The molecular determinants of PABPC-mediated deadenylation rate

Deadenylation, the enzymatic shortening of the poly(A) tail, is typically the first committed step of mRNA decay. Deadenylation rates span nearly a 1000-fold range between transcripts and are governed by protein-RNA interactions, including those involving cytoplasmic poly(A)-binding protein (PABPC). Previous work shows that PABPC can straddle the junction between the poly(A) tail and the 3' untranslated region (UTR), but whether this conformation influences deadenylation has not been tested. To investigate how straddling influences deadenylation kinetics, we designed a library of tailed RNA substrates and measured both in vitro deadenylation rates in the presence of PABPC and PABPC binding propensity for each substrate. We found that 3' UTR sequences influence deadenylation through two mechanisms. First, structured UTRs are deadenylated more slowly in the absence of PABPC1, an effect that is alleviated by PABPC1. Second, sequences upstream of the poly(A) tail modulate PABPC1 binding propensity, with tighter binding correlating with slower deadenylation. This relationship is abolished with a PABPC1 mutant lacking UTR-binding capacity. Together, these results show that sequences upstream of the poly(A) tail tune PABPC1 binding and deadenylation rates, likely contributing to the range of deadenylation rates observed for cellular mRNAs.