KARR-seq reveals principles of high-order ribonucleoprotein structure assembly

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.