Nuclear RNA cap-chaperones eIF4E and NCBP2 elicit distinct fates for 1000s of RNAs uncovering an unexpected regulatory point in gene expressioncells

Nuclear mRNA processing occurs in a stepwise manner to generate the protein blueprints required for cellular function. The addition of the methyl-7-guanosine (m7G) cap on the 5’end of mRNAs is conserved in humans, plants and fungi. The m7G cap recruits the nuclear cap-binding protein NCBP2 co-/peri-transcriptionally where it mediates interactions between capped-RNAs and the processing machinery. Convention posits that NCBP2 is the sole cap-binding protein in the nucleus positioning cap-chaperoning as an important constitutive, housekeeping function. However, the eukaryotic translation initiation factor eIF4E is also found in the nucleus across Kingdoms. Both eIF4E and NCBP2 employ highly similar structural strategies to directly bind the m7G cap. The presence of two cap-binding factors in the nucleus could arise to provide redundancy to ensure gene expression security or it could provide the basis for tandem regulation of selected subsets of capped-mRNAs driving distinct gene expression programmes. To dissect these possibilities, we compared the spatial localizations, interactomes and impacts on gene expression of eIF4E and NCBP2. We found that like NCBP2, eIF4E physically and spatially associated with active sites of transcription and splicing machinery. However, contrary to expectations, eIF4E and NCBP2 drove distinct transcription and splicing signatures impacting ~1000 transcripts which in turn elicit different biological programmes. RNAs segregated with specific cap-binding proteins with only an overlap of only ~130 transcripts between eIF4E and NCBP2. Clearly, the cap-interaction was not sufficient to elicit sensitivity to these cap-binding proteins given the absence of generalized impacts on the transcriptome. We uncovered the molecular mechanism for cap-chaperone selectivity which lay in differences in conserved sequences motifs within introns of selected mRNAs, their mainly distinct spatial localizations, and differences in the capacity to alter splice factor production. Relevant to the 130 common targets, a fraction of eIF4E and NCBP2 did interact and spatially overlap. Despite their common m7G cap-binding activity, eIF4E and NCBP2 elicit substantively different impacts on gene expression. In contrast to the conventional paradigm, our data support a model whereby cap-chaperones direct processing of distinct subsets of mRNAs thereby eliciting diverse biological programmes. Differential programming by cap-chaperones reveals an unexpected regulatory point in gene expression..