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The volume presents a small selection of state-of-the-art approaches for studying transposable elements(TE). Chapters guide readers through HTS-based approaches, bioinformatic tools, methods to studyTE protein complexes, and the functional impact on the host. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, Transposable Elements: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.
An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes
Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE
Detecting Horizontal Transfer of Transposons
Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments
A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms
Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR)
Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM
Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq
Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications
Targeted Nanopore Resequencing and Methylation Analysis of LINE-1 Retrotransposons​
Inferring Protein-DNA Binding Profiles at Interspersed Repeats Using HiChIP and PAtChER
Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules
LINE-1 Retrotranspositi​on Assays in Embryonic Stem Cells
Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing
Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering
Epigenetic Manipulation of Transposable and Repetitive Elements
Genetic Knockout of TE Insertions by CRISPR-Cas9