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Fig. 1 | Genome Biology

Fig. 1

From: Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

Fig. 1

mRNAs that are less soluble are enriched in non-optimal codons. A Scatterplot comparing RPKMs of mRNAs in soluble (sol) and total (tot) mRNA pools in WT. 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 Distribution of solubility of mRNAs, defined as log2FC soluble/total from DESeq2 in RNA-Seq. C Distribution of relative degradation levels of 5′P mRNA intermediates compared to the RNA abundance (log2FC 5′P-Seq/RNA-Seq from DESeq2 using spike-in) in soluble versus total RNA pools. D Metagene profile dividing each CDS into 20 equal bins and finding the mean normalized reads of 5′P mRNA intermediates in each for soluble and total RNA pools in wild type cells. E Scatterplot comparing differential 5′P-RDOs in total versus soluble RNA pools with the tRNA adaptation index (tAI). The 15 most optimal codons are indicated in blue, and the 15 most non-optimal codons are shown in green. The optimal and non-optimal codon relative RDOs were compared with a one-sided Wilcoxon rank-sum test giving a p-value of 5.627e − 05

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