A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance

The RNA exosome is an RNA degradation machine that is critical for eukaryotic transcriptome surveillance and mutations in exosome components cause numerous human diseases. The exosome is directed to specific RNAs by adaptor protein complexes. However, it remains unclear how these adaptors specifically recognize their target RNAs. The PAXT connection is an adaptor that recruits the exosome to polyadenylated RNAs in the nucleus, especially transcripts polyadenylated at intronic poly(A) sites. Here we show that PAXT-mediated degradation is induced by the combination of a 5' splice site and a poly(A) junction, which includes the poly(A) signal and the poly(A) tail, but not by either sequence alone. These two sequences are bound by the splicing factor U1 snRNP and pre-mRNA 3' processing factors, which in turn cooperatively recruit PAXT. As 5' splice sites and poly(A) junctions are typically found on unspliced precursors and processed RNAs respectively, we propose that their presence on the same RNA molecule constitutes an “RNA degradation code”. Consistent with this model, disease-associated single nucleotide polymorphisms that create novel 5' splice sites near poly(A) sites induce aberrant RNA degradation. Our results revealed the first nuclear RNA degradation code that plays important roles in transcriptome surveillance and may also influence gene evolution. Overall design: Examination of 16 samples by PAS-seq, a type of 3' end mRNA-sequencing. There are 3 biological replicates of control siRNA treatment, 3 biological replicates of EXOSC3 siRNA treatment, 3 biological replicates of scramble shRNA treatment, 2 biological replicates of MTR4 shRNA treatment, 3 biological replicates of ZFC3H1 shRNA treatment, and 2 biological replicates of PABPN1 shRNA treatment. All samples were prepared from HEK293T cells.