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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
List of contents
A New Toolbox to Analyze Enhancer-Promoter Functions.- Global Run-on Sequencing (GRO-Seq).- Illuminating Enhancer Transcription at Nucleotide Resolution with Native Elongating Transcript Sequencing (NET-Seq).- Low Quantity single strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters.- Analyses of Promoter, Enhancer and Nucleosome Organisation in Mammalian Cells by MNase-Seq.- Measuring Chromatin Accessibility: ATAC-Seq.- High-resolution ChIP-MNase Mapping of Nucleosome Positions at Selected Genomic Loci And Alleles.- Sequential Chromatin Immunoprecipitation to Identify Heterotypic Nucleosomes.- Low Input Targeted Chromatin Capture (low-T2C).- Proximity Ligation-assisted ChIP-Seq (PLAC-Seq).- Analysis of Enhancer-promoter Interactions using CAGE and RADICL-Seq technologies.- Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to identify open chromatin interactions.- Assessment of 3D Interactions Between Promoters and Distal Regulatory Elements with Promoter Capture Hi-C (PCHi-C).- Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-Translational Modification (PTM) Combinatorics At Distinct Genomic Regions.- Using ChIP-SICAP to Identify Proteins That Co-Localize in Chromatin.- Genome-wide profiling of protein-DNA Interactions with Chromatin Endogenous Cleavage And High-Throughput Sequencing (ChEC-Seq).- Transcriptional Activation Of Heterochromatin by Recruitment of dCas9 Activators.- Deletion of Regulatory Elements with All-in-One CRISPR-Cas9 Vectors.- Simultaneous Tagmentation-based detection of ChIP/ATAC Signal with Bisulfite Sequencing.- Low Input Whole-Genome Bisulfite Sequencing.
