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mRNA Decay

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Cover of 'mRNA Decay'

Table of Contents

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    Book Overview
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    Chapter 1 5′-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives
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    Chapter 2 Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)
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    Chapter 3 Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay
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    Chapter 4 Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH
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    Chapter 5 PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins
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    Chapter 6 Characterizing mRNA Sequence Motifs in the 3′-UTR Using GFP Reporter Constructs
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    Chapter 7 iCLIP of the PIWI Protein Aubergine in Drosophila Embryos
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    Chapter 8 Integration of ENCODE RNAseq and eCLIP Data Sets
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    Chapter 9 Identifying miRNA Targets Using AGO-RIPseq
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    Chapter 10 Integrated Analysis of miRNA and mRNA Expression Profiles to Identify miRNA Targets
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    Chapter 11 Identifying RISC Components Using Ago2 Immunoprecipitation and Mass Spectrometry
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    Chapter 12 Using Tet-Off Cells and RNAi Knockdown to Assay mRNA Decay
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    Chapter 13 Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP−Seq)
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    Chapter 14 Generation of Cell Lines Stably Expressing a Fluorescent Reporter of Nonsense-Mediated mRNA Decay Activity
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    Chapter 15 Reactivation Assay to Identify Direct Targets of the Nonsense-Mediated mRNA Decay Pathway in Drosophila
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    Chapter 16 Studying Nonsense-Mediated mRNA Decay in Mammalian Cells Using a Multicolored Bioluminescence-Based Reporter System
Attention for Chapter 3: Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay
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Chapter title
Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay
Chapter number 3
Book title
mRNA Decay
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7540-2_3
Pubmed ID
Book ISBNs
978-1-4939-7539-6, 978-1-4939-7540-2
Authors

Wei Sun, Wei Chen

Abstract

The development of genome-wide RNA profiling technologies greatly facilitates the global analysis of gene expression. However, such technologies alone could not distinguish the contribution to cellular RNA abundance by transcription versus decay. To overcome such limitation, metabolic labeling of newly synthesized RNA with 4-thiouridine (4sU) combined with genome-wide RNA profiling was used to in parallel measure RNA transcription and decay. Here, we describe the detailed protocol for using metabolic labeling with 4sU to separate newly synthesized RNA from the preexisting RNA in mammalian cells.

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Mendeley readers

The data shown below were compiled from readership statistics for 17 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 17 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 29%
Student > Doctoral Student 4 24%
Professor 2 12%
Other 1 6%
Researcher 1 6%
Other 1 6%
Unknown 3 18%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 8 47%
Agricultural and Biological Sciences 4 24%
Arts and Humanities 1 6%
Medicine and Dentistry 1 6%
Neuroscience 1 6%
Other 0 0%
Unknown 2 12%