Comparative SHAPE-MaP data on endogenous TP53 mRNA 5-prime regulatory region

The secondary structure of the TP53 mRNA 5' end has been reported to regulate translation initiation. This region has been shown to include regulatory motifs. We use the SHAPE reagent 5 nitroisatoic anhydride (5NIA) to probe the secondary structure under cell-free conditions to construct a secondary structure model under extracted, gently deproteinated conditions for TP53 transcript variant 1 (NM_000546.6) from human A549 lung carcinoma cell line. We compare the cell-free SHAPE profile with the targeted region (25-475) with RNA extracted after in-cell chemical probing with 5NIA. We also collect SHAPE-MaP data from live cells subjected to chemical stress treatments known to induce TP53 expression namely 15 uM etoposide (DNA damage), 100 mM cobalt chloride (hypoxia), and 50 uM 4EGI-1 (inhibition of cap-dependent translation).