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Enhancer RNAs

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Ulf Andersson Ørom

    1. Max Planck Institute Molecular Genetics, Berlin, Germany

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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 1468)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Cellular Fractionation and Isolation of Chromatin-Associated RNA

    • Thomas Conrad, Ulf Andersson Ørom
    Pages 1-9

  3. Knockdown of Nuclear-Located Enhancer RNAs and Long ncRNAs Using Locked Nucleic Acid GapmeRs

    • Benoit T. Roux, Mark A. Lindsay, James A. Heward
    Pages 11-18

  4. Visualization of Enhancer-Derived Noncoding RNA

    • Youtaro Shibayama, Stephanie Fanucchi, Musa M. Mhlanga
    Pages 19-32

  5. UV-RNA Immunoprecipitation (UV-RIP) Protocol in Neurons

    • Katie Schaukowitch, Jae-Yeol Joo, Tae-Kyung Kim
    Pages 33-38

  6. Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART)

    • Keith W. Vance
    Pages 39-50

  7. Detecting Long-Range Enhancer–Promoter Interactions by Quantitative Chromosome Conformation Capture

    • Wulan Deng, Gerd A. Blobel
    Pages 51-62

  8. Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET)

    • Jocelyn Choy, Melissa J. Fullwood
    Pages 63-89

  9. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing

    • Steven Blinka, Michael H. Reimer Jr., Kirthi Pulakanti, Luca Pinello, Guo-Cheng Yuan, Sridhar Rao
    Pages 91-109

  10. Global Run-On Sequencing (GRO-Seq)

    • Alessandro Gardini
    Pages 111-120

  11. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers

    • Anusha Nagari, Shino Murakami, Venkat S. Malladi, W. Lee Kraus
    Pages 121-138

  12. Evaluating the Stability of mRNAs and Noncoding RNAs

    • Ana Carolina Ayupe, Eduardo M. Reis
    Pages 139-153

  13. A Novel Method to Quantify RNA–Protein Interactions In Situ Using FMTRIP and Proximity Ligation

    • C. Zurla, J. Jung, E. L. Blanchard, P. J. Santangelo
    Pages 155-170

  14. In Silico Promoter Recognition from deepCAGE Data

    • Xinyi Yang, Annalisa Marsico
    Pages 171-199

  15. Bioinformatics Pipeline for Transcriptome Sequencing Analysis

    • Sarah Djebali, Valentin Wucher, Sylvain Foissac, Christophe Hitte, Erwan Corre, Thomas Derrien
    Pages 201-219

  16. CRISPR/Cas9 Genome Editing in Embryonic Stem Cells

    • Guillaume Andrey, Malte Spielmann
    Pages 221-234

  17. Targeted Gene Activation Using RNA-Guided Nucleases

    • Alexander Brown, Wendy S. Woods, Pablo Perez-Pinera
    Pages 235-250

  18. Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis

    • Sarah Djebali, Valentin Wucher, Sylvain Foissac, Christophe Hitte, Erwan Corre, Thomas Derrien
    Pages E1-E1

  19. Back Matter

    Pages 251-252
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Keywords

About this book

This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long ncRNAs and exploring transcription by assessing where transcription starts and generally how it occurs.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, Enhancer RNAs: Methods and Protocols aims to ensure successful results in this rapidly developing field.

Editors and Affiliations

  • Max Planck Institute Molecular Genetics, Berlin, Germany

    Ulf Andersson Ørom

Bibliographic Information

  • Book Title: Enhancer RNAs

  • Book Subtitle: Methods and Protocols

  • Editors: Ulf Andersson Ørom

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-4035-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2017

  • Hardcover ISBN: 978-1-4939-4033-2Published: 23 September 2016

  • Softcover ISBN: 978-1-4939-8160-1Published: 08 June 2018

  • eBook ISBN: 978-1-4939-4035-6Published: 23 September 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 252

  • Number of Illustrations: 8 b/w illustrations, 43 illustrations in colour

  • Topics: Human Genetics

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