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With our approach, we have discovered that rapid histone deacetylase inhibition disrupts super enhancer function by creating many new aberrant contacts. The code for data analysis is available at https//github.com/GryderArt/AQuA-HiChIP. This protocol reports both experimental and bioinformatic details to perform AQuA-HiChIP, going from cell culture to ranking chromatin interactions within 6 d.An amendment to this paper has been published and can be accessed via a link at the top of the paper.PURPOSE CTNNA1 is a potential diffuse gastric