ChIP-seq (detect DNA-binding factor occupancy and histone modification profiles) |
Co-factors (EP300, Mediator) |
Assays enhancers mediated by specific co-factors; TFs need not be specified in advance. |
Blow et al., 2010; He et al., 2011; May et al., 2012
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Co-occupancy of multiple TFs |
Reveals specific trans factors but requires specific antibodies for each factor and often each species. Typically requires large numbers of nuclei. |
He et al., 2011, 2014; Luna-Zurita et al., 2016; Akerberg et al., 2019
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Active histone marks (H3K27ac, H3K4me1) |
Robust antibodies that work across metazoans; reveals enhancer states;requires less input than for TFs. |
Wamstad et al., 2012; Nord et al., 2013; He et al., 2014
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Enzyme tethering ChIP alternative (use factor-mediated in-situ genome fragmentation to profile epigenome) |
CUT&RUN (pA-MNase fusion protein) |
Unfixed in-situ procedure, requires lower cell numbers (∼100 for histone modification) and less sequencing reads |
Skene and Henikoff, 2017; Meers et al., 2019
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CUT&Tag (pA-Tn5) |
Similar to CUT&RUN with a simpler barcoding step; streamlined workflow in a single tube; works on low cell numbers or even single cells |
Kaya-Okur et al., 2019; Henikoff et al., 2020
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CUTAC (pA-Tn5, low salt) |
Similar to CUT&Tag with a small modification that detects accessible chromatin in parallel with adjacent histone modifications |
Henikoff et al., 2020 |
Accessible chromatin profiling (detect nucleosome-depleted regions that are enriched for enhancers) |
DNase-seq |
High quality TF footprintscan be generated. |
Thurman et al., 2012; Vierstra et al., 2014, 2020
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ATAC-seq |
Simple and robust method that requires low cell numbers, widely applied; can be used on frozen sections; produces a comprehensive list of where CREs may be located. |
Buenrostro et al., 2013; Corces et al., 2017
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Nascent RNA sequencing run-on assays (depict the real-time activity of RNA polymerases and detect eRNAs) |
GRO-seq |
Detect actively transcribed eRNAs which is a hallmark of active enhancers |
Core et al., 2008 |
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PRO-seq |
Refined version of GRO-seq that uses biotinylated nucleotide to reach nucleotide-resolution, low background, and large dynamic ranges |
Kwak et al., 2013; Core et al., 2014
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ChRO-seq |
Similar to PRO-seq but use chromatin as starting materials; can be applied to solid tissues and samples with degraded RNAs |
Chu et al., 2018 |
Chromosome conformation capture (use proximity ligation and detect enhancer-promoter interaction) |
Hi-C |
Maps genome-wide chromatin contacts (‘all-to-all’); requires substantial sequencing to reveal local enhancer-promoter interactions |
Lieberman-Aiden et al., 2009 |
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Promoter capture Hi-C |
Maps promoter-centric chromatin interactions; requires less reads for detecting promoter-enhancer interactions |
Mifsud et al., 2015; Schoenfelder et al., 2015
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ChIA-PET |
Detect chromatin interactions mediated by a specific DNA-binding factor; can enrich rare factor-specific chromatin interactions |
Fullwood et al., 2009; Grubert et al., 2020
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HiChIP& PLAC-seq (Use in-situ Hi-C followed by ChIP) |
Detects factor-centric chromatin interaction similar to ChIA-PET but require 10-fold to 100-fold fewer cells, also more robust and less time-consuming |
Fang et al., 2016; Mumbach et al., 2016
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4C |
Identifies all genomic regions that interacts a reference locus (‘one-to-all’); can be used for studying specific enhancers |
Simonis et al., 2006 |