U1 snRNA rewrites the "script"

Abstract

Expression of eukaryotic mRNAs requires the collaboration of a host of RNA processing factors acting upon the transcript. Berg et al. describe how a pre-mRNA splicing factor modulates the activity of the polyadenylation machinery to regulate mRNA length, with important implications for isoform expression in activated neuronal and immune cells.

Figure 1. U1 Levels Determine the Use of Premature Cleavage and Polyadenylation Sites

(A) At wild-type levels of U1, U1 snRNA base pairing at the 5′ss inhibits the use of proximal PASs, leading to generation of a full-length transcript polyadenylated at the 3′ end. Potential cleavage sites far downstream of the 5′ss are also inhibited by the activity of U1, presumably via 5′ss-independent interactions (or perhaps by recognition of cryptic 5′ss signals). (B) When U1 snRNA is depleted experimentally, as with AMO, it is not available to splice pre-mRNAs or to inhibit the use of PASs in the first intron, and as a consequence, short cleaved and polyadenylated RNAs are generated through PCPA. (C) When U1 snRNA is decreased experimentally (by titrating AMO levels), the 3′ end of the RNA becomes shorter due to a decrease in U1-mediated protection from PCPA. A greater decrease in U1 snRNA levels leads to usage of cryptic PASs closer to the 5′ end of the RNA. (D) 3′ UTR shortening and 3′ exon switching have been observed in activated neuronal and immune cells to produce shortened transcripts similar to the observed effects of decreasing U1 levels. Rapid and transient transcriptional upregulation of pre-mRNAs creates a shortage of U1 snRNA relative to the amount of nascent pre-mRNA, leading to the production of short isoforms under activated conditions (For example, homer-1 long is produced in unactivated neuronal cells, whereas homer-1 short predominates in activated cells). It is unclear whether other, perhaps unstable, isoforms are also produced. For each panel, RNA polymerase II is shown synthesizing PAS-containing pre-mRNA from a chromatin template. The pre-mRNA is shown with exons (colored boxes), introns, the 5′ cap (red ball), and multiple PAS sequences. The purple ovals represent components of the polyadenylation machinery that associate with the C-terminal domain (CTD) of RNA polymerase II. The U1 snRNA is depicted in association with spliceosomal proteins (light blue ovals).