Enhancers and Promoters Methods and Protocols

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.

Part I – Introduction

1.     A New Toolbox to Analyze Enhancer-Promoter Functions

Benedetto Daniele Giaimo, Tobias Friedrich, and Tilman Borggrefe

Part II – Enhancer-Promoter transcripts

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

Petros Tzerpos, Bence Daniel, and Laszlo Nagy

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

Olga Jasnovidova, Mirjam Arnold, and Andreas Mayer

4.     Low Quantity single strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters

Hazuki Takahashi, Hiromi Nishiyori-Sueki, Jordan A. Ramilowski, Masayoshi Itoh, andPiero Carninci

Part III – Nucleosome Occupancy and DNA Accessibility

5.     Analyses of Promoter, Enhancer and Nucleosome Organisation in Mammalian Cells by MNase-Seq

Cyril Esnault, Talha Magat, Encar García-Oliver, and Jean-Christophe Andrau

6.     Measuring Chromatin Accessibility: ATAC-Seq

Sanjeeb Kumar Sahu, Amitava Basu, and Vijay K. Tiwari

7.     High-resolution ChIP-MNase Mapping of Nucleosome Positions at Selected Genomic Loci And Alleles

Dominic van Essen, Agata Oruba, and Simona Saccani

8.     Sequential Chromatin Immunoprecipitation to Identify Heterotypic Nucleosomes

Maxim Nekrasov and David J. Tremethick

Part IV – Chromatin Interactions

9.     Low Input Targeted Chromatin Capture (low-T2C)

Ilias Boltsis, Karol Nowosad, Rutger W. W. Brouwer, Przemko Tylzanowski, Wilfred F.J. van IJcken, Danny Huylebroeck, Frank Grosveld, and Petros Kolovos

10.  Proximity Ligation-assisted ChIP-Seq (PLAC-Seq)

Miao Yu, Ivan Juric, Armen Abnousi, Ming Hu, and Bing Ren

11.  Analysis of Enhancer-promoter Interactions using CAGE and RADICL-Seq technologies

Alessandro Bonetti, Andrew Tae-Jun Kwon, Erik Arner, and Piero Carninci

12.  Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to identify open chromatin interactions

Lumeng Jia, Cheng Li, and Tingting Li

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

Nezih Karasu and Tom Sexton

Part V – Protein-DNA Interactions

14.  Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-Translational Modification (PTM) Combinatorics At Distinct Genomic Regions

Luciano Nicosia and Tiziana Bonaldi

15.  Using ChIP-SICAP to Identify Proteins That Co-Localize in Chromatin

Mahmoud-Reza Rafiee and Jeroen Krijgsveld

16.  Genome-wide profiling of protein-DNA Interactions with Chromatin Endogenous Cleavage And High-Throughput Sequencing (ChEC-Seq)

Moustafa M. Saleh, Jason P. Tourigny, and Gabriel E. Zentner

Part VI – Functional analysis

17.  Transcriptional Activation Of Heterochromatin by Recruitment of dCas9 Activators

Lukas Frank, Robin Weinmann, Fabian Erdel, Jorge Trojanowski, and Karsten Rippe

18.  Deletion of Regulatory Elements with All-in-One CRISPR-Cas9 Vectors

Inês Cebola

Part VII– DNA methylation

19.  Simultaneous Tagmentation-based detection of ChIP/ATAC Signal with Bisulfite Sequencing

Priscillia Lhoumaud and Jane Skok

20.  Low Input Whole-Genome Bisulfite Sequencing

Anna Krepelova and Francesco Neri