MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.
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.
Pardo
Carolina E
CE
Department of Biochemistry and Molecular Biology, University of Florida Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, Gainesville, FL 32610-3633, USA.
Carr
Ian M
IM
Hoffman
Christopher J
CJ
Darst
Russell P
RP
Markham
Alexander F
AF
Bonthron
David T
DT
Kladde
Michael P
MP
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D045744:Cell Line, Tumor; D002843:Chromatin / Q000378:metabolism; D019295:Computational Biology; D018899:CpG Islands; D003562:Cytidine / Q000032:analysis / Q000378:metabolism; D003596:Cytosine / Q000378:metabolism; D004247:DNA / Q000737:chemistry; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D006801:Humans; D007089:Image Enhancement; D000070957:MutL Protein Homolog 1; D009687:Nuclear Proteins / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry*
D048868:Adaptor Proteins, Signal Transducing; D002843:Chromatin; C501486:MLH1 protein, human; D009687:Nuclear Proteins; D013447:Sulfites; D003562:Cytidine; D003596:Cytosine; D004247:DNA; D004248:DNA (Cytosine-5-)-Methyltransferases; D000070957:MutL Protein Homolog 1; C042345:hydrogen sulfite