Transposable Elements

Methods and Protocols

Miguel R. Branco, Alexandre de Mendoza Soler (Herausgeber)

Buch | Softcover

382 Seiten

2023 | 1st ed. 2023
Springer-Verlag New York Inc.
978-1-0716-2885-0 (ISBN)

Artikel merken

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 annotation and quantification of transposable elements with dnaPipeTE.- Best practice for the identification of horizontally transferred transposons.- Genotyping of transposable elements insertions segregating in the human populations using short-read re-alignments.- A Pangenome approach to detect and genotype TE insertion polymorphisms.0 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 profiling of L1 DNA methylation by bs-ATLAS-seq.- Nanopore epigenomic analysis of transposable element DNA modifications.- Targeted resequencing and methylation analysis of L1 elements by nanopore sequencing.- Inferring protein-DNA binding profiles at interspersed repeats using HiChIP and PatChER.- Affinity-based Interactome Analysis of Endogenous LINE-1 Macromolecules.- LINE-1 retrotransposition assays in embryonic stem cells.- Detecting somatic transposable element insertions in Drosophila tissues.- Precise and scarless insertion of transposable elements by Cas9-mediated genome engineering.- Epigenetic editing of transposable and repetitive elements.- Using CRISPR to investigate the regulatory activity of transposable elements.

Erscheinungsdatum	02.12.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	60 Illustrations, color; 5 Illustrations, black and white; XII, 382 p. 65 illus., 60 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Mathematik / Informatik ► Informatik ► Theorie / Studium
	Informatik ► Weitere Themen ► Bioinformatik
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	ChIP-Seq • CRISPR-Cas9 • KZNFs • Nanopore • polymorphic transposons
ISBN-10	1-0716-2885-2 / 1071628852
ISBN-13	978-1-0716-2885-0 / 9781071628850
Zustand	Neuware