RNA turnover in eukaryotes : Analysis of specialized and quality control RNA decay pathways / edited by Lynne E. Maquat, Megerditch Kiledjian.

Contributor(s): Maquat, Lynne [editor.] | Kiledjian, Megerditch [editor.]
Material type: TextTextSeries: Methods in enzymology: volume 449.Publisher: San Diego, California : Academic Press/Elsevier, ©2008Description: 1 online resource (xliv, 417 pages, 1 unnumbered leaf of plates) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9780080923321; 0080923321; 0123745845; 9780123745842Other title: Analysis of specialized and quality control RNA decay pathwaysSubject(s): Protista | RNA | RNA Precursors | RNA Stability -- physiology | Eukaryotic Cells -- metabolism | RNA, Messenger -- metabolism | mRNA Cleavage and Polyadenylation Factors | SCIENCE -- Life Sciences -- Biology | SCIENCE -- Life Sciences -- Microbiology | Protista | RNA | rna | metabolisme | metabolism | degradatie | degradation | Metabolic Processes | Metabole processenGenre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: RNA turnover in eukaryotes.DDC classification: 579 LOC classification: QP601 | .M49eb v. 449Online resources: Click here to access online
Contents:
Section I. Analysis of Specialized mRNA Decay Pathways -- Section II: Nonsense-Mediated mRNA Decay (How Do You Study NMD; What Defines An NMD Target) -- Section III. Analysis of Nuclear mRNA Decay and Non-mRNA Decay -- Section IV. Identifying Targets of an RNA Decay Factor -- Section V. RNAi-Mediated mRNA Decay.
Front Cover; RNA Turnover in Eukaryotes: Analysis of Specialized and Quality Control RNA Decay Pathways; Copyright Page; Contents; Contributors; Preface; Volumes in Series; Section I: Analysis of Specialized mRNA Decay Pathways; Chapter 1: Methods to Study No-Go mRNA Decay in Saccharomyces Cerevisiae; 1. Introduction; 2. Design and Construction of an NGD Substrate mRNA; 4. Conclusion; References; Chapter 2: Cell-Cycle Regulation of Histone mRNA Degradation in Mammalian Cells: Role of Translation and Oligouridylation; 1. Introduction.
2. Use of the Iron Response Protein to Study the Role of Translation in Histone mRNA Degradation3. Expression of a Dominant Negative Stem-Loop Binding Protein; 5. Oligo(dA) RT-PCR to Visualize Oligo(U) Tails on Histone mRNA following Inhibition of DNA Synthesis or at the End of S Phase; Chapter 3: Assays of Adenylate Uridylate-Rich Element-Mediated mRNA Decay in Cells; 1. Introduction; 2. Reporter Gene System; 6. Quantitation of mRNA Levels; Acknowledgments; References; Chapter 4: Evaluating the Control of mRNA Decay in Fission Yeast; 1. Introduction.
3. Systems for Studying TZF Protein-Mediated mRNA Decay5. Use of the nmt Expression System to Evaluate zfs1-Mediated mRNA Decay; 6. Northern Blot Analysis and Transcript Quantitation; Acknowledgments; References; Chapter 5: In Vivo Analysis of the Decay of Transcripts Generated by Cytoplasmic RNA Viruses; 1. Introduction; 3. Viral RNA Decay Systems; 5. Analysis of the 3prime End of Viral RNA; 6. Isolation of Small RNAs; Acknowledgments; References; Section II: Nonsense-Mediated MRNA Decay (How Do You Study NMD; What Defines An NMD Target).
Chapter 6: Qualitative and Quantitative Assessment of the Activity of the Yeast Nonsense-Mediated mRNA Decay Pathway1. Introduction; 2. Methods and Discussion; 3. Summary; Acknowledgment; References; Chapter 7: Nonsense-Mediated mRNA Decay in Caenorhabditis Elegans; 1. Introduction; 3. Protocol for a Genome-Wide RNAi-Based NMD Screen; 4. Protocol: Genetic Screen for Novel NMD Factors; References; Chapter 8: In Vivo Analysis of Plant Nonsense-Mediated mRNA Decay; 1. Introduction.
5. Experiment 1 (Analysis of Endogeneous NMD Target: The Fate of At3g63340 Splicing Variants in Arabidopsis Thaliana)6. Experiment 2 (Recognition of Termination Codon Contexts as NMD Targets in Nicotiana Benthamiana); References; Chapter 9: Studying Nonsense-Mediated mRNA Decay in Mammalian Cells; 1. Introduction; 2. Criteria for Nonsense-Mediated mRNA Decay in Mammalian Cells; 3. Methods Used to Study NMD in Cultured Mammalian Cells; Acknowledgments; Section III: Analysis of Nuclear MRNA Decay and Non-MRNA Decay; Chapter 10: Estimating Nuclear mRNA Decay in Saccharomyces Cerevisiae.
Summary: Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation. * Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway * Expert researchers introduce the most advanced technologies and techniques * Offers step-by-step lab instructions, including necessary equipment and reagents.
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Includes bibliographical references and indexes.

