Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism

Fan

et al. 2021

Nucleic Acids Research

Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.

Section: Discussionmentioning

confidence: 99%

ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation

Fan

et al. 2021

Nucleic Acids Research

“…Let-7a supplementation alone was previously shown to have no effect on AKT1 abundance [ 27 ]. Similarly, a recent study on HEK 293T cells showed that the deletion of DIS3L2 also results in increased phosphorylation of AKT at T308 [ 59 ]. Although TUT4/7 were previously suggested as chemotherapeutic targets, perturbation of uridylation-dependent RNA decay leads to potentially carcinogenic, increased AKT phosphorylation.…”

Section: Discussionmentioning

confidence: 94%

Terminal Uridylyltransferases TUT4/7 Regulate microRNA and mRNA Homeostasis

Zhang¹,

Frederick²,

Heinemann³

2022

Cells

The terminal nucleotidyltransferases TUT4 and TUT7 (TUT4/7) regulate miRNA and mRNA stability by 3′ end uridylation. In humans, TUT4/7 polyuridylates both mRNA and pre-miRNA, leading to degradation by the U-specific exonuclease DIS3L2. We investigate the role of uridylation-dependent decay in maintaining the transcriptome by transcriptionally profiling TUT4/7 deleted cells. We found that while the disruption of TUT4/7 expression increases the abundance of a variety of miRNAs, the let-7 family of miRNAs is the most impacted. Eight let-7 family miRNAs were increased in abundance in TUT4/7 deleted cells, and many let-7 mRNA targets are decreased in abundance. The mRNAs with increased abundance in the deletion strain are potential direct targets of TUT4/7, with transcripts coding for proteins involved in cellular stress response, rRNA processing, ribonucleoprotein complex biogenesis, cell–cell signaling, and regulation of metabolic processes most affected in the TUT4/7 knockout cells. We found that TUT4/7 indirectly control oncogenic signaling via the miRNA let-7a, which regulates AKT phosphorylation status. Finally, we find that, similar to fission yeast, the disruption of uridylation-dependent decay leads to major rearrangements of the transcriptome and reduces cell proliferation and adhesion.

“…RNA quality control and turnover are vital for cellular function, yet little is known about how nucleases deal with the diverse universe of structured RNAs. Dis3L2 is an RNAse II/R family 3’-5’ hydrolytic exoribonuclease that plays an important role in development and differentiation 1,7 , cell proliferation 8–11 , calcium homeostasis 12 , and apoptosis 13,14 by effectively removing or processing 3’ uridylated RNAs. Dis3L2 targets are oligo-uridylated by the terminal uridylyl-transferases (or TUTs) 15–17 .…”

Section: Initial Binding Of Dis3l2 To Structured Substratesmentioning

confidence: 99%

A shape-shifting nuclease unravels structured RNA

Meze

Axhemi

Thomas

et al. 2021

Preprint

RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts that may otherwise interfere with cellular programs. The enzyme Dis3-like protein 2 (Dis3L2) is a 3’-5’ exoribonuclease that, through its RNA turnover activity, plays a critical role in human development1. Dis3L2 can independently degrade structured substrates and its targets include many coding and non-coding 3’-uridylated RNAs1–5. While the basis for Dis3L2’s substrate recognition has been well-characterized6, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining electron cryo-microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for single-stranded (ss) and double-stranded (ds) RNA processing. We discovered a dramatic conformational change that is triggered by the dsRNA, involving repositioning of two cold shock domains by 70 Å. This movement exposes a trihelix-linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not ssRNA, degradation. These findings reveal the conformational plasticity of this enzyme, and detail a novel mechanism of structured RNA degradation.