Enhancers and Promoters: Methods and Protocols

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

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

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

Dominic van Essen, Agata Oruba, and Simona Saccani

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

Inês Cebola

Part VII- DNA methylation

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

Priscillia Lhoumaud and Jane Skok

Anna Krepelova and Francesco Neri