DNA Methylation Protocols

Preface .............................................................................................................v Contributors ..................................................................................................... ix 1 Overview Ken I. Mills and Bernard H. Ramsahoye ............................................. 1 2 Nearest-Neighbor Analysis Bernard H. Ramsahoye ......................................................................... 9 3 Measurement of Genome-Wide DNA Cytosine-5 Methylation by Reversed-Phase High-Pressure Liquid Chromatography Bernard H. Ramsahoye ....................................................................... 17 4 Methylation Analysis by Chemical DNA Sequencing Piroska E. Szabó, Jeffrey R. Mann, and Gerd P. Pfeifer ................. 29 5 Methylation-Sensitive Restriction Fingerprinting Catherine S. Davies ............................................................................. 43 6 Restriction Landmark Genome Scanning Joseph F. Costello, Christoph Plass, and Webster K. Cavenee ... 53 7 Combined Bisulfite Restriction Analysis (COBRA) Cindy A. Eads and Peter W. Laird ..................................................... 71 8 Differential Methylation Hybridization Using CpG Island Arrays Pearlly S. Yan, Susan H. Wei, and Tim Hui-Ming Huang ................ 87 9 Methylated CpG Island Amplification for Methylation Analysis and Cloning Differentially Methylated Sequences Minoru Toyota and Jean-Pierre J. Issa ........................................... 101 10 Isolation of CpG Islands Using a Methyl-CpG Binding Column Sally H. Cross ..................................................................................... 111 11 Purification of MeCP2-Containing Deacetylase from Xenopus laevis Peter L. Jones, Paul A. Wade, and Alan P. Wolffe ........................ 131 12 DNA-Methylation Analysis by the Bisulfite-Assisted Genomic Sequencing Method Petra Hajkova, Osman El-Maarri, Sabine Engemann, Joachim Oswald, Alexander Olek, and Jörn Walter ................. 143 13 Measuring DNA Demethylase Activity In Vitro Moshe Szyf and Sanjoy K. Bhattacharya ....................................... 155 vii viii Contents 14 Extracting DNA Demethylase Activity from Mammalian Cells Moshe Szyf and Sanjoy K. Bhattacharya ....................................... 163 Index ............................................................................................................ 177