ArticleNucleic acids research2011
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data.Bioinformatics (Oxford, England) · 2021Article
- A prelude to the proximity interaction mapping of CXXC5.Scientific reports · 2021Article
- A CpG island promoter drives the CXXC5 gene expression.Scientific reports · 2021Article
- DNA Methylation Patterns of a Satellite Non-coding Sequence -Frontiers in genetics · 2019Article
- FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes.Genome biology and evolution · 2017Article
- Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo.The Journal of biological chemistry · 2015Article
- Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin.Molecular and cellular biology · 2015Article
- Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.Genome research · 2014Article
- Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter.The Journal of biological chemistry · 2013Article
- DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11.Epigenetics · 2013Article
- The ZEB1 pathway links glioblastoma initiation, invasion and chemoresistance.EMBO molecular medicine · 2013Article
- Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.Nucleic acids research · 2013Article
- Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.Genome research · 2012Article
- DNA methyltransferase accessibility protocol for individual templates by deep sequencing.Methods in enzymology · 2012Article
- WIF1 is a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix.Carcinogenesis · 2011Article
- Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit.Current protocols in molecular biology · 2011Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at nucleotide resolution along single DNA strands. Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) is an effective technique for mapping protein-DNA interactions. Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we previously cloned and characterized, was used to probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells. Because M.CviPI-probed samples contain both CG and GC methylation, we developed a versatile, visually-intuitive program, called MethylViewer, for evaluating the bisulfite sequencing results. Uniquely, MethylViewer can simultaneously query cytosine methylation status in bisulfite-converted sequences at as many as four different user-defined motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data can also be exported for statistical analysis and as publication-quality images. Analysis of hMLH1 MAPit data with MethylViewer showed that endogenous CG methylation and accessible GC sites were both mapped on single molecules at high resolution. Disruption of positioned nucleosomes on single molecules of the PHO5 promoter was detected in budding yeast using M.CviPII, increasing the number of enzymes available for probing protein-DNA interactions. MethylViewer provides an integrated solution for primer design and rapid, accurate and detailed analysis of bisulfite sequencing or MAPit datasets from virtually any biological or biochemical system.
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