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Enhancers and Promoters

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Tilman Borggrefe

    1. Institute of Biochemistry, University of Giessen, Gießen, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Benedetto Daniele Giaimo

    1. Institute of Biochemistry, University of Giessen, Gießen, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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 2351)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Introduction

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. A Comprehensive Toolbox to Analyze Enhancer–Promoter Functions

      • Benedetto Daniele Giaimo, Tobias Friedrich, Tilman Borggrefe
      Pages 3-22

  3. Enhancer-Promoter Transcripts

    1. Front Matter

      Pages 23-23
      Download chapter PDF

    2. Global Run-on Sequencing (GRO-Seq)

      • Petros Tzerpos, Bence Daniel, Laszlo Nagy
      Pages 25-39

    3. Illuminating Enhancer Transcription at Nucleotide Resolution with Native Elongating Transcript Sequencing (NET-Seq)

      • Olga Jasnovidova, Mirjam Arnold, Andreas Mayer
      Pages 41-65

    4. Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters

      • Hazuki Takahashi, Hiromi Nishiyori-Sueki, Jordan A. Ramilowski, Masayoshi Itoh, Piero Carninci
      Pages 67-90Open Access

  4. Nucleosome Occupancy and DNA Accessibility

    1. Front Matter

      Pages 91-91
      Download chapter PDF

    2. Analyses of Promoter , Enhancer, and Nucleosome Organization in Mammalian Cells by MNase-Seq

      • Cyril Esnault, Talha Magat, Encar García-Oliver, Jean-Christophe Andrau
      Pages 93-104

    3. Measuring Chromatin Accessibility: ATAC-Seq

      • Sanjeeb Kumar Sahu, Amitava Basu, Vijay K. Tiwari
      Pages 105-121

    4. High-Resolution ChIP-MNase Mapping of Nucleosome Positions at Selected Genomic Loci and Alleles

      • Dominic van Essen, Agata Oruba, Simona Saccani
      Pages 123-145

    5. Sequential Chromatin Immunoprecipitation to Identify Heterotypic Nucleosomes

      • Maxim Nekrasov, David J. Tremethick
      Pages 147-161

  5. Chromatin Interactions

    1. Front Matter

      Pages 163-163
      Download chapter PDF

    2. Low Input Targeted Chromatin Capture (Low-T2C)

      • Ilias Boltsis, Karol Nowosad, Rutger W. W. Brouwer, Przemko Tylzanowski, Wilfred F. J. van IJcken, Danny Huylebroeck et al.
      Pages 165-179

    3. Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq)

      • Miao Yu, Ivan Juric, Armen Abnousi, Ming Hu, Bing Ren
      Pages 181-199

    4. Analysis of Enhancer–Promoter Interactions using CAGE and RADICL-Seq Technologies

      • Alessandro Bonetti, Andrew Tae-Jun Kwon, Erik Arner, Piero Carninci
      Pages 201-210Open Access

    5. Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions

      • Lumeng Jia, Cheng Li, Tingting Li
      Pages 211-227

    6. Assessment of 3D Interactions Between Promoters and Distal Regulatory Elements with Promoter Capture Hi-C (PCHi-C)

      • Nezih Karasu, Tom Sexton
      Pages 229-248
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Keywords

About this book

This volume contains cutting-edge techniques to study the function of enhancers and promoters in depth. Chapters are divided into six sections and describe enhancer-promoter transcripts, nucleosome occupancy, DNA accessibility, chromatin interactions, protein-DNA interactions, functional analyses, and DNA methylation assays. Written in the Methods in Molecular Biology series format, chapters include comprehensive introductions, lists of the necessary materials and reagents, step-by-step laboratory protocols, and useful suggestions for troubleshooting.

Authoritative and cutting-edge, Enhancers and Promoters: Methods and Protocols is a useful guide for future experiments.

Chapters 4 and 11 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com

Editors and Affiliations

  • Institute of Biochemistry, University of Giessen, Gießen, Germany

    Tilman Borggrefe, Benedetto Daniele Giaimo

Bibliographic Information

  • Book Title: Enhancers and Promoters

  • Book Subtitle: Methods and Protocols

  • Editors: Tilman Borggrefe, Benedetto Daniele Giaimo

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1597-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1596-6Published: 13 August 2021

  • Softcover ISBN: 978-1-0716-1599-7Published: 14 August 2022

  • eBook ISBN: 978-1-0716-1597-3Published: 11 August 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 376

  • Number of Illustrations: 12 b/w illustrations, 57 illustrations in colour

  • Topics: Genetics and Genomics, Human Genetics

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