-
Nature Communications Nov 2021Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers and is characterized by high recurrence and heterogeneity, yet its mechanism is not...
Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers and is characterized by high recurrence and heterogeneity, yet its mechanism is not well understood. Here we show that N-methyladenosine methylation (mA) in tRNA is remarkably elevated in hepatocellular carcinoma (HCC) patient tumour tissues. Moreover, mA methylation signals are increased in liver cancer stem cells (CSCs) and are negatively correlated with HCC patient survival. TRMT6 and TRMT61A, forming mA methyltransferase complex, are highly expressed in advanced HCC tumours and are negatively correlated with HCC survival. TRMT6/TRMT61A-mediated mA methylation is required for liver tumourigenesis. Mechanistically, TRMT6/TRMT61A elevates the mA methylation in a subset of tRNA to increase PPARδ translation, which in turn triggers cholesterol synthesis to activate Hedgehog signaling, eventually driving self-renewal of liver CSCs and tumourigenesis. Finally, we identify a potent inhibitor against TRMT6/TRMT61A complex that exerts effective therapeutic effect on liver cancer.
Topics: Adenosine; Animals; Carcinoma, Hepatocellular; Cell Line, Tumor; Cell Self Renewal; Cholesterol; Disease Models, Animal; Female; Humans; Liver Neoplasms; Male; Membrane Proteins; Methylation; Mice; Mice, Inbred C57BL; Mice, Knockout; Middle Aged; Neoplastic Stem Cells; PPAR gamma; RNA, Transfer; Survival Rate; tRNA Methyltransferases
PubMed: 34728628
DOI: 10.1038/s41467-021-26718-6 -
Nucleic Acids Research Jan 2021The highly abundant N6-methyladenosine (m6A) RNA modification affects most aspects of mRNA function, yet the precise function of the rarer 5-methylcytidine (m5C) remains...
The highly abundant N6-methyladenosine (m6A) RNA modification affects most aspects of mRNA function, yet the precise function of the rarer 5-methylcytidine (m5C) remains largely unknown. Here, we map m5C in the human transcriptome using methylation-dependent individual-nucleotide resolution cross-linking and immunoprecipitation (miCLIP) combined with RNA bisulfite sequencing. We identify NSUN6 as a methyltransferase with strong substrate specificity towards mRNA. NSUN6 primarily targeted three prime untranslated regions (3'UTR) at the consensus sequence motif CTCCA, located in loops of hairpin structures. Knockout and rescue experiments revealed enhanced mRNA and translation levels when NSUN6-targeted mRNAs were methylated. Ribosome profiling further demonstrated that NSUN6-specific methylation correlated with translation termination. While NSUN6 was dispensable for mouse embryonic development, it was down-regulated in human tumours and high expression of NSUN6 indicated better patient outcome of certain cancer types. In summary, our study identifies NSUN6 as a methyltransferase targeting mRNA, potentially as part of a quality control mechanism involved in translation termination fidelity.
Topics: 3' Untranslated Regions; Animals; Base Sequence; Cell Line, Tumor; Codon Usage; Consensus Sequence; Cytidine; Embryonic Stem Cells; Gene Knockout Techniques; Genes, Reporter; HEK293 Cells; Humans; Immunoprecipitation; Methylation; Mice; Mice, Knockout; Mutagenesis, Site-Directed; RNA Processing, Post-Transcriptional; RNA, Messenger; Transcriptome; tRNA Methyltransferases
PubMed: 33330931
DOI: 10.1093/nar/gkaa1193 -
Molecular Cell Dec 2017Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N-methyladenosine (mA) is a recently identified mRNA modification;...
Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N-methyladenosine (mA) is a recently identified mRNA modification; however, little is known about its precise location and biogenesis. Here, we develop a base-resolution mA profiling method, based on mA-induced misincorporation during reverse transcription, and report distinct classes of mA methylome in the human transcriptome. mA in 5' UTR, particularly those at the mRNA cap, associate with increased translation efficiency. A different, small subset of mA exhibit a GUUCRA tRNA-like motif, are evenly distributed in the transcriptome, and are dependent on the methyltransferase TRMT6/61A. Additionally, we show that mA is prevalent in the mitochondrial-encoded transcripts. Manipulation of mA level via TRMT61B, a mitochondria-localizing mA methyltransferase, demonstrates that mA in mitochondrial mRNA interferes with translation. Collectively, our approaches reveal distinct classes of mA methylome and provide a resource for functional studies of mA-mediated epitranscriptomic regulation.
Topics: 5' Untranslated Regions; Adenosine; Cell Nucleus; HEK293 Cells; Humans; Mitochondria; Mitochondrial Proteins; Nuclear Proteins; Protein Biosynthesis; RNA Caps; RNA Interference; RNA Processing, Post-Transcriptional; RNA, Messenger; RNA, Transfer; Single Molecule Imaging; Transfection; tRNA Methyltransferases
PubMed: 29107537
DOI: 10.1016/j.molcel.2017.10.019 -
EBioMedicine Jan 2021Pancreatic cancer (PC) is one of the most lethal solid malignancies in the world due to its excessive cell proliferation and aggressive metastatic features. Emerging...
BACKGROUND
Pancreatic cancer (PC) is one of the most lethal solid malignancies in the world due to its excessive cell proliferation and aggressive metastatic features. Emerging evidences revealed the importance of posttranscriptional modifications of RNAs in PC progression. However, knowledge about the 5-methylcytosine (m5C) RNA modification in PC is still extremely limited. In this study, we attempted to explore the expression changes and clinical significances of 12 known m5C-related genes among PC patients.
METHODS
A total of 362 normal and 382 tumor specimens from PC patients were examined for candidate m5C-related gene and protein expression by using quantitative PCR (qPCR) and immunohistochemistry (IHC). The proliferation rate of PC cells was detected by MTS assay. Xenograft mouse models were used to assess the role of NSUN6 in PC tumor formation.
FINDINGS
Through analyzing the four Gene Expression Omnibus (GEO) databases, six m5C-related genes shown significant and consistent alterations were selected for further examination in our 3 independent PC cohorts. Finally, we identified the reduction of NSUN6 as a common feature of all PC sample sets examined. NSUN6 expression correlated with clinicopathologic parameters including T stage, and Ki67 cell rate. Further assessing the transcriptional profiles of 50 PC tissues, we found biological processes associated with cell proliferation like cell cycle and G2M checkpoint were enriched in NSUN6 lower expression group. Helped by in vitro PC cell lines and in vivo xenograft mouse models, we confirmed the role of NSUN6 in regulating cell proliferation and PC tumor growth. Last but also importantly, we also show the good performance of NSUN6 in evaluating tumor recurrence and survival among PC patients.
INTERPRETATION
Our data suggested that NSUN6 is an important factor involved in regulating cell proliferation of PC, and highlights the potential of novel m5C-based clinical modalities as a therapeutic approach in PC patients.
FUNDING
This study was supported by the National Natural Science Foundation of China (Grant Nos. 81803014, 81802424, and 81802911).
Topics: Animals; Cell Cycle; Cell Line, Tumor; Cell Proliferation; Cell Transformation, Neoplastic; Computational Biology; