Translational regulation by uORFs and start codon selection stringency

Dever, Thomas E.; Ivanov, Ivaylo P.; Hinnebusch, Alan G.

doi:10.1101/gad.350752.123

Cited by 45 publications

(31 citation statements)

References 144 publications

(225 reference statements)

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“…To determine whether RNase L had an effect on uORF-based regulation, we quantified the ratio of ribosome footprints in the 5’UTR and compared it to footprints that mapped to the main ORF (Figure 6B-C, see Methods). We noted a substantial decrease in uORF translation relative to main ORF translation in poly I:C treated WT or RNASEL KO cells due to eIF2α phosphorylation, as expected (Dever et al ., 2023). However, this decrease was less in the case of the WT cells compared to RNASEL KO cells (Figure 6B-C), suggesting that RNase L activation may have some role in affecting this shift.…”

Section: Resultssupporting

confidence: 89%

“…The GADD34 mRNA was identified as a strong target of RNase L driven degradation (Burke et al ., 2019) and thus absolute levels of GADD34 are likely lower in WT cells as compared to RNASEL KO cells. The transcripts for ATF4 , CHOP , and GADD34 contain one or more open reading frames in their 5’UTR (uORFs) with unique features that allow them to suppress translation of the main ORF in non-stressed cells, but activate it when eIF2α becomes phosphorylated (Dever et al, 2023; Young and Wek, 2016). As noted above, the TE for GADD34 was observed to increase 2-4-fold in in poly(I:C) treated cells (WT or RNASEL KO) (Figure 6A).…”

Section: Resultsmentioning

confidence: 99%

“…We also focused on changes in translation efficiency related to the ISR since it is a well-established regulatory pathway known to rely on control of translation via phosphorylation of eIF2α by the dsRNA sensor PKR (Dever et al ., 2023; Young and Wek, 2016). One consequence of eIF2α phosphorylation is the translational activation of a set of genes, such as GADD34 , due to a shift in translation initiation from uORFs to the main ORF (Young and Wek, 2016).…”

Section: Discussionmentioning

confidence: 99%

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Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Karasik,

Lorenzi,

DePass

et al. 2023

Preprint

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SummaryDuring viral infection, several dsRNA sensors are activated in the cell and trigger signaling that leads to changes in gene expression. One of these sensors activates an endonuclease, RNase L, that cleaves many types of RNA in the cell. However, how the resultant widespread RNA decay affects gene expression is not fully understood. Here we found that gene expression changes caused by activating dsRNA sensing pathways are tuned by RNase L activation, pointing to intricacy in the innate immune response where multiple inputs are integrated to create an optimized output. We show that RNase-L-dependent RNA fragmentation induces the activation of the Ribotoxic Stress Response, potentially through ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L appears to limit the translation of genes that are regulated by another dsRNA-induced pathway, the Integrated Stress Response. Intriguingly, we found the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage events can directly evoke an antiviral program.Key summaryActivated RNase L acts together with other dsRNA-sensing pathways to induce a strong immune response via JNK and p38 signalingGeneric RNA fragmentation plays a key role in inducing transcription, potentially through ribosome collisionsActivation of RNase L inhibits the effects of eIF2α phosphorylationTranslation of the antiviral IFIT mRNAs is inhibited by active RNase L

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Karasik,

Lorenzi,

DePass

et al. 2023

Preprint

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“…Interestingly, protein-coding genes with similarly high EJC-NMD prediction (> 90%) were mostly driven by short upstream ORFs (uORFs; 13/20 genes). Among those 13 genes with uORF-translation coupled to NMD are well characterized examples such as DDIT3 (CHOP) and PPP1R15A (GADD34), which play an important role in the integrated stress response (ISR) [105][106][107][108] . Conversely, genes that were predicted to be EJC-independent (< 10% EJC-NMD ORF usage) included GADD45B (Figure S7C), which was previously shown in reporter assays to induce NMD by its GCrich 3 ′ UTR 103 .…”

Section: Nmd Rna Substrate Regulation Supports Biological Functionmentioning

confidence: 99%

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells

Boehm,

Wallmeroth,

Wulf

et al. 2024

Preprint

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The helicase UPF1 acts as the central essential factor in human nonsense-mediated mRNA decay (NMD) and is involved in various other mRNA degradation processes. Given its multifunctionality, distinguishing between mRNAs regulated directly and indirectly by UPF1 remains a critical challenge. We engineered two different conditional degron tags into endogenous UPF1 in human cell lines to probe the consequences of UPF1 rapid depletion. UPF1 degradation inhibits NMD within hours and strongly stabilizes endogenous NMD substrates, which can be classified into different groups based on their expression kinetics. Extended UPF1 depletion results in massive transcript and isoform alterations, partially driven by secondary effects. We define a high-confidence UPF1-regulated core set of transcripts, which consists mostly of NMD substrates. NMD-regulated genes are involved in brain development and the integrated stress response, among other biological processes. In summary, UPF1 degron systems rapidly inhibit NMD, providing valuable insights into its roles across various experimental systems.

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“…The 5'-proximal AUG-initiated uORF in GCN4 mRNA, uORF1, is the best characterized such uORF in yeast, being optimized for eIF3 and eIF4G binding and retention of post-termination 40S subunits by the presence of cis-acting reinitiation promoting elements (RPEs) rendering it highly permissive for REI downstream (Fig. 2) 5,27,28 . Accordingly, the 40S post-termination complexes at the uORF1 stop codon should not spontaneously dissociate from mRNA on release of the deacylated tRNA, enabling high-level REI in WT cells whether or not tRNA release depends on the Tma factors (Fig.…”

Section: (Cf Wt and Tma∆∆)mentioning

confidence: 99%

Impacts of yeast Tma20/MCTS1, Tma22/DENR and Tma64/eIF2D on translation reinitiation and ribosome recycling

Jendruchová,

Gaikwad,

Poncová

et al. 2024

Preprint

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Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S subunit from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation at short upstream open reading frames (uORFs) harboring penultimate codons that confer dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited reinitiation at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on reinitiation at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) reinitiation. We found that the Tma proteins generally impede reinitiation at native uORF4 and uORF4 variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on reinitiation at native uORF1, and equipping uORF1 with Tma-dependent penultimate codons generally did not confer Tma-dependent reinitiation; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the reinitiation potential of the uORF and the penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.

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Translational regulation by uORFs and start codon selection stringency

Cited by 45 publications

References 144 publications

Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells

Impacts of yeast Tma20/MCTS1, Tma22/DENR and Tma64/eIF2D on translation reinitiation and ribosome recycling

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