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.
Table of Contents
Study of Transposable Elements and their Genomic Impact.- Bacterial Group II Introns: Identification and Mobility Assay.- In silico Methods to Identify Exapted Transposable Element Families.- Retrotransposon Capture Sequencing (RC-seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans.- Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome.- Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High Throughput Sequencing.- RNA-seq Analysis to Measure the Expression of SINE Retroelements.- Qualitative and Quantitative Assays of Transposition and Homologous Recombination of the Retrotransposon Tf1 in Schizosaccharomyces pombe.- LINE Retrotransposition Assays in Saccharomyces cerevisiae.- LINE-1 Cultured Cell Retrotransposition Assay.- L1 Retrotransposition in Neural Progenitor Cells.- Characterization of Engineered L1 Retrotransposition Events: The Recovery Method.- SINE Retrotransposition: Evaluation of Alu Activity and Recovery of de novo Inserts.- The Engineered SVA Trans-Mobilization Assay.- Detection of LINE-1 RNAs by Northern Blot.- Monitoring Long Interspersed Nuclear Element 1 Expression during Mouse Embryonic Stem Cells Differentiation.- Immuno-Detection of Human LINE-1 Expression in Cultured Cells and Human Tissues.- Cellular Localization of Engineered Human LINE-1 RNA and Proteins.- Purification of L1-ribonucleoprotein Particles (L1-RNPs) from Cultured Human Cells.- Characterization of L1-RiboNucleoprotein Particles.- LEAP: L1 Element Amplification Protocol.- Biochemical Approaches to Study LINE-1 Reverse Transcriptase Activity In Vitro.- Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.- Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements.- A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression.- Reprogramming of Human Fibroblasts to Induced Pluripotent Stem Cells with Sleeping Beauty Transposon-based Stable Gene Delivery.