The quantitative impact of 3′UTRs on gene expression [PRO-seq]

Control of gene expression is fundamental to biology, and post transcriptional regulation is an important component of this process. In mammals, the 3′UTR in particular serves as a major source of regulatory information within the transcript. Here, we developed an accurate, high throughput, reporter based system to evaluate the impact of >1,400 full length human 3′UTRs on RNA stability, translational regulation, and total protein output. We used this data to model the relative contributions of RNA stability and translational efficiency towards total 3′UTR mediated regulation, revealing an unexpectedly large role for 3′UTR specified translational control. We observed relationships between GC content and 3′UTR length and different modes of regulation, and identified candidate RNA binding proteins involved in 3′UTR dependent gene expression. We compared regulation from >1,400 3′UTRs under control of two dissimilar promoters, which revealed promoter driven differences in post transcriptional regulation for certain 3′UTRs. Together, this dataset represents a comprehensive characterization of 3′UTR mediated quantitative regulation. Nascent RNA profiling (PRO-seq) of monoclonal landing pad cell lines containing either the PGK or CAG promoter, to measure transcriptome-wide RNA stability (used in combination with RNA-seq performed in parallel)