Fig. 2

Not1 and Not4 inversely regulate mRNA solubilities. A Scatterplot comparing RPKMs of mRNAs in soluble (sol) and total (tot) mRNA pools before and after Not1 (not1d), Not4 (not4d), and Not5 (not5d) depletion (from left to right) in soluble and total mRNA pools. mRNAs significantly less soluble after depletion are indicated in black and more soluble in purple (cutoffs from DESeq2 RNA-Seq sol/tot—high solubility: [log2FC > 0, FDR < 0.05] OR [log2FC > 1, p-value < 0.05]; low solubility: [log2FC < 0, FDR < 0.05] OR [log2FC <  − 1, p-value < 0.05]). B Box plot analysis indicating mRNA solubilities in cells before (WT) or after Not1, Not4, and Not5 depletion. C Scatterplot comparing changes in mRNA solubilities before and after Not1 and Not4 depletion. D–G Box plot analysis comparing features of mRNAs falling into the four categories defined by changes in mRNA solubilities upon Not1 and Not4 depletion color coded in panel C with regard to D content in non-optimal codons, E abundance (RPF RPKMs), F length, and G solubility in wild-type cells. Number of mRNAs in box plots, left to right: 823, 637, 522, and 1040. 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