Genomic Imprinting: Methods and Protocols

ISBN-13: 9781627030106 / Angielski / Twarda / 2012 / 297 str.

Nora Engel

Opis

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 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.

Spis treści

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. Szabó

 

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

            Sébastien 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 Rocío 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-Esperón

 

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-Esperón

 

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-Esperón

            Raffaella Nativio, Yoko Ito, and Adele Murrell

 

12. Genome-Wide Analysis of DNA Methylation in Low Cell Numbers by Reduced Representation Bisulfite Sequencing

            Sébastien 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 Rocío 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-Esperón

 

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-Esperón

            Sébastien 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 Rocío 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-Esperón

 

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-Esperón