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Transposons and Retrotransposons

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Jose L. Garcia-Pérez

    1. Institute of Genetics and Molecular Medi, Genyo (Center for Genomics and Oncologic, Granada, Spain

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1400)

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About this book

This volume covers the latest protocols designed to identify and characterize TEs in genomes, ancient or recently inserted. Additionally, this book includes a series of protocols designed to understand how host genomes act to regulate the activity of TEs, from elegant genetic mobilization assays to key biochemical methods. Finally, this book also includes chapters that describe how TEs can be used for biotechnological applications. Written for the Methods in Molecular Biology series, 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 practical, Transposons and Retrotransposons: Methods and Protocols aims to ensure successful results in the further study of this vital field.

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Study of Transposable Elements and Their Genomic Impact

    • Martin Muñoz-Lopez, Raquel Vilar-Astasio, Pablo Tristan-Ramos, Cesar Lopez-Ruiz, Jose L. Garcia-Pérez
    Pages 1-19

  3. Bacterial Group II Introns: Identification and Mobility Assay

    • Nicolás Toro, María Dolores Molina-Sánchez, Rafael Nisa-Martínez, Francisco Martínez-Abarca, Fernando Manuel García-Rodríguez
    Pages 21-32

  4. In Silico Methods to Identify Exapted Transposable Element Families

    • LeeAnn Ramsay, Guillaume Bourque
    Pages 33-45

  5. Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans

    • Francisco J. Sanchez-Luque, Sandra R. Richardson, Geoffrey J. Faulkner
    Pages 47-77

  6. Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome

    • Tara T. Doucet, Haig H. Kazazian Jr.
    Pages 79-93

  7. Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing

    • Raheleh Rahbari, Richard M. Badge
    Pages 95-106

  8. RNA-Seq Analysis to Measure the Expression of SINE Retroelements

    • Ángel Carlos Román, Antonio Morales-Hernández, Pedro M. Fernández-Salguero
    Pages 107-116

  9. Qualitative and Quantitative Assays of Transposition and Homologous Recombination of the Retrotransposon Tf1 in Schizosaccharomyces pombe

    • Maya Sangesland, Angela Atwood-Moore, Sudhir K. Rai, Henry L. Levin
    Pages 117-130

  10. LINE Retrotransposition Assays in Saccharomyces cerevisiae

    • Axel V. Horn, Jeffrey S. Han
    Pages 131-137

  11. LINE-1 Cultured Cell Retrotransposition Assay

    • Huira C. Kopera, Peter A. Larson, John B. Moldovan, Sandra R. Richardson, Ying Liu, John V. Moran
    Pages 139-156

  12. L1 Retrotransposition in Neural Progenitor Cells

    • Alysson R. Muotri
    Pages 157-163

  13. Characterization of Engineered L1 Retrotransposition Events: The Recovery Method

    • David Cano, Santiago Morell, Andres J. Pulgarin, Suyapa Amador, Jose L. Garcia-Pérez
    Pages 165-182

  14. SINE Retrotransposition: Evaluation of Alu Activity and Recovery of De Novo Inserts

    • Catherine Ade, Astrid M. Roy-Engel
    Pages 183-201

  15. The Engineered SVA Trans-mobilization Assay

    • Anja Bock, Gerald G. Schumann
    Pages 203-222

  16. Detection of LINE-1 RNAs by Northern Blot

    • Prescott Deininger, Victoria P. Belancio
    Pages 223-236

  17. Monitoring Long Interspersed Nuclear Element 1 Expression During Mouse Embryonic Stem Cell Differentiation

    • Maxime Bodak, Constance Ciaudo
    Pages 237-259

  18. Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues

    • Reema Sharma, Nemanja Rodić, Kathleen H. Burns, Martin S. Taylor
    Pages 261-280

  19. Cellular Localization of Engineered Human LINE-1 RNA and Proteins

    • Aurélien J. Doucet, Eugénia Basyuk, Nicolas Gilbert
    Pages 281-297

  20. Purification of L1-Ribonucleoprotein Particles (L1-RNPs) from Cultured Human Cells

    • Prabhat K. Mandal, Haig H. Kazazian Jr.
    Pages 299-310
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Editors and Affiliations

  • Institute of Genetics and Molecular Medi, Genyo (Center for Genomics and Oncologic, Granada, Spain

    Jose L. Garcia-Pérez

Bibliographic Information

  • Book Title: Transposons and Retrotransposons

  • Book Subtitle: Methods and Protocols

  • Editors: Jose L. Garcia-Pérez

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3372-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3370-9Published: 20 February 2016

  • Softcover ISBN: 978-1-4939-8033-8Published: 31 March 2018

  • eBook ISBN: 978-1-4939-3372-3Published: 19 February 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 434

  • Number of Illustrations: 17 b/w illustrations, 56 illustrations in colour

  • Topics: Human Genetics

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