How is polyadenylation restricted to 3′-untranslated regions?

Polyadenylation occurs at numerous sites within 3 '-untranslated regions (3 '-UTRs) but rarely within coding regions. How does Pol II travel through long coding regions without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3 '-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3 '-UTRs, but it is unknown how its recruitment is restricted to 3 '- UTRs during Pol II elongation. Unlike coding regions, 3 '-UTRs have long AT-rich stretches of DNA that may be important for restricting polyadenylation to 3 '-UTRs. Recognition of the 3 '-UTR could occur at the DNA (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA-and/or rA:dT-rich) level. Based on the nucleic acid critical for 3 '-UTR recognition, there are three classes of models, not mutually exclusive, for how the CpA machinery is selectively recruited to 3 '-UTRs, thereby restricting where polyadenylation occurs: (1) RNA-based models suggest that the CpA complex directly (or indirectly through one or more intermediary proteins) binds long AU-rich stretches that are exposed after Pol II passes through these regions. (2) DNA-based models suggest that the AT-rich sequence affects nucleosome depletion or the elongating Pol II machinery, resulting in dissociation of some elongation factors and subsequent recruitment of the CpA machinery. (3) RNA:DNA hybrid models suggest that preferential destabilization of the Pol II elongation complex at rU:dA-and/or rA:dT-rich duplexes bridging the nucleotide addition and RNA exit sites permits preferential association of the CpA machinery with 3 '-UTRs. Experiments to provide evidence for one or more of these models are suggested.

Automated summary

Polyadenylation commonly occurs in 3'-untranslated regions (UTRs) but rarely in coding regions. The recruitment of a complex called CpA to the 3'-UTRs restricts polyadenylation to these regions during Pol II elongation. Three models propose different mechanisms for the selective recruitment of CpA to the 3'-UTRs based on RNA, DNA, or RNA:DNA hybrid recognition. Experimental evidence is suggested to support these models.