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Promoter Associated RNA

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Sara Napoli

    1. Experimental Therapeutics Group, Institute of Oncology Research, Bellinzona, Switzerland

    View editor publications

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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
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1543)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Identification of Promoter-Associated RNAs

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. ChIP-seq for the Identification of Functional Elements in the Human Genome

      • Georgi K. Marinov
      Pages 3-18

    3. Identification of Candidate Functional Elements in the Genome from ChIP-seq Data

      • Georgi K. Marinov
      Pages 19-43

    4. GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression

      • Rui Lopes, Reuven Agami, Gozde Korkmaz
      Pages 45-55

    5. NanoCAGE: A Method for the Analysis of Coding and Noncoding 5′-Capped Transcriptomes

      • Stéphane Poulain, Sachi Kato, Ophélie Arnaud, Jean-Étienne Morlighem, Makoto Suzuki, Charles Plessy et al.
      Pages 57-109

    6. Deep Cap Analysis of Gene Expression (CAGE): Genome-Wide Identification of Promoters, Quantification of Their Activity, and Transcriptional Network Inference

      • Alexandre Fort, Richard J. Fish
      Pages 111-126

  3. Characterization of Promoter-Associated RNA Features

    1. Front Matter

      Pages 127-127
      Download chapter PDF

    2. Deep-RACE: Comprehensive Search for Novel ncRNAs Associated to a Specific Locus

      • Chiara Pastori, Dmitry Velmeshev, Veronica Julia Peschansky
      Pages 129-143

    3. In Silico Prediction of RNA Secondary Structure

      • Fariza Tahi, Van Du T. Tran, Anouar Boucheham
      Pages 145-168

    4. Computational Prediction of RNA-Protein Interactions

      • Carla M. Mann, Usha K. Muppirala, Drena Dobbs
      Pages 169-185

    5. Isolation of Nuclear RNA-Associated Protein Complexes

      • Ranveer Singh Jayani, Amanjot Singh, Dimple Notani
      Pages 187-193

  4. Functional Studies of Promoter-Associated RNAs

    1. Front Matter

      Pages 195-195
      Download chapter PDF

    2. Identification of Long Noncoding RNAs Associated to Human Disease Susceptibility

      • Marco Magistri, Dmitry Velmeshev
      Pages 197-208

    3. Targeting Promoter-Associated RNAs by siRNAs

      • Sara Napoli
      Pages 209-219

    4. RNA-FISH to Study Regulatory RNA at the Site of Transcription

      • Marta Soler, Raquel Boque-Sastre, Sonia Guil
      Pages 221-229

    5. Detection and Characterization of R Loop Structures

      • Raquel Boque-Sastre, Marta Soler, Sonia Guil
      Pages 231-242

  5. Therapeutic Potential of Promoter-Associated RNAs Targeting

    1. Front Matter

      Pages 243-243
      Download chapter PDF

    2. Induction of Transcriptional Gene Silencing by Expression of shRNA Directed to c-Myc P2 Promoter in Hepatocellular Carcinoma by Tissue-Specific Virosomal Delivery

      • Mohammad Khalid Zakaria, Debi P. Sarkar, Parthaprasad Chattopadhyay
      Pages 245-257

    3. Targeting Promoter-Associated Noncoding RNA In Vivo

      • Gianluca Civenni
      Pages 259-270
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Keywords

About this book

This volume is divided in four sections; covering genome wide approaches, techniques for characterize of paRNA structural features are described, selecting pa-RNA, and paRNA therapeutic potential. Chapters describe how siRNAsdirected against paRNAs can be applied in vivo to modulate transcription of important genes controlled by paRNAs. 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 tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Promoter Associated RNA: Methods and Protocols aims to demonstrate paRNAs as new class of regulatory molecules, to further investigate and value as tools for fine transcriptional tuning.


Editors and Affiliations

  • Experimental Therapeutics Group, Institute of Oncology Research, Bellinzona, Switzerland

    Sara Napoli

Bibliographic Information

  • Book Title: Promoter Associated RNA

  • Book Subtitle: Methods and Protocols

  • Editors: Sara Napoli

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6716-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-6714-8Published: 28 March 2017

  • Softcover ISBN: 978-1-4939-8281-3Published: 09 June 2018

  • eBook ISBN: 978-1-4939-6716-2Published: 27 March 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 287

  • Number of Illustrations: 101 b/w illustrations, 182 illustrations in colour

  • Topics: Human Genetics

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