ADAT2/3-mediated tRNA editing promotes cancer cell growth and tumorigenicity
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE272218 | GEO | 2026/07/31
REPOSITORIES: GEO
Similar Datasets
Project description:In most eukaryotes, the wobble position of tRNA with a GUN anticodon is queuosine-modified (Q34). Q is synthesized exclusively by eubacteria and salvaged by eukaryotes as a nutrient to replace G34 in tRNAs. Q34 modification stimulates Dnmt2/Pmt1-dependent C38 methylation in the tRNAAsp anticodon loop in Schizosaccharomyces pombe. Due to the location of both modification in the anticodon loop, we anticipated an influence on translation. Our experimental setup allowed for the analysis of effects from each modification alone or a combination of both.
2019-02-13 | GSE102376 | GEO
Project description:Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed translational changes that occur upon CHIKV infection at the ER and the cytosol. We show that CHIKV infection induces codon-specific reprogramming of the host translation machinery to favor the translation of viral RNA genomes over host mRNAs with an otherwise optimal codon usage. This reprogramming was mostly apparent at the ER, where CHIKV RNAs are efficiently translated. Mechanistically, it involves CHIKV-induced overexpression of KIAA1456, an enzyme that modifies the wobble U34 position in the anticodon of tRNAs, which we find is required for proper decoding of codons that are highly enriched in CHIKV RNAs. Our findings demonstrate an unprecedented interplay of viruses with the host tRNA epitranscriptome to adapt the host translation machinery to viral production.
2025-06-16 | MTBLS2443 | MetaboLights
Project description:The tRNA epitranscriptome is composed of a wide variety of base modifications in tRNAs and is emerging as a potential key vulnerability of cancer. Wobble tRNA modifications are required for specific codon decoding during translation and maintenance of protein homeostasis and support cancer metastasis and resistance to therapy. Here we show that ablation of enzymes catalyzing wobble uridine (U34) tRNA modification (U34 enzymes) remodels the MHC-II-associated antigen repertoire of melanoma by perturbing codon-specific mRNA translation. This perturbation in translation triggers the formation of aggregates that are subsequently degraded through the autophagy-lysosomal pathway and presented on MHC-II. The remodeled MHC-II repertoire in turn induces a CD4+ effector T cell-mediated anti-tumor response displaying specific clonal selection and immunodominance in melanoma. Our results identify a novel, potentially tractable, vulnerability of melanoma, in which codon-specific mRNA translation through wobble uridine tRNA modification, optimizes proteome homeostasis, prevents excessive antigen presentation, and limits T cell activity in melanoma.
2025-03-01 | E-MTAB-13867 | biostudies-arrayexpress
Project description:The tRNA epitranscriptome is composed of a wide variety of base modifications in tRNAs and is emerging as a potential key vulnerability of cancer. Wobble tRNA modifications are required for specific codon decoding during translation and maintenance of protein homeostasis and support cancer metastasis and resistance to therapy. Here we show that ablation of enzymes catalyzing wobble uridine (U34) tRNA modification (U34 enzymes) remodels the MHC-II-associated antigen repertoire of melanoma by perturbing codon-specific mRNA translation. This perturbation in translation triggers the formation of aggregates that are subsequently degraded through the autophagy-lysosomal pathway and presented on MHC-II. The remodeled MHC-II repertoire in turn induces a CD4+ effector T cell-mediated anti-tumor response displaying specific clonal selection and immunodominance in melanoma. Our results identify a novel, potentially tractable, vulnerability of melanoma, in which codon-specific mRNA translation through wobble uridine tRNA modification, optimizes proteome homeostasis, prevents excessive antigen presentation, and limits T cell activity in melanoma.
2026-02-27 | E-MTAB-13868 | biostudies-arrayexpress
Project description:Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. Despite decades of study, cellular roles of Q modification remain to be fully elucidated. Here we show that in human cells, Q modification specifically protects its cognate tRNAHis and tRNAAsn against cleavage by ribonucleases. We generated cell lines that contain completely depleted or fully Q-modified tRNAs. Using these resources, we found that Q modification significantly reduces angiogenin cleavage of its cognate tRNAs in vitro. Q modification does not change the cellular abundance of the cognate full-length tRNAs, but alters the cellular content of their fragments in vivo in the absence and presence of stress. Our results provide a new biological aspect of Q modification and a mechanism of how Q modification alters small RNA pool in human cells.
2018-08-10 | GSE102570 | GEO
Project description:Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Yeast cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress and accumulate aggregates of endogenous proteins with key cellular functions. Moreover, these cells are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA anticodon modifications in maintaining proteome integrity. Ribosome profiling of wild-type and tRNA modification-deficient yeast and nematodes. Yeast samples were generated in various growth conditions (rich medium versus stress induced by treatment with diamide or rapamycin) and paired mRNA-Seq was performed on a subset of samples. Dataset contains three biological replicates for yeast samples and two biological replicates for nematode samples.
