Main description:

This volume aims to provide the most recent advances in techniques for studying gene expression regulation at the post-transcriptional level. Post-Transcriptional Gene Regulation, Second Edition is organized in six sections describing bioinformatics approaches for studying post-transcriptional regulation, various expression profiling approaches, protein-RNA interaction and non-coding RNA investigation techniques, methods for profiling RNA modifications, and other techniques such as alternative translation initiation or polyadenylation sites determination. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Post-Transcriptional Gene Regulation, Second Edition is a versatile resource to researchers studying post-transcriptional regulation, introducing the most recent techniques and providing a comprehensive guide to their implementation.

Contents:

PART I: Bioinformatics

1. Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene Expression

Alessandro Quattrone and Erik Dassi

2. A Computational Approach for the Discovery of Protein-RNA Networks

Domenica Marchese, Carmen Maria Livi, and Gian Gaetano Tartaglia

PART II: Expression Studies

3. Transcriptional Regulation with CRISPR/Cas9 Effectors in Mammalian Cells

Hannah Pham, Nicola A. Kearns, and Rene Maehr

4. Studying the Translatome with Polysome Profiling

Paola Zuccotti and Angelika Modelska

5. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling

Pieter Spealman, Hao Wang, Gemma May, Carl Kingsford, and C. Joel Mcmanus

6. Studying Isoform-Specific Recruitment to Polyribosomes with Frac-Seq

Rocio T. Martinez-Nunez and Jeremy Sanford

7. Use of the Pbutr Reporter System for Scalable Analysis of 3' UTR-Mediated Gene Regulation

Arindam Chaudhury and Joel R. Neilson

PART III: RBP Interactomics

8. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture

Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M. Steinmetz, Jeroen Krijgsveld, and Matthias W. Hentze

9. Identifying RBP Targets with RIP-Seq

Hans-Herman Wessels, Antje Hirsekorn, Uwe Ohler, and Neelanjan Mukherjee

10. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites

Charles Danan, Sudhir Manickavel, and Markus Hafner

11. Profiling the Binding Sites of RNA-Binding Proteins with Nucleotide Resolution Using Iclip

FX Reymond Sutandy, Andrea Hildebrandt, and Julian Koenig

12. A Pipeline for PAR-CLIP Data Analysis

Marvin Jens

PART IV: Non-Coding RNAs

13. Capture and Identification Of Mirna Targets By Biotin Pulldown And RNA-Seq

Shen Mynn Tan and Judy Lieberman

14. Identification of Mirna-Target RNA Interactions Using CLASH

Alexandra Helwak and David Tollervey

PART V: RNA Modifications

15. Genome-Wide Analysis of A-To-I RNA Editing

Yiannis A. Savva, Georges St. Laurent, and Robert A. Reenan

16. Nucleotide-Level Profiling Of M5c RNA Methylation

Tennille Sibbritt, Andrew Shafik, Susan J. Clark, and Thomas Preiss

17. Probing N6-Methyladenosine (M6a) RNA Modification in Total RNA with SCARLET

Nian Liu and Tao Pan

PART VI: Other Aspects Of PTR

18. Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill

Stefan Wilkening, Vicent Pelechano, and Lars M. Steinmetz

19. Genome-Wide Profiling Of Alternative Translation Initiation Sites

Xiangwei Gao, Ji Wan, and Shu-Bing Qian

20. Genome-Wide Study Of Mrna Isoform Half-Lives

Joseph V. Geisberg and Zarmik Moqtaderi

21. Visualizing Mrna Dynamics in Live Neurons and Brain Tissues

Hye Yoon Park and Minho Song

22. Single Molecule Live-Cell Visualization of Pre-Mrna Splicing

Robert M. Martin, Jose Rino, Ana C. De Jesus, and Maria Carmo-Fonseca