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Fig. 4 | Genome Biology

Fig. 4

From: Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization

Fig. 4

mRNA features that distinguish the role of the Ccr4-Not complex in the regulation of mRNA translation v stability. A Data shows the log2FC in mRNA half-life after CNOT1 depletion (x-axis) compared to the log2FC translational efficiency (y-axis). mRNAs are first classified based on their mRNA stability change—a low log2FC mRNA half-life (dark colors) or a high log2FC mRNA half-life (light colors) and second by their TE change—increased TE (red), no TE change (yellow), or decreased TE (blue). B Pulsed SILAC data for three biological repeats conducted with forward and reverse labelling (Additional File 1: Fig. S8A-C). Displayed is the protein production change (siCNOT1/siControl) for the proteins that were detected in at least two biological repeats for the groups of mRNAs classified in (A). Non-significant comparisons are indicated, and all statistical comparisons are shown in Additional File 9: Fig. S1A. C The influence of mRNA sequence features on the classification of mRNAs into groups based how the Ccr4-Not complex differentially regulates their stability and/or translation (Fig. 4A) was determined by gradient boosting. D–F The presence of the top three features identified in (D) in the differentially regulated groups of mRNAs. D CDS length, E CDS G/C nucleotide content, and F CDS A/G nucleotide content. For clarity, non-significant comparisons are indicated, and all statistical comparisons are shown in Additional File 9: Fig. S1BCD

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