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Autor: Joanna Rorbach
ISBN-13: 9781627039703
Einband: Book
Seiten: 377
Gewicht: 885 g
Format: 262x187x27 mm
Sprache: Englisch


1125, Methods in Molecular Biology
Methods and Protocols
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Includes cutting-edge methods and protocols
PART I: SECTION I: 3 -END PROCESSING IN EUKARYOTES 1. 3 end Formation and Regulation of Eukaryotic mRNAs
Thomas J. Sweet and Donny D. Licatalosi
PART II: I-A General Methods
2. Poly(A) Polymerase-based Poly(A) Length Assay
Deepak P. Patil, Baskar Bakthavachalu, and Daniel R. Schoenberg
3 . Using Klenow Mediated Extension to Measure Poly(A)-tail Length and Position in the Transcriptome
Man C. Lee, Amrei Jänicke, and Traude H. Beilharz
4 . Detection of Uridylated mRNAs
François M. Sement, Dominique Gagliardi
5 . Cytoplasmic Polyadenylation Assays
Olga Coll, Ana Villalba, Fátima Gebauer
6 . In vitro Analysis of Transcriptional Activators and Polyadenylation
Takashi Nagaike and James L. Manley
7 . Fluorescence Detection of Polyadenylation Reaction through the Coordination of Adensoine 2 -coralyne-adensoine 2
Jia-Hui Lin and Wei-Lung Tseng
8 . Small Molecule Recognition of Poly(A)
Özgül Persil Çetinkol
9 . The Stem-loop Luciferase Assay for Polyadenylation (SLAP) Method for Determining CstF-64-dependent Polyadenylation Activity
J. Andrew Hockert and Clinton C. MacDonald
PART III: I-B Alternative Polyadenylation
I-B-1 Prediction of Polyadenylation Sites
10 . Accurate Mapping of Cleavage and Polyadenylation Sites by 3' Region Extraction and Deep Sequencing
Mainul Hoque, Wencheng Li, and Bin Tian
11 . Polyadenylation Site Prediction using PolyA-iEP Method
Ioannis Kavakiotis, George Tzanis, and Ioannis Vlahavas
12 . Detecting Alternative Polyadenylation from Microarray Data
Antonio Lembo and Paolo Provero
Part IV: I-B-2 Large Scale/Genome Wide Analysis of mRNA Polyadenylation and Application of the Next Generation DNA Sequencing in Polyadenylation Study
13 . Quantitative Polyadenylation Site Mapping with Single-molecule Direct RNA Sequencing
Fatih Ozsolak
14 . RHAPA: A New Method to Quantify Alternative Polyadenylation
Ashley L. Cornett and Carol S. Lutz
15 . Multiplex Analysis of PolyA-linked Sequences (MAPS): An RNA-seq Strategy to Profile poly(A+) RNA
Yu Zhou, Hai-Ri Li, Jie Huang, Ge Jin, and Xiang-Dong Fu
16 . Global and Quantitative Profiling of Polyadenylated RNAs using PAS-seq
Chengguo Yao and Yongsheng Shi
17 . High-throughput Sequencing of RNA Isolated by Crosslinking and Immunoprecipitation (HITS-CLIP) to Determine Sites of Binding of CstF-64 on Nascent RNAs
Petar N. Grozdanov and Clinton C. MacDonald
18. Polyadenylation in Bacteria and Organelles
Joanna Rorbach, Agnieszka J. Bobrowicz, Sarah Pearce, and Michal Minczuk.
19 . In vivo Analysis of Polyadenylation in Prokaryotes
Bijoy K. Mohanty and Sidney R. Kushner
20 . Polyadenylation of RNA in E. coli : RNA Polymerase-associated (rA)n-synthetic Activities
Grant A. Encalade and Maxim V. Sukhodolets
21 . Analysis of the Human Mitochondrial Transcriptome using Directional Deep sequencing and Parallel Analysis of RNA Ends
Oliver Rackham and Aleksandra Filipovska
22. Measurement of Mitochondrial RNA Stability by Metabolic Labeling of Transcripts with 4-Thiouridine
Lukasz S. Borowski and Roman J. Szczesny
23. Deadenylation and its Regulation in Eukaryotic Cells
Xiaokan Zhang, Frida E. Kleiman, and Emral Devany
24 . Assaying mRNA Deadenylation in vitro
Mandy Jeske, Claudia Temme, and Elmar Wahle
25 . Assaying mRNA Deadenylation in vivo
Claudia Temme and Elmar Wahle
26 . In vitro Analysis of RNA Degradation Catalyzed by Deadenylase Enzymes
Joel Hrit, Nathan Raynard, Jamie Van Etten, Kamya Sankar, Adam Petterson, and Aaron C. Goldstrohm
27 . microRNA-mediated Deadenylation in a Mammalian Cell-free System
Motoaki Wakiyama, Shigeyuki Yokoyama
28 . Quantitative Analysis of Deadenylation-independent mRNA Decay by a Modified MBRACE Assay
Julie A. Dougherty, Roshan Mascarenhas, and Daniel R. Schoenberg.
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.

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Autor: Joanna Rorbach
ISBN-13 :: 9781627039703
ISBN: 1627039708
Erscheinungsjahr: 31.03.2014
Verlag: Springer-Verlag GmbH
Gewicht: 885g
Seiten: 377
Sprache: Englisch
Auflage 2014
Sonstiges: Buch, 262x187x27 mm, 50 schwarz-weiße und 18 farbige Abbildungen, 11 schwarz-weiße Tabellen, Bibliographie