Genomic imprinting

Preface ............................................................................................................ v Contributors .................................................................................................... ix 1 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 Kingdom JUSTIN F.-X. AINSCOUGH • Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom MIRA ARIEL • Department of Cellular Biochemistry and Human Genetics, Hadassah Medical School, The Hebrew University, Jerusalem, Israel MARISA S. BARTOLOMEI • Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA SHEILA C. BARTON • Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom DÉBORAH BOURC’HIS • INSERM U383, Hôpital Necker-Enfants Malades, Paris Cedex, France GIOVANNA BRAIDOTTI • Department of Cell Biology and Genetics, Erasmus University, Rotterdam, The Netherlands MARIKA CHARALAMBOUS • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom HENGMI CUI • Departments of Medicine, Oncology, and Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD WENDY L. DEAN • Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge, United Kingdom GHISLAINE DELL • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom HUGH G. DICKINSON • Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom OSMAN EL-MAARRI • Institute of Experimental Haematology and Transfusion Medicine, Bonn, Germany SABINE ENGEMANN • Max-Planck-Institut für molekulare Genetik, Ihnestr, Berlin, Germany ix Contributors x Contributors ROBERT FEIL • Institute of Molecular Genetics, CNRS-UMR5535, Montpellier, France ANNE C. FERGUSON-SMITH • Department of Anatomy, University of Cambridge, Downing Street, Cambridge, United Kingdom CHUNGUANG GAO • Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA PANTELIS GEORGIADES • Department of Anatomy, University of Cambridge, Downing Street, Cambridge, United Kingdom VALERIE GRANDJEAN • Department of Anatomy, University of Cambridge, Downing Street, Cambridge, United Kingdom RICHARD I. GREGORY • Fox Chase Cancer Center, Philadelphia, Pennsylvania PETRA HAJKOVA • Department of Genetics, University of Saarland, Saarbrücken, Germany IZUHO HATADA • Gene Research Center, Gunma University, Maebashi, Japan ANDREW R. HOFFMAN • Medical Service, VA Palo Alto Health Care System and Department of Medicine, Stanford University School of Medicine, Palo Alto, CA JI-FAN HU • Medical Service, VA Palo Alto Health Care System and Department of Medicine, Stanford University School of Medicine, Palo Alto, CA FUMITOSHI ISHINO • Gene Research Center, Tokyo Institute of Technology, Yokohama; CREST, Japan Science and Technology Corporation (JST), Kawaguchi, Japan ROSALIND M. JOHN • Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom PETER L. JONES • Department of Cell and Structural Biology, University of Illinois, Urbana-Champaign, Urbana, IL YASUFUMI KANEDA • Division of Gene Therapy Science, Osaka University School of Medicine, Suita, Osaka, Japan TOMOKO KANEKO-ISHINO • School of Health Sciences, Tokyo University, Isehara, Japan STEFAN U. KASS • Department of Genomic Technologies, Janssen Research Foundation, Beerse, Belgium GAVIN KELSEY • Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge, United Kingdom SANJEEV KHOSLA • Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom SHIN KOBAYASHI • Gene Research Center, Tokyo Institute of Technology, Yokohama, Japan TAKASHI KOHDA • Gene Research Center, Tokyo Institute of Technology, Yokohama, Japan YOSHIMI KUROIWA • Pharmaceutical Research Laboratory, Kirin Brewery Co. Ltd., Takasaki, Gunma, Japan MARC LALANDE • Department of Genetics and Developmental Biology, School of Medicine, University of Connecticut, Farmington, CT JANINE LASALLE • Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA HELENA MALMIKUMPU • Department of Animal Development & Genetics, Uppsala University, Norbyvägen, Uppsala, Sweden JEFFREY R MANN • Division of Biology, Beckman Research Institute of the City of Hope, CA NAOKI MIYOSHI • Gene Research Center, Tokyo Institute of Technology, Yokohama, Japan TOM MOORE • Department of Biochemistry, University College Cork, Ireland. TSUNEHIRO MUKAI • Department of Biochemistry, Saga Medical School, Saga, Japan. ROLF OHLSSON • Department of Animal Development and Genetics, Uppsala University, Norbyvägen, Uppsala, Sweden JOACHIM OSWALD • Institut für Polymerforschung e.V., Dresden, Germany KERSTIN OTTE • Wellcome/CRC Institute, Cambridge United Kingdom WOLF REIK • Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge, United Kingdom BJÖRN ROZELL • Unit for Morphological Phenotype Analysis and Unit for Embryology and Genetics, Clinical Research Center, Huddinge University Hospital, Stockholm, Sweden. ROD J. SCOTT • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom JUDITH SINGER-SAM • Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA RACHEL J. SMITH • Developmental Genetics Programme, The Babraham Institute, Babraham, Cambridge, United Kingdom MELISSA SPIELMAN • Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom KRISTIAN SVENSSON • Department of Pharmacology, Pharmacia-Upjohn, Stockholm, Sweden MAXINE TEVENDALE • Department of Anatomy, University of Cambridge, Downing Street, Cambridge, United Kingdom JOANNE L. THORVALDSEN • Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA Contributors xi xii Contributors KIYOE URA • Division of Gene Therapy Science, Osaka University School of Medicine, Suita, Osaka Japan ILSE VAN DEN WYNGAERT • Department of Genomic Technologies, Janssen Research Foundation, Beerse, Belgium EVANI VIEGAS-PÉQUIGNOT • INSERM U383, Hôpital Necker-Enfants Malades, Paris Cedex, France RINKE VINKENOOG • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom PAUL A. WADE • Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD JOERN WALTER • Department of Genetics, University of Saarland, Saarbrücken, Germany ANDREW WARD • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom ALAN P. WOLFFE • Sangamo BioSciences Inc., Richmond, CA