Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

By Michael Weber, Jonathan J. Davies, David Wittig, E. Oakeley, M. Haase, Wan L. Lam, Dirk Schübeler. Nature Genetics, 2005

1,856 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b4f249781ae06568c7e1d41c357c27a78f5d2dbc

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Citations in the corpus

• DNA methylation and cancer. (2010, background): “Moreover, the development of the antibodies against 5-methylcytosine presents the opportunity to identify multiple distinct CpG sites across the genome, when combined with DNA microarray analyses (Me-DIP strategy) (Weber et al., 2005).”
• The mammalian epigenome. (2007, background): “, 2004) or normal and tumor samples (Hu et al., 2005; Keshet et al., 2006; Weber et al., 2005; Weisenberger et al., 2006).”
• High density DNA methylation array with single CpG site resolution. (2011, background): “Many microarray and next-generation sequencing based technologies have emerged, and analyses that were previously restricted to specific loci in a limited number of genes can now be performed on a genome-wide scale [1–10].”
• Acute exercise remodels promoter methylation in human skeletal muscle. (2012, methodology): “Digested DNA (4 mg) was used for a standard MeDIP assay as described (Weber et al., 2005) and 1–2 mg for methylcytosine capture.”
• DNA hypomethylation and human diseases. (2007, background): “[159] identified a number of largely gene-poor, LINE rich regions on chromosomes 3, 7, 11 and 14, individually spanning up to 20 Mb that exhibited marked hypomethylation in transformed cells.”
• Differential methylation analysis for BS-seq data under general experimental design (2016, background): “, 2006) or capture-based sequencing like MeDIP-seq (Weber et al., 2005), BS-seq has improved accuracy, reduced background bias, and higher spatial resolution.”
• Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome (2007, methodology): “Results Profiling promoter DNA methylation in the human genome To determine the methylation status for a comprehensive set of human promoters, we enriched methylated DNA from human primary fibroblasts using methylated DNA immunoprecipitation (MeDIP) methodolog”
• Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation (2010, positive): “MeDIP was performed based on published protocol (Weber et al., 2005).”
• R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters (2012, positive): “For DRIP, DNA was further processed essentially as described for MeDIP (Weber et al., 2005), except the S9.”
• DNA methylation: a historical perspective. (2022, neutral): “Interestingly, this cell line also showed notable hypomethylation across large gene-poor domains and the inactive X chromosome [202].”
• SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips (2012, background): “Currently, several microarray and next-generation sequencing technologies are available that allow the interrogation of DNA methylation on a genome-wide scale [5-14].”
• Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis (2005, methodology): “Another, more recent genome-wide approach used immunopreciptation with a methyl cytosine antibody rather than restriction digestion to enrich for the methylated fraction ( 26 ).”