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
Inhaltsverzeichnis
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.
