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…mehr
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
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.
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.
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