mRNA Decay: Methods and Protocols

Front Matter ....Pages i-xi
 5′-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives  (Toshimichi Yamada, Naoto Imamachi, Rena Onoguchi-Mizutani, Katsutoshi Imamura, Yutaka Suzuki, Nobuyoshi Akimitsu)....Pages 1-13
 Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)  (Farah Abdul-Rahman, David Gresham)....Pages 15-24
 Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay  (Wei Sun, Wei Chen)....Pages 25-34
 Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH  (Tatjana Trcek, Samir Rahman, Daniel Zenklusen)....Pages 35-54
 PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins  (Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl)....Pages 55-75
 Characterizing mRNA Sequence Motifs in the 3′-UTR Using GFP Reporter Constructs  (Rene Geissler, Andrew Grimson)....Pages 77-88
 iCLIP of the PIWI Protein Aubergine in Drosophila Embryos  (Bridlin Barckmann, Jérémy Dufourt, Martine Simonelig)....Pages 89-110
 Integration of ENCODE RNAseq and eCLIP Data Sets  (Jorge Boucas)....Pages 111-129
 Identifying miRNA Targets Using AGO-RIPseq  (Rebecca Petri, Johan Jakobsson)....Pages 131-140
 Integrated Analysis of miRNA and mRNA Expression Profiles to Identify miRNA Targets  (Zhiming Li, Chi-Meng Tzeng)....Pages 141-148
 Identifying RISC Components Using Ago2 Immunoprecipitation and Mass Spectrometry  (Tingfang Yi)....Pages 149-159
 Using Tet-Off Cells and RNAi Knockdown to Assay mRNA Decay  (Thomas D. Baird, J. Robert Hogg)....Pages 161-173
 Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP−Seq)  (Tatsuaki Kurosaki, Mainul Hoque, Lynne E. Maquat)....Pages 175-186
 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, Nadya G. Gurskaya)....Pages 187-204
 Reactivation Assay to Identify Direct Targets of the Nonsense-Mediated mRNA Decay Pathway in Drosophila  (Jonathan O. Nelson, Mark M. Metzstein)....Pages 205-211
 Studying Nonsense-Mediated mRNA Decay in Mammalian Cells Using a Multicolored Bioluminescence-Based Reporter System  (Andrew Nickless, Zhongsheng You)....Pages 213-224
Back Matter ....Pages 225-227