title: DNA methyltransferase accessibility protocol for individual templates by deep sequencing.
abstract: A single-molecule probe of chromatin structure can uncover dynamic chromatin states and rare epigenetic variants of biological importance that bulk measures of chromatin structure miss. In bisulfite genomic sequencing, each sequenced clone records the methylation status of multiple sites on an individual molecule of DNA. An exogenous DNA methyltransferase can thus be used to image nucleosomes and other protein-DNA complexes. In this chapter, we describe the adaptation of this technique, termed Methylation Accessibility Protocol for individual templates, to modern high-throughput sequencing, which both simplifies the workflow and extends its utility.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Florida Shands Cancer Center Program in Cancer Genetics, Epigenetics, and Tumor Virology, Gainesville, Florida, USA.
authors.forename: Russell P
authors.initials: RP
authors.lastname: Darst
authors.forename: Nancy H
authors.initials: NH
authors.lastname: Nabilsi
authors.forename: Carolina E
authors.initials: CE
authors.lastname: Pardo
authors.forename: Alberto
authors.initials: A
authors.lastname: Riva
authors.forename: Michael P
authors.initials: MP
authors.lastname: Kladde
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018899:CpG Islands; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D015723:Gene Library; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D025542:Neurofibromin 1 / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D013447:Sulfites / Q000378:metabolism; D013698:Templates, Genetic
chemical_list: D025542:Neurofibromin 1; D009707:Nucleosomes; D013447:Sulfites; D004247:DNA; D004248:DNA (Cytosine-5-)-Methyltransferases; C042345:hydrogen sulfite