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mRNA decay : methods and protocols

Author: Shireen R Lamande
Publisher: New York, NY : Humana Press ; Springer, [2018] ©2018
Series: Methods in molecular biology (Clifton, N.J.), v. 1720.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets. Subjects include metabolic labelling and RNAseq methods for determining RNA decay rates, approaches for discovering RNA-binding protein targets, bioinformatics, miRNA targets and novel components of the miRNA-directed decay pathway, and recently developed  Read more...
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Details

Genre/Form: Electronic books
Laboratory manuals
Additional Physical Format: Print version:
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Shireen R Lamande
ISBN: 9781493975402 1493975404
OCLC Number: 1015338398
Description: 1 online resource (xi, 227 pages) : illustrations (some color).
Contents: 50-bromouridine IP chase (BRIC)-seq to determine RNA half-lives / Toshimichi Yamada, Naoto Imamachi, Rena Onoguchi-Mizutani, Katsutoshi Imamura, Yutaka Suzuki, and Nobuyoshi Akimitsu --
Determining mRNA decay rates using RNA approach to equilibrium sequencing (RATE-Seq) / Farah Abdul-Rahman and David Gresham --
Metabolic labeling of newly synthesized RNA with 4sU to in parallel assess RNA transcription and decay / Wei Sun and Wei Chen --
Measuring mRNA decay in budding yeast using single molecule FISH / Tatjana Trcek, Samir Rahman, and Daniel Zenklusen --
PAR-CLIP for discovering target sites of RNA-binding proteins / Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, and Thomas Tuschl --
Characterizing mRNA sequence motifs in the 3'-UTR using GFP reporter constructs / Rene Geissler and Andrew Grimson --
iCLIP of the PIWI protein aubergine in Drosophila embryos / Bridlin Barckmann, Jeremy Dufourt, and Martine Simonelig --
Integration of ENCODE RNAseq and eCLIP data sets / Jorge Boucas --
Identifying miRNA targets using AGO-RIPseq / Rebecca Petri and Johan Jakobsson --
Integrated analysis of miRNA and mRNA expression profiles to identify miRNA targets / Zhiming Li and Chi-Meng Tzeng --
Identifying RISC components using Ago2 immunoprecipitation and mass spectrometry / Tingfang Yi --
Using tet-off cells and RNAi knockdown to assay mRNA decay / Thomas D. Baird and J. Robert Hogg --
Identifying cellular nonsense-mediated mRNA decay (NMD) targets : immunoprecipitation of phosphorylated UPF1 followed by RNA sequencing (p-UPF1 RIP seq) / Tatsuaki Kurosaki, Mainul Hoque, and Lynne E. Maquat --
Generation of cell lines stably expressing a fluorescent reporter of nonsense-mediated mRNA decay activity / Nadezhda M. Markina, Anton P. Pereverzev, Dmitry B. Staroverov, Konstantin A. Lukyanov, and Nadya G. Gurskaya --
Reactivation assay to identify direct targets of the nonsense-mediated mRNA decay pathway in Drosophila / Jonathan O. Nelson and Mark M. Metzstein --
Studying nonsense-mediated mRNA decay in mammalian cells using a multicolored bioluminescence-based reporter system / Andrew Nickless and Zhongsheng You.
Series Title: Methods in molecular biology (Clifton, N.J.), v. 1720.
Responsibility: edited by Shireen R. Lamandé.

Abstract:

This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets.  Read more...

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