SHAPE-MaP probing of RNA structures in E. coli cells

E. coli total RNA was subjected to modification with SHAPE reagent (1M7) or mock treatment under three experimental conditions: in living cells, in cells with kasugamycin treatment, and in protein-free RNA extracts. After modification, ribosomal RNAs were depleted using Epicentre Ribo-zero kits. SHAPE adduct locations were converted into sequencing libraries using random primers and mutational profiling (MaP), which exploits error-prone reverse transcription.