We designed KARR-seq, which reveals RNA-RNA interactions transcriptome-wide. The frequency of KARR-seq chimeras accurately reveals the physical distances between RNAs in vivo. Using KARR-seq, we systematically analyzed celullar effect on RNA-RNA interactions.
Overall design
KARR-seq were performed in difference cell lines under normal or treatment conditions. Treatments include knocking down selective RBPs, adding tranlation inhibitors, adding arsenite stress, etc. KARR-seq for in vitro refolded RNA and intact nuclei were also perfromed.
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