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Post-Transcriptional Gene Regulation

  • Book
  • © 2016

Overview

Editors:
  1. Erik Dassi

    1. Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Mattarello, Italy

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1358)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Bioinformatics

    1. Front Matter

      Pages 1-1
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    2. Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression

      • Alessandro Quattrone, Erik Dassi
      Pages 3-28

    3. A Computational Approach for the Discovery of Protein–RNA Networks

      • Domenica Marchese, Carmen Maria Livi, Gian Gaetano Tartaglia
      Pages 29-39

  3. Expression Studies

    1. Front Matter

      Pages 41-41
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    2. Transcriptional Regulation with CRISPR/Cas9 Effectors in Mammalian Cells

      • Hannah Pham, Nicola A. Kearns, René Maehr
      Pages 43-57

    3. Studying the Translatome with Polysome Profiling

      • Paola Zuccotti, Angelika Modelska
      Pages 59-69

    4. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling

      • Pieter Spealman, Hao Wang, Gemma May, Carl Kingsford, C. Joel McManus
      Pages 71-97

    5. Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq

      • Rocio T. Martinez-Nunez, Jeremy R. Sanford
      Pages 99-108

    6. Use of the pBUTR Reporter System for Scalable Analysis of 3′ UTR-Mediated Gene Regulation

      • Arindam Chaudhury, Joel R. Neilson
      Pages 109-128

  4. RBP Interactomics

    1. Front Matter

      Pages 129-129
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    2. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture

      • Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M. Steinmetz et al.
      Pages 131-139

    3. Identifying RBP Targets with RIP-seq

      • Hans-Herman Wessels, Antje Hirsekorn, Uwe Ohler, Neelanjan Mukherjee
      Pages 141-152

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

      • Charles Danan, Sudhir Manickavel, Markus Hafner
      Pages 153-173

    5. Profiling the Binding Sites of RNA-Binding Proteins with Nucleotide Resolution Using iCLIP

      • FX Reymond Sutandy, Andrea Hildebrandt, Julian König
      Pages 175-195

    6. A Pipeline for PAR-CLIP Data Analysis

      • Marvin Jens
      Pages 197-207

  5. Non-coding RNAs

    1. Front Matter

      Pages 207-207
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    2. Capture and Identification of miRNA Targets by Biotin Pulldown and RNA-seq

      • Shen Mynn Tan, Judy Lieberman
      Pages 211-228

    3. Identification of miRNA-Target RNA Interactions Using CLASH

      • Aleksandra Helwak, David Tollervey
      Pages 229-251

  6. RNA Modifications

    1. Front Matter

      Pages 253-253
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Keywords

About this book

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.

Editors and Affiliations

  • Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Mattarello, Italy

    Erik Dassi

Bibliographic Information

  • Book Title: Post-Transcriptional Gene Regulation

  • Editors: Erik Dassi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3067-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3066-1Published: 14 October 2015

  • Softcover ISBN: 978-1-4939-4969-4Published: 23 August 2016

  • eBook ISBN: 978-1-4939-3067-8Published: 13 October 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIII, 353

  • Number of Illustrations: 13 b/w illustrations, 30 illustrations in colour

  • Topics: Human Genetics, Gene Function

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