RNA secondary structome of different cellular compartments in human and mouse

We resolved the RNA secondary structure of three cellular compartments including chromatin (ch), nucleoplasm(np) and cytoplasm(cy) in HEK293 and mES cells based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyze the RNA structure dynamics among cellular compartments and different RNA processings. Also, we study which factors perturb the RNA structures. Subcellular fractionation for HEK293 cells and mES cells was performed and tested by western and RT-qPCR. libraries of subcellular fractions were constructed as the icSHAPE protocol. The RNA structure in vivo and in vitro was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) and in vitro NAI-N3 treatment samples (T). irCLIP was constructed in Mettl3 WT and KO mES cells. Anti-Lin28A and anti-GFP (control) antibody was used in the two condition (Mettl3 WT and KO).