2015-06-04 | E-GEOD-67387 | biostudies-arrayexpress
Project description:In eukaryotes, the genetic code is transcribed into messenger RNA (mRNA) in the nucleus and decoded by transfer RNA (tRNA) in the cytosol. Nuclear mRNA processing events that do not affect the nucleotide sequence of an mRNA are thought to be invisible to tRNAs during protein translation in the cytosol. Here, we report a mechanism by which the modified mRNA nucleotide N6‑methyladenosine (m6A) connects nuclear mRNA processing to tRNA decoding. m6A is deposited in the protein coding sequence (CDS) of mRNAs with long exons, where it slows the decoding of a subset of m6A-modified codons in vivo. Translation of codons with m6A at the wobble position is facilitated by 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a modified nucleotide of the tRNA anticodon loop that juxtaposes the wobble-m6A. This unanticipated link between the mRNA and tRNA epitranscriptomes controls mRNA half-life in a translation-dependent manner and connects the exon-intron architecture of mRNAs to their turnover. The pathways for m6A and mcm5s2U biogenesis are tightly co-regulated in human tissues but deregulated in cancer cells. In breast cancer, a shift towards more mcm5s2U is associated with tumor aggressiveness and poor prognosis. Thus, the m6A/mcm5s2U-balance has evolved as a pan-epitranscriptomic mechanism that coordinates gene expression changes and curtails tumorigenesis.
2025-05-09 | GSE173971 | GEO
Project description:Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas the substrate for Q-modification in tRNA in mammals is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method of biological RNA samples that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method Periodate-dependent analysis of queuosine and thio modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
2022-06-22 | GSE196016 | GEO
Project description:The mammalian mitochondrial protein synthesis system produces thirteen essential subunits of oxidative phosphorylation (OXPHOS) complexes. Translation initiation in mammalian mitochondria is characterized by the use of leaderless mRNAs and non-AUG start codons, where the proofreading function of IF-3mt still remains elusive. Here, we developed a reconstituted mammalian mitochondrial translation system using in vitro transcribed and native mitochondrial tRNAs to investigate IF-3mt’s proofreading function. Similar to bacterial IF-3, IF-3mt permits initiator tRNA to participate in initiation by discriminating the three G-C pairs in its anticodon stem, and the cognate interaction of its anticodon with the AUG start codon. As a result, IF-3mt promotes the accurate initiation of leaderless mRNAs. Nevertheless, IF-3mt can also facilitate initiation from the non-AUG(AUA) start codon through its unique N- and C-terminal extensions in concert with the 5-methylcytidine (m5C) or 5-formylcytidine (f5C) modification at the anticodon wobble position of mt-tRNAMet. This is partly because the IF-3mt-specific N- and C-terminal extensions and the KKGK-motif favor leaderless mRNA initiation and relax non-AUG start codon discrimination. Analyses of IF-3mt-depleted cells revealed that, in human cells, IF-3mt indeed participates in translating the ORFs of leaderless mRNAs, as well as the internal ORFs of bicistronic mRNAs.
2025-02-05 | GSE282838 | GEO
Project description:tRNA fragments (tRFs) are natural, small non-coding RNAs produced by endogenous ribonucleolytic cleavage of tRNAs. tRFs play a role in many biological pathways including regulation of cell proliferation. Specific modifications also affect tRF abundance and the abundance of their cognate, full-length tRNA. Queuosine (Q) modification occurs at the wobble anticodon nucleotide of 4 mammalian tRNAs and protects these tRNAs from fragmentation. Here, we investigated cell-type and tRNA Q-modification-dependences on cell proliferation. We found that Q-modified tRNA can either increase, decrease, or make no difference on proliferation. Among the six cell lines tested, proliferation only decreased in MCF7, a breast cancer cell line, when tRNAs were Q-modified, but the proliferation can be restored by the transfection of Q-modification-dependent tRFHis. tRNA-seq showed that in MCF7 cells, tRNA Q-modification reduced m1A58 and m3C32 modification levels, consistent with reduced translation. Additionally, polysome profiling showed a Q-modification associated codon usage pattern that corresponded with altered translation efficiency of ribosomal proteins required for faster proliferation. Protein pull-down using tRFHis identified Musashi RNA binding protein 2 (Msi2) as a tRFHis binding protein. Msi2 is known to enhance mitochondrial activities, and Msi2 knockdown reduced the tRFHis dependent cell proliferation effect. Our results illustrate a highly cell-type dependent proliferation effect of tRNA Q-modification, suggesting multi-faceted mechanisms in studying this ubiquitous tRNA modification.
2026-03-31 | GSE293476 | GEO