Section I. Analysis of Specialized mRNA Decay Pathways -- Section II: Nonsense-Mediated mRNA Decay (How Do You Study NMD; What Defines An NMD Target) -- Section III. Analysis of Nuclear mRNA Decay and Non-mRNA Decay -- Section IV. Identifying Targets of an RNA Decay Factor -- Section V. RNAi-Mediated mRNA Decay.

Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation. * Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway * Expert researchers introduce the most advanced technologies and techniques * Offers step-by-step lab instructions, including necessary equipment and reagents.

Front Cover; RNA Turnover in Eukaryotes: Analysis of Specialized and Quality Control RNA Decay Pathways; Copyright Page; Contents; Contributors; Preface; Volumes in Series; Section I: Analysis of Specialized mRNA Decay Pathways; Chapter 1: Methods to Study No-Go mRNA Decay in Saccharomyces Cerevisiae; 1. Introduction; 2. Design and Construction of an NGD Substrate mRNA; 4. Conclusion; References; Chapter 2: Cell-Cycle Regulation of Histone mRNA Degradation in Mammalian Cells: Role of Translation and Oligouridylation; 1. Introduction.

2. Use of the Iron Response Protein to Study the Role of Translation in Histone mRNA Degradation3. Expression of a Dominant Negative Stem-Loop Binding Protein; 5. Oligo(dA) RT-PCR to Visualize Oligo(U) Tails on Histone mRNA following Inhibition of DNA Synthesis or at the End of S Phase; Chapter 3: Assays of Adenylate Uridylate-Rich Element-Mediated mRNA Decay in Cells; 1. Introduction; 2. Reporter Gene System; 6. Quantitation of mRNA Levels; Acknowledgments; References; Chapter 4: Evaluating the Control of mRNA Decay in Fission Yeast; 1. Introduction.

3. Systems for Studying TZF Protein-Mediated mRNA Decay5. Use of the nmt Expression System to Evaluate zfs1-Mediated mRNA Decay; 6. Northern Blot Analysis and Transcript Quantitation; Acknowledgments; References; Chapter 5: In Vivo Analysis of the Decay of Transcripts Generated by Cytoplasmic RNA Viruses; 1. Introduction; 3. Viral RNA Decay Systems; 5. Analysis of the 3prime End of Viral RNA; 6. Isolation of Small RNAs; Acknowledgments; References; Section II: Nonsense-Mediated MRNA Decay (How Do You Study NMD; What Defines An NMD Target).

Chapter 6: Qualitative and Quantitative Assessment of the Activity of the Yeast Nonsense-Mediated mRNA Decay Pathway1. Introduction; 2. Methods and Discussion; 3. Summary; Acknowledgment; References; Chapter 7: Nonsense-Mediated mRNA Decay in Caenorhabditis Elegans; 1. Introduction; 3. Protocol for a Genome-Wide RNAi-Based NMD Screen; 4. Protocol: Genetic Screen for Novel NMD Factors; References; Chapter 8: In Vivo Analysis of Plant Nonsense-Mediated mRNA Decay; 1. Introduction.

5. Experiment 1 (Analysis of Endogeneous NMD Target: The Fate of At3g63340 Splicing Variants in Arabidopsis Thaliana)6. Experiment 2 (Recognition of Termination Codon Contexts as NMD Targets in Nicotiana Benthamiana); References; Chapter 9: Studying Nonsense-Mediated mRNA Decay in Mammalian Cells; 1. Introduction; 2. Criteria for Nonsense-Mediated mRNA Decay in Mammalian Cells; 3. Methods Used to Study NMD in Cultured Mammalian Cells; Acknowledgments; Section III: Analysis of Nuclear MRNA Decay and Non-MRNA Decay; Chapter 10: Estimating Nuclear mRNA Decay in Saccharomyces Cerevisiae.

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RNA turnover in eukaryotes : ©2008
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