Genomic imprinting : methods and protocols

Generation of Monoparental Embryos for Investigation into Genomic Imprinting Wendy L. Dean, Gavin Kelsey, and Wolf Reik ................................... 1 2 Deriving and Propagating Mouse Embryonic Stem Cell Lines for Studying Genomic Imprinting Jeffrey R. Mann .................................................................................... 21 3 Balanced Translocations for the Analysis of Imprinted Regions of the Mouse Genome Anne C. Ferguson-Smith, Maxine Tevendale, Pantelis Georgiades, and Valerie Grandjean.............................. 41 4 Production of YAC Transgenic Mice by Pronuclear Injection Justin F.-X. Ainscough, Rosalind M. John, and Sheila C. Barton ....................................................................... 55 5 A Transgenic Approach to Studying Imprinted Genes: Modified BACs and PACs Rosalind M. John, Justin F.-X. Ainscough, and Sheila C. Barton .... 67 6 Methylation-Sensitive Genome Scanning Izuho Hatada and Tsunehiro Mukai................................................... 83 7 Subtraction-Hybridization Method for the Identification of Imprinted Genes Fumitoshi Ishino, Yoshimi Kuroiwa, Naoki Miyoshi, Shin Kobayashi, Takashi Kohda, and Tomoko Kaneko-Ishino ........ 101 8 Identification of Imprinted Loci by Methylation: Use of Methylation- Sensitive Representational Difference Analysis (Me-RDA) Rachel J. Smith and Gavin Kelsey .................................................. 113 9 Ribonuclease Protection Joanne L. Thorvaldsen and Marisa S. Bartolomei ........................ 133 10 Quantitative RT-PCR-Based Analysis of Allele-Specific Gene Expression Judith Singer-Sam and Chunguang Gao ........................................ 145 11 Allele-Specific In Situ Hybridization (ASISH) Rolf Ohlsson, Kristian Svensson, Hengmi Cui, Helena Malmikumpu, and Gail Adam .......................................... 153 vii Contents viii Contents 12 RNA-FISH to Analyze Allele-Specific Expression Giovanna Braidotti............................................................................. 169 13 Flow Cytometry and FISH to Investigate Allele-Specific Replication Timing and Homologous Association of Imprinted Chromosomes Janine LaSalle and Marc Lalande .................................................... 181 14 Southern Analysis Using Methyl-Sensitive Restriction Enzymes Tom Moore .......................................................................................... 193 15 A PCR-Based Method for Studying DNA Methylation Mira Ariel ............................................................................................. 205 16 Bisulfite-Based Methylation Analysis of Imprinted Genes Sabine Engemann, Osman El-Maarri, Petra Hajkova, Joachim Oswald, and Joern Walter ............................................ 217 17 Direct Analysis of Chromosome Methylation Déborah Bourc’his and Evani Viegas-Péquignot .......................... 229 18 In Vitro Methylation of Predetermined Regions in Recombinant DNA Constructs Ilse Van den Wyngaert, Roger L. P. Adams, and Stefan U. Kass ........................................................................ 243 19 In Vitro Methylation of Specific Regions in Recombinant DNA Constructs by Excision and Religation Ghislaine Dell, Marika Charalambous, and Andrew Ward ........... 251 20 Detection of Methyl-Sensitive DNA-Binding Proteins with Possible Involvement in the Imprinting Phenomenon Kerstin Otte and Björn Rozell ........................................................... 259 21 Probing Chromatin Structure with Nuclease Sensitivity Assays Richard I. Gregory, Sanjeev Khosla, and Robert Feil ................... 269 22 Examining Histone Acetylation at Specific Genomic Regions Ji-Fan Hu and Andrew R. Hoffman .................................................. 285 23 Purification of the MeCP2/Histone Deacetylase Complex from Xenopus laevis Peter L. Jones, Paul A. Wade, and Alan P. Wolffe ....................... 297 24 Reconstitution of Chromatin In Vitro Kiyoe Ura and Yasufumi Kaneda ..................................................... 309 25 Genomic Imprinting in Plants Rinke Vinkenoog, Melissa Spielman, Sally Adams, Hugh G. Dickinson, and Rod J. Scott ......................................... 327 Index ............................................................................................................ 371 GAIL ADAM , Eurona Medical AB, Kungsängsvägen, Uppsala, Sweden ROGER L. P. ADAMS , IBLS, University of Glasgow, Scotland, UK SALLY ADAMS , Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United