,8(3):445-452
Glucose provokes a transient stimulation of phospholipid methylation in rat pancreatic islets, possibly by increasing phospholipid methyltransferase activity. The association of DL-homocysteine and 3-deazaadenosine inhibits phospholipid methylation. The methylation of phospholipids may play a role in the stimulus-secretion coupling for glucose-induced insulin release. 相似文献
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Marchal R Chicheportiche A Dutrillaux B Bernardino-Sgherri J 《Cytogenetic and genome research》2004,105(2-4):316-324
DNA methylation is involved in many biological processes and is particularly important for both development and germ cell differentiation. Several waves of demethylation and de novo methylation occur during both male and female germ line development. This has been found at both the gene and all genome levels, but there is no demonstrated correlation between them. During the postnatal germ line development of spermatogenesis, we found very complex and drastic DNA methylation changes that we could correlate with chromatin structure changes. Thus, detailed studies focused on localization and expression pattern of the chromatin proteins involved in both DNA methylation, histone tails modification, condensin and cohesin complex formation, should help to gain insights into the mechanisms at the origin of the deep changes occurring during this particular period. 相似文献
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DNA methylation in prostate cancer 总被引:7,自引:0,他引:7
Prostate cancer is the most common malignancy and the second leading cause of cancer death among men in the United States. There are three well-established risk factors for prostate cancer: age, race and family history. The molecular bases for these risk factors are unclear; however, they may be influenced by epigenetic events. Epigenetic events covalently modify chromatin and alter gene expression. Methylation of cytosine residues within CpG islands on gene promoters is a primary epigenetic event that acts to suppress gene expression. In tumorigenesis, the normal functioning of the epigenetic-regulatory system is disrupted leading to inappropriate CpG island hypermethylation and aberrant expression of a battery of genes involved in critical cellular processes. Cancer-dependent epigenetic regulation of genes involved in DNA damage repair, hormone response, cell cycle control and tumor-cell adhesion/metastasis can contribute significantly to tumor initiation, progression and metastasis and, thereby, increase prostate cancer susceptibility and risk. In this review, we will discuss current research on genes that are hypermethylated in human prostate cancer. We will also discuss the potential involvement of DNA methylation in age-related, race-related and hereditary prostate cancer, and the potential use of hypermethylated genes as biomarkers to detect prostate cancer and assess its risk. 相似文献
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dam methylation in the archaebacteria 总被引:6,自引:0,他引:6
D Lodwick H N Ross J E Harris J W Almond W D Grant 《Journal of general microbiology》1986,132(11):3055-3059
The DNA of certain species of halophilic and methanogenic archaebacteria is dam methylated, as shown by restriction endonuclease sensitivities. The Dam+ phenotype appears to be confined to particular taxonomic groupings defined by DNA:rRNA hybridization or 16S RNA oligonucleotide cataloguing. 相似文献
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DNA methylation in early development 总被引:1,自引:0,他引:1
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R Versteeg 《American journal of human genetics》1997,60(4):751-754
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