mRNA Imprinting: transcription apparatus can remotely control cytoplasmic post-transcriptional mechanisms by dozens of proteins

Proper regulation of gene expression requires the harmonious coordination of transcription with other stages of the mRNA lifecycle. We have previously demonstrated that proteins can bind to nascent transcripts co-transcriptionally – a phenomenon named “mRNA imprinting” because the bound proteins modulate subsequent stages of the mRNA lifecycle. Using a novel high-throughput approach, “PRofiling OF Imprinted Transcripts” (“PROFIT”), to identify proteins involved in mRNA imprinting, we uncovered several dozen candidates. The RNA polymerase II (Pol II) subunit Rpb4, which can itself imprint mRNAs, mediates the imprinting of a large subset of these proteins. Imprinting repertoire and profile is responsive to environmental changes and include HSP70 variants. Interestingly, PROFIT identified proteins previously thought to function mainly or exclusively in the cytoplasm, including a translation factors, mRNA decay factor, protein chaperones, substrate-delivering factors of the proteasome, targeting factors that deliver mRNAs to mitochondria and more. Using proximity labeling, we validated several hits, including two translation initiation factors: eIF4G and the eIF3 component Rpg1. Importantly, we found that the same Rpg1 molecule, which had been transiently localized near Pol II, co-sediments with polyribosomes - similar to the bulk Rpg1. Our results suggest that the transcription machinery can regulate translation by recruiting specific translation factors, which later participate in protein synthesis. mRNA imprinting appears to be a widespread phenomenon, and we speculate that it may not be limited to the transcription stage alone. Interestingly, the PROFIT experiments identified proteins with known cytoplasmic function, including a translation factor (Rpg1), mRNA decay factor (Xrn1), protein chaperones (Ssa1/2), substrate-delivering factors of the proteasome, targeting factors that deliver mRNAs to mitochondria, and actin-binding factors.