The EDC4-XRN1 axis controls P-body dynamics to link mRNA decapping with decay

Abstract

Deadenylation-dependent mRNA decapping and decay is the major cytoplasmic mRNA turnover pathway in eukaryotes. Many mRNA decapping and decay factors associate with each other via protein-protein interaction motifs. For example, the decapping enzyme DCP2 and the 5’-3’ exoribonuclease XRN1 interact with enhancer of mRNA decapping protein 4 (EDC4), a large scaffold that has been reported to stimulate mRNA decapping. mRNA decapping and decay factors are also found in processing bodies (P-bodies), evolutionarily conserved ribonucleoprotein (RNP) granules that are often enriched with mRNAs targeted for decay, such as microRNA (miRNA)-targeted mRNAs, yet paradoxically are not required for mRNA decay to occur. In this study, we show that disrupting the interaction between XRN1 and EDC4 or altering their stoichiometry leads to an inhibition of mRNA decapping, with miRNA-targeted mRNAs being stabilized in a translationally repressed state. Importantly, we demonstrate that this concomitantly leads to larger P-bodies that are directly responsible for preventing mRNA decapping under these conditions. Finally, we demonstrate that P-bodies act to support cell viability and prevent stress granule formation under conditions when XRN1 is limiting. Taken together, these data demonstrate that the interaction between XRN1 and EDC4 regulates P-body dynamics to properly coordinate mRNA decapping with 5’-3’ decay in human cells.HIGHLIGHTSXRN1-EDC4 interaction couples mRNA decapping with mRNA decay.Disrupting XRN1-EDC4 contact generates larger P-bodies that, in turn, inhibit decapping.P-bodies support cellular fitness in the absence of XRN1.

Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress

“…6d, e). To test whether the observed enrichment of shortened genes is specific to the SGs, we also tested for association with processing bodies (P-bodies), membraneless organelles enriched in de-capping factors and exoribonucleases, essential for RNA decay under normal, non-stress conditions (Brothers et al, 2023). We re-analyzed previously published data from HEK293 cells (Matheny et al, 2019), but in contrast to SGs, we found no association between P-body localization and gene lengths (Sup.…”

The RNA-binding activity of the TRIM-NHL protein NHL-2 is essential for miRNA-mediated gene regulation

“…Conversely, inhibition of deadenylation results in smaller P-bodies (59). Interestingly, disrupting the EDC4-XRN1 interaction inhibits mRNA decapping, stabilizes miRNA-targeted mRNAs, and increases Pbody size in HeLa cells (60). The increase in P-body size in nhl-2(RBlf) but not in the RING mutant, correlates with the severity of the alae defects observed.…”

EDC-3 and EDC-4 Regulate Embryonic mRNA Clearance and Biomolecular Condensate Specialization

“…On its own, this hypomorphic allele exhibited ~70% embryonic lethality at 16°C (Figure 4C). dcap-2(0) was synthetic lethal with mir-35-41(nDf50), as we could not obtain a single viable homozygous dcap-2(0); mir- [35][36][37][38][39][40][41] animal. Individual edc-3(0) or edc-4(0) mutants exacerbated mir-35-41(nDf50) embryonic lethality to 91% and 93%, while their combined deletion exacerbated lethality to ~99% (Figure 4C).…”

“…In C. elegans embryos, P-bodies are found in the somatic and germline blastomeres and are distinct from P/germ granules, which specifically form in the germline lineage 36,37 . Originally proposed to be active sites for mRNA decay 38 , several lines of evidence support the idea that P-bodies instead store and protect silent mRNAs from decapping and decay 33,[39][40][41] . However, as P-bodies seem to form as a consequence of translational repression, some papers even challenged whether they represent active regulatory sites per se 21,42 .…”