Genomic imprinting : methods and protocols

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Genomic imprinting : methods and protocols

edited by Nora Engel

（Methods in molecular biology / John M. Walker, series editor, 925）（Springer protocols）

Humana Press, c2012

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Includes bibliographical references and index

Description and Table of Contents

Description

Genomic imprinting, the process by which the non-equivalence of the paternal and maternal genomes is established, has been fascinating us for over three decades and has provided many emerging scientists with the chance to hit their stride in a frontier posing many unexpected questions and even more surprising answers. In Genomic Imprinting: Methods and Protocols, experts in the field provide a survey of the technologies that are being applied to advance the study of imprinting. This detailed volume features new technologies that are accelerating the pace of discovery of imprinted genes and characterization of their epigenetic profile, bioinformatic procedures for prediction and comparative analyses of imprinted genes, as well as methods in embryology and basic molecular biology that have been employed for many years, some appearing in new versions for small cell numbers. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easy to use, Genomic Imprinting: Methods and Protocols will aid scientists in unveiling both much awaited answers and all-new questions to keep this vital field busy for many exciting years to come.

Table of Contents

Part I: Parent-of-Origin Effects 1. Uniparental Embryos in the Study of Genomic Imprinting Yong Cheng, Dasari Amarnath, and Keith E. Latham 2. Derivation of Induced Pluripotent Stem Cells by Retroviral Gene Transduction in Mammalian Species Masanori Imamura, Hironobu Okuno, Ikuo Tomioka, Yoshimi Kawamura, Zachary Yu-Ching Lin, Ryusuke Nakajima, Wado Akamatsu, Hirotaka James Okano, Yumi Matsuzaki, Erika Sasaki, and Hideyuki Okano 3. Generation of Trophoblast Stem Cells Michael C. Golding 4. Immunomagnetic Purification of Murine Primordial Germ Cells Emily Y. Smith and James L. Resnick Part II: Identifying Imprinted Genes 5. Whole Genome Methylation Profiling by Immunoprecipitation of Methylated DNA Andrew J. Sharp 6. Identification of Imprinted Loci by Transcriptome Sequencing Tomas Babak 7. Data Mining as a Discovery Tool for Imprinted Genes Chelsea Brideau and Paul Soloway Part III: Identifying the Regulatory Features of Imprinted Domains 8. Engineering of Large Deletions and Duplications In Vivo Louis Lefebvre Part IV: Epigenetics of Imprinted Regions 9. Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells Julie Borgel, Sylvain Guibert, and Michael Weber 10. Chromatin Immunoprecipitation to Characterize the Epigenetic Profiles of Imprinted Domains Purnima Singh and Piroska E. Szabo 11. Quantitative Chromosome Conformation Capture Raffaella Nativio, Yoko Ito, and Adele Murrell 12. Genome-Wide Analysis of DNA Methylation in Low Cell Numbers by Reduced Representation Bisulfite Sequencing Sebastien A. Smallwood and Gavin Kelsey Part V: Analysis of Imprinted Expression 13. Isolation of RNA and DNA from Single Preimplantation Embryos and a Small Number of Mammalian Oocytes for Imprinting Studies Sarah Rose Huffman, Md Almamun, and Rocio Melissa Rivera 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon Raffaella Nativio, Yoko Ito, and Adele Murrell 12. Genome-Wide Analysis of DNA Methylation in Low Cell Numbers by Reduced Representation Bisulfite Sequencing Sebastien A. Smallwood and Gavin Kelsey Part V: Analysis of Imprinted Expression 13. Isolation of RNA and DNA from Single Preimplantation Embryos and a Small Number of Mammalian Oocytes for Imprinting Studies Sarah Rose Huffman, Md Almamun, and Rocio Melissa Rivera 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon Sebastien A. Smallwood and Gavin Kelsey Part V: Analysis of Imprinted Expression 13. Isolation of RNA and DNA from Single Preimplantation Embryos and a Small Number of Mammalian Oocytes for Imprinting Studies Sarah Rose Huffman, Md Almamun, and Rocio Melissa Rivera 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon 14. Generation of cDNA Libraries from RNP-Derived Regulatory Non-Coding RNAs Mathieu Rederstorff 15. Co-Immunoprecipitation of Long Non-Coding RNAs Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil Part VI: Imprinting in Plants 16. Specialized Technologies for Epigenetics in Plants Wenyan Xiao Part VII: Evolution of Imprinted Genes 17. Computational Studies of Imprinted Genes Martina Paulsen 18. Insights on Imprinting from Beyond Mice and Men Andrew Pask 19. Non-Mammalian Parent-Of-Origin Effects Elena de la Casa-Esperon

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