Transposons and Retrotransposons: Methods and Protocols

1 Study of Transposable Elements and Their Genomic Impact - Martin Muñoz-Lopez, Raquel Vilar-Astasio, Pablo Tristan-Ramos, Cesar Lopez-Ruiz, and Jose L. Garcia-Pérez
2 Bacterial Group II Introns: Identification and Mobility Assay - Nicolás Toro, María Dolores Molina-Sánchez, Rafael Nisa-Martínez, Francisco Martínez- Abarca, and Fernando Manuel García-Rodríguez
3 In Silico Methods to Identify Exapted Transposable Element Families - LeeAnn Ramsay and Guillaume Bourque
4 Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans - Francisco J. Sanchez-Luque, Sandra R. Richardson, and Geoffrey J. Faulkner
5 Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome - Tara T. Doucet and Haig H. Kazazian Jr.
6 Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing - Raheleh Rahbari and Richard M. Badge
7 RNA-Seq Analysis to Measure the Expression of SINE Retroelements - Ángel Carlos Román, Antonio Morales-Hernández, and Pedro M. Fernández-Salguero
8 Qualitative and Quantitative Assays of Transposition and Homologous Recombination of the Retrotransposon Tf1 in Schizosaccharomyces pombe - Maya Sangesland , Angela Atwood-Moore, Sudhir K. Rai, and Henry L. Levin
9 LINE Retrotransposition Assays in Saccharomyces cerevisiae - Axel V. Horn and Jeffrey S. Han
10 LINE-1 Cultured Cell Retrotransposition Assay - Huira C. Kopera, Peter A. Larson, John B. Moldovan, Sandra R. Richardson, Ying Liu, and John V. Moran
11 L1 Retrotransposition in Neural Progenitor Cells - Alysson R. Muotri
12 Characterization of Engineered L1 Retrotransposition Events: The Recovery Method - David Cano, Santiago Morell, Andres J. Pulgarin, Suyapa Amador, and Jose L. Garcia-Pérez
13 SINE Retrotransposition: Evaluation of Alu Activity and Recovery of De Novo Inserts - Catherine Ade and Astrid M. Roy-Engel
14 The Engineered SVA Trans-mobilization Assay - Anja Bock and Gerald G. Schumann
15 Detection of LINE-1 RNAs by Northern Blot - Prescott Deininger and Victoria P. Belancio
16 Monitoring Long Interspersed Nuclear Element 1 Expression During Mouse Embryonic Stem Cell Differentiation - Maxime Bodak and Constance Ciaudo
17 Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues - Reema Sharma, Nemanja Rodić, Kathleen H. Burns, and Martin S. Taylor
18 Cellular Localization of Engineered Human LINE-1 RNA and Proteins - Aurélien J. Doucet, Eugénia Basyuk, and Nicolas Gilbert
19 Purification of L1-Ribonucleoprotein Particles (L1-RNPs) from Cultured Human Cells - Prabhat K. Mandal and Haig H. Kazazian Jr.
20 Characterization of L1-Ribonucleoprotein Particles - Martin S. Taylor, John LaCava, Lixin Dai, Paolo Mita, Kathleen H. Burns, Michael P. Rout, and Jef D. Boeke
21 LEAP: L1 Element Amplification Protocol - Huira C. Kopera, Diane A. Flasch, Mitsuhiro Nakamura, Tomoichiro Miyoshi, Aurélien J. Doucet, and John V. Moran
22 Biochemical Approaches to Study LINE-1 Reverse Transcriptase Activity In Vitro - Sébastien Viollet, Aurélien J. Doucet, and Gaël Cristofari
23 Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses - Rita Rebollo and Dixie L. Mager
24 Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements - Lorenzo de la Rica, Jatinder S. Stanley, and Miguel R. Branco
25 A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression - Gabriela Ecco, Helen M. Rowe, and Didier Trono
26 Reprogramming of Human Fibroblasts to Induced Pluripotent Stem Cells with Sleeping Beauty Transposon-­Based Stable Gene Delivery - Attila Sebe and Zoltán Ivics