Cis-element acquisition converts pervasive transcripts into translated mRNAs

Abstract

Mammalian genomes produce many unstable non-coding transcripts (e.g., PROMPTs and eRNAs) that are rapidly degraded by the nuclear exosome. This study tests whether adding splicing and polyadenylation signals to endogenous non-coding loci can convert them into stable mRNAs. Using CRISPR-Cas9 knock-in in murine cancer cells, the authors show that both signals together render transcripts stable, polyadenylated, exported, and translated into protein. Quantitatively, polyadenylation extends half-life from ~20 minutes to ~12 hours, while splicing primarily drives nuclear export, with export efficiency predicting protein output. Interestingly, untranslated regions of naturally intronless genes can substitute for splicing, mainly by enhancing export. A genome-wide CRISPR screen implicates export, processing, and translation factors such as NXF1, PABPN1, and EIF3G in this conversion. Overall, defined cis-elements suffice to transform pervasive transcripts into functional mRNAs, with nuclear export as the key rate-limiting step. This provides experimental evidence for a potential evolutionary path by which non-coding loci can be co-opted into the coding genome.