A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

Abstract

Summary: Degradation of transcripts in human nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, those adaptors are the nuclear exosome-targeting (NEXT) complex and the poly(A) (pA) exosome-targeting (PAXT) connection. How these adaptors guide exosome targeting remains enigmatic. Employing high-resolution 3′ end sequencing, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA− 3′ ends often covering kilobase-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3′ ends defined by canonical pA site use. Irrespective of this clear division, NEXT and PAXT act redundantly in two ways: (1) regional redundancy, where the majority of exosome-targeted transcription units produce NEXT- and PAXT-sensitive RNA isoforms, and (2) isoform redundancy, where the PAXT connection ensures fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides a two-layered targeting mechanism for efficient nuclear sorting of the human transcriptome. : Wu et al. demonstrate that the nuclear exosome adaptor NEXT targets poly(A)− RNAs with poorly defined 3′ ends, whereas the PAXT connection targets poly(A)+ RNAs derived from canonical poly(A) sites. NEXT substrates become polyadenylated in the absence of NEXT, causing fail-safe RNA decay via PAXT. Keywords: nuclear RNA turnover, NEXT complex, PAXT connection, 3′ end sequencing, pA+/pA− RNA