OGD-induced changes to initiation, elongation and termination. (A) Distribution of sequenced fragments across functional regions of mRNAs under different conditions. (B) Metagene profile of the ribosome density obtained under normal condition and after 1 h of OGD. Positions of footprints 5′ ends are shown relative to the coordinates of the start and stop codons of acORFs, which are set to 0. Over 5,000 mRNA profiles were aggregated to produce the profile. (C) Ribosomal density at Polr2l mRNA. The density in the 3′ UTR indicates leaky termination (readthrough). (D) Sequence logo of the nucleotide context surrounding stop codons in the 19 mRNAs exhibiting high levels of readthrough (top) and the change of stop codon readthrough efficiency during the time course of OGD. (E) Distribution of the Pearson’s correlations of ribosome densities for individual mRNA profiles between replicas and across conditions. (F) An example of mRNA (Mapk3) with changes in footprint density distribution between conditions and replicas.