Description
Book SynopsisThe 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.
Table of Contents1. An overview of best practices for transposable element identification, classification and annotation in eukaryotic genomes
Fernando Rodriguez and Irina R. Arkhipova
2. Assembly-free annotation and quantification of transposable elements with dnaPipeTE
Clément Goubert
3. Best practice for the identification of horizontally transferred transposons
James D Galbraith, Zhipeng Qu, Atma M Ivancevic, David L Adelson
4. Genotyping of transposable elements insertions segregating in the human populations using short-read re-alignments
Xun Chen, Guillaume Bourque, and Clément Goubert
5. A Pangenome approach to detect and genotype TE insertion polymorphisms
Cristian Groza, Guillaume Bourque, and Clément Goubert
6. Experimental validation of transposable element insertions using the Polymerase Chain Reaction (PCR)
Miriam Merenciano, Marta Coronado-Zamora, and Josefa González
7. Quantification of LINE-1 RNA expression from bulk RNA-seq using L1EM
Wilson McKerrow
8. Genome-wide profiling of L1 DNA methylation by bs-ATLAS-seq
Claude Philippe and Gael Cristofari
9. Nanopore epigenomic analysis of transposable element DNA modifications
Nathan Smits and Geoffrey Faulkner
10. Targeted resequencing and methylation analysis of L1 elements by nanopore sequencing
Arpita Sarkar, Sophie Lanciano, and Gael Cristofari
11. Inferring protein-DNA binding profiles at interspersed repeats using HiChIP and PatChER
Darren Taylor and Miguel R Branco
12. Affinity-based Interactome Analysis of Endogenous LINE-1 Macromolecules
Luciano H. Di Stefano, Leila Saba, Mehrnoosh Oghbaie, Hua Jiang, Wilson McKerrow, Maria Benitez-Guijarro, Martin S. Taylor, and John LaCava
13. LINE-1 retrotransposition assays in embryonic stem cells
Marta Garcia-Canadas, Francisco Sanchez-Luque, Laura Sanchez, Johana Rojas, and Jose Garcia Perez
14. Detecting somatic transposable element insertions in Drosophila tissues
Katarzyna Siudeja
15. Precise and scarless insertion of transposable elements by Cas9-mediated genome engineering”
Vivien M Weber, Aurelien J Doucet, and Gael Cristofari
16. Epigenetic editing of transposable and repetitive elements
Joanna M Jachowicz
17. Using CRISPR to investigate the regulatory activity of transposable elements
David M Simpson, Conor R Kelly, and Edward B Chuong
