Competition between maturation and degradation drives human snRNA 3′ end quality control

Abstract

Polymerases and exonucleases act on 3 ′ ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood.Here, we identify a central role for the human DEDD deadenylase TOE1 in distinguishing the fates of small nuclear (sn)RNAs of the spliceosome from unstable genome-encoded snRNA variants. We found that TOE1 promotes maturation of all regular RNA polymerase II transcribed snRNAs of the major and minor spliceosomes by removing posttranscriptional oligo(A) tails, trimming 3 ′ ends, and preventing nuclear exosome targeting. In contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3 ′ end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of noncoding RNAs processed by DEDD deadenylases.

Integrator-Dependent and Allosteric/Intrinsic Mechanisms Ensure Efficient Termination of snRNA Transcription

“…As primers span the Integrator cleavage sites, this suggests that DIS3 targets transcripts that escape maturation rather than competing with processing. This idea is supported by recent findings that mature snRNA accumulation is unaffected by exosome depletion (Lardelli and Lykke-Andersen, 2020). Following INTS1 depletion, a substantial fraction of precursors are lost after actD treatment either because of residual Integrator activity or degradation of the resulting unprocessed products.…”

ISG20 and nuclear exosome promote destabilization of nascent transcripts for spliceosomal U snRNAs and U1 variants

“…RNA was prepared from HeLa cells in which ISG20, EXO10, or TOE1 (positive control) was knocked down (Figure 4a), and the 3′‐end of U1 snRNA was analyzed by Next‐Generation Sequencing (NGS) analyses. The results in Figure 4b,c clearly showed that the 3′‐end of U1 snRNA was not extended in ISG20‐ or EXO10‐KD cells, whereas a clear extension was detected in TOE1‐KD cells (positive control) (Lardelli & Andersen, 2020; Lardelli et al., 2017; Son et al., 2018). Even the ISG20‐ and EXO10‐ double KD cells did not show the 3′‐end extension of U1 snRNA (Figure S3c,d).…”

“…During the preparation of this manuscript, a paper was published showing that the nuclear exosome cooperates with TOE1 and degrades 3′‐unprocessed U snRNAs and U1 variants (Lardelli & Andersen, 2020). Our conclusion with the nuclear exosome was supported by their data (Lardelli & Andersen, 2020). However, our results also called attention to ISG20, a novel factor controlling the stability of the nascent transcript for U snRNAs and U1 variants.…”

“…Recent studies revealed that the DEDD family deadenylase TOE1 is the enzyme critical for snRNA 3′ end trimming in human cells (Lardelli et al., 2017; Wagner et al., 2007). The immature 3′‐end of U snRNAs are first adenylated, and the adenylated tails are subsequently trimmed to the mature end by TOE1 (Lardelli & Andersen, 2020; Lardelli et al., 2017; Son et al., 2018). TOE1 is mainly localized in the nucleus and concentrated in the Cajal bodies (Son et al., 2018; Wagner et al., 2007), suggesting that the final 3′‐end maturation may occur in the nucleus, although classical Xenopus oocytes microinjection experiments suggested that the trimming may occur before or upon nuclear import (Neuman de Vegvar & Dahlberg, 1990).…”

The integrity of the U12 snRNA 3′ stem–loop is necessary for its overall stability

“…Recent work revealed TOE1, a primarily Cajal body-localized deadenylase with nucleo-cytoplasmic shuttling activity ( 42 , 43 ), as the enzyme responsible for the 3′ trimming of human snRNA precursors to their mature length ( 44 , 45 ). TOE1 thus represents another 3′-to-5′ exonucleolytic activity targeting the 3′ end of snRNAs.…”