Fig. 3

Soluble mRNAs show more relative degradation but less detectable co-translational decay than insoluble mRNAs. A Box plot analysis indicating levels of 5′P mRNA decay intermediates compared to total RNA normalized by spike in control RNA in cells before (WT) and after Not1 (not1d), Not4 (not4d), and Not5 (not5d) depletion, in soluble and total RNA pools. Significance of differences is indicated at the top of the box plots—p-values are calculated using a two-sided Welch two-sample t-test. B–E Positions of 5′ ends of decay intermediates were shifted 17nt downstream to simulate the A-site of the adjacent ribosome and create metagene profiles of 5′P mRNA decay intermediates for WT and after Not1, Not4, and Not5 depletion; B and C over the whole CDS for soluble (B) and total (C) RNA pools; D around the start codon for the total (upper panel) or the soluble (lower panel) RNA pools; E before the stop codon in soluble (left) and total (right) RNA pools, with an indication of the percentage of 5′P decay intermediate 5′ ends (no shift) in each of the reading frames over the entire ORFs for the cells before (WT, first row) and after Not1 (not1d, second row), Not4 (not4d, third row), and Not5 (not5d, fourth row) depletion. F Scatterplot representing percentage of 5′P decay intermediate 5′ ends in Frame 1 within the soluble and total RNA pools for the indicated strains. G Scatterplot comparing relative degradation (corrected to WT) in not1d tot and not4d total RNAs. Transcripts with solubility high in not1d and low in not4d are indicated in green, and low in not1d and high in not4d are red, related to Fig. 2C. H Same analysis as Fig. 2D but for relative degradation in wild-type cells