ArticleGenome research2008
Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 104 citations in OpenAlex.
- Genome-wide analysis of strand-specific transcription and DNA methylation inFrontiers in microbiology · 2026Article
- DNA methylation as a contributor to dysregulation of STX6 and other frontotemporal Lobar degeneration genetic risk-associated loci.Acta neuropathologica communications · 2025Article
- DNA methylation as a contributor to dysregulation ofbioRxiv : the preprint server for biology · 2025Article
- JmjC catalysed histone H2a N-methyl arginine demethylation and C4-arginine hydroxylation reveals importance of sequence-reactivity relationships.Communications biology · 2024Article
- Systematic integrated analyses of methylomic and transcriptomic impacts of early combined botanicals on estrogen receptor-negative mammary cancer.Scientific reports · 2021Article
- Inhibition of P53-mediated cell cycle control as the determinant in dedifferentiated liposarcomas development.American journal of cancer research · 2021Article
- Role of DNA Methylation in the Resistance to Therapy in Solid Tumors.Frontiers in oncology · 2020Review
- Epigenetic silencing of SALL2 confers tamoxifen resistance in breast cancer.EMBO molecular medicine · 2019Article
- A new correlation clustering method for cancer mutation analysis.Bioinformatics (Oxford, England) · 2016Article
- Nucleic Acid Modifications in Regulation of Gene Expression.Cell chemical biology · 2016Review
- Circadian disruption and breast cancer: an epigenetic link?Oncotarget · 2015Review
- Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.Genome biology · 2015Article
- Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.PloS one · 2015Article
- Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways.Frontiers in genetics · 2015Article
- An H2A histone isotype regulates estrogen receptor target genes by mediating enhancer-promoter-3'-UTR interactions in breast cancer cells.Nucleic acids research · 2014Article
- Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition.Genome biology · 2013Article
- How has the study of the human placenta aided our understanding of partially methylated genes?Epigenomics · 2013Article
- Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network.Scientific reports · 2013Article
- The human placenta methylome.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- DNA methylation signatures of peripheral leukocytes in schizophrenia.Neuromolecular medicine · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a method for mapping unmethylated sites in the human genome based on the resistance of TspRI-digested ends to ExoIII nuclease degradation. Digestion with TspRI and methylation-sensitive restriction endonuclease HpaII, followed by ExoIII and single-strand DNA nuclease allowed removal of DNA fragments containing unmethylated HpaII sites. We then used array comparative genomic hybridization (CGH) to map the sequences depleted by these procedures in human genomes derived from five human tissues, a primary breast tumor, and two breast tumor cell lines. Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5' end of widely expressed genes, including promoter, first exon, and first intron. In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas the primary tumor exhibits a pattern between those of the normal tissue and the cell lines. A striking characteristic of tumor cell lines is the presence of megabase-sized hypomethylated zones. These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor suppressor genes, and with regions containing tissue-specific gene clusters or with gene-poor regions containing novel tissue-specific genes. Correlation with microarray analysis shows that genes with a hypomethylated sequence 2 kb up- or downstream of the transcription start site are highly expressed, whereas genes with extensive intragenic and 3' untranslated region (UTR) hypomethylation are silenced. The method described herein can be used for large-scale screening of changes in the methylation pattern in the genome of interest.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.