A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X.

The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled. Synopsis: Monitoring the dynamics of mRNA changes after DDX3X depletion indicates translation suppression followed by mRNA stabilization. GC content in the CDS is a strong predictor of mRNA stabilization and it is detectable in multiple transcriptomics datasets, with a potential link to cell-cycle regulation. RNA-seq and Ribo-seq on a time course of DDX3X depletion show regulation of translation and mRNA levels. Intron-exon count modeling and SLAM-seq demonstrate post-transcriptional mRNA stabilization. Random Forest and Lasso show GC content in the CDS (GCcds) as a main predictor of mRNA stabilization. ENCODE RBP knockdowns and in vivo datasets show widespread GCcds-dependent mRNA stabilization. Monitoring the dynamics of mRNA changes after DDX3X depletion indicates translation suppression followed by mRNA stabilization. GC content in the CDS is a strong predictor of mRNA stabilization and it is detectable in multiple transcriptomics datasets, with a potential link to cell-cycle regulation. [ABSTRACT FROM AUTHOR]