Chromatin Interaction Analysis by Paired-End Tag Sequencing ChIA-PET features an immunoprecipitation step to map long-range DNA interactions, similar to Hi-C (Li et al., 2010) (Fullwood et al., 2009). In this method, DNA-protein complexes are crosslinked and fragmented. Specific antibodies are used to immunoprecipitate proteins of […]
Identify Sites Bound by Small Chemical Molecules Chem-seq can be used to detect the binding of small-molecule ligands, such as therapeutic drugs, to proteins associated with the genome. This information may provide important insights into the perturbation of cellular function by small-molecule drugs (Anders et […]
Covalent Attachment of Tags to Capture Histones and Identify Turnover CATCH-IT is a direct method for measuring nucleosome turnover dynamics genome-wide (Deal et al., 2010). In this method, cells are treated briefly with the methionine surrogate azidohomoalanine (Aha), which couples biotin to nucleosomes containing newly […]
Chromatin Conformation Capture Carbon Copy 5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA […]
Chromatin Conformation Capture Carbon Copy 5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA […]
Chromatin Conformation Capture Carbon Copy 5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA […]
Chromatin Conformation Capture Carbon Copy 5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA […]
Assay for Transposase-Accessible Chromatin Sequencing / ATAC-seq Optimized for Blood Cells ATAC-Seq uses the Tn5 transposome to detect nucleosome-free regions of the genome (Buenrostro et al., 2013). The method is commonly used, and optimized protocols are available for tissues, such as blood (Fast-ATAC) (Corces et […]
Chromatin Conformation Capture Carbon Copy 5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA […]
Circular Chromatin Conformation Capture 4C (Zhao et al., 2006), (Simonis et al., 2006), also called 4C-seq, is a method similar to 3C and is sometimes called circular 3C. It allows the unbiased detection of all genomic regions that interact with a particular region of interest […]
