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In Polyadenylation: Methods and Protocols , expert researchers in the field detail many of the protocols which are now commonly used to study polyadenylation. Focusing on recent advances in the fast-moving polyadenylation filed, that has recently been recognized as a key contributor to the complexity of mammalian gene expression. Written in the highly 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 laboratory protocols and key tips on troubleshooting and avoiding known pitfalls.
List of contents
3' end Formation and Regulation of Eukaryotic mRNAs.- Poly(A) Polymerase-based Poly(A) Length assay.- Using Klenow Mediated Extension to Measure Poly(A)-tail Length and Position in the Transcriptome.- Detection of Uridylated mRNAs.- Cytoplasmic Polyadenylation Assays.- In vitro Analysis of Transcriptional Activators and Polyadenylation.- Fluorescence Detection of Polyadenylation Reaction through the Coordination of Adensoine2-coralyne-adensoine2.- Small molecule recognition of poly(A).-The Stem-loop Luciferase assay for Polyadenylation (SLAP) Method for Determining CstF-64-dependent Polyadenylation Activity.- Accurate Mapping of Cleavage and Polyadenylation Sites by 3' Region Extraction and Deep Sequencing.- Polyadenylation Site Prediction using PolyA-iEP Method.- Detecting alternative polyadenylation from Microarray Data.- Quantitative Polyadenylation Site Mapping with Single-molecule Direct RNA Sequencing.- RHAPA: A New Method to Quantify Alternative Polyadenylation.- Multiplex Analysis of PolyA-linked Sequences (MAPS): An RNA-seq Strategy to Profile poly(A+) RNA.- Global and Quantitative Profiling of Polyadenylated RNAs using PAS-seq.- High-throughput Sequencing of RNA Isolated by Crosslinking and Immunoprecipitation (HITS-CLIP) to Determine Sites of Binding of CstF-64 on Nascent RNAs.- Polyadenylation in Bacteria and Organelles.- In vivo Analysis of Polyadenylation in Prokaryotes.- Polyadenylation of RNA in E. coli: RNA Polymerase-associated (rA)n-synthetic Activities.- Analysis of the Human Mitochondrial Transcriptome using Directional Deep sequencing and Parallel Analysis of RNA Ends.- Measurement of Mitochondrial RNA Stability by Metabolic Labeling of Transcripts with 4-Thiouridine .- Deadenylation and its Regulation in Eukaryotic Cells.- Assaying mRNA Deadenylation in vitro.- Assaying mRNA Deadenylation in vivo.- In vitro Analysis of RNA Degradation Catalyzed by Deadenylase Enzymes.-microRNA-mediated Deadenylation in a Mammalian Cell-free System.- Quantitative Analysis of Deadenylation-independent mRNA Decay by a Modified MBRACE Assay.
Summary
In Polyadenylation: Methods and Protocols, expert researchers in the field detail many of the protocols which are now commonly used to study polyadenylation. Focusing on recent advances in the fast-moving polyadenylation filed, that has recently been recognized as a key contributor to the complexity of mammalian gene expression. Written in the highly 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 laboratory protocols and key tips on troubleshooting and avoiding known pitfalls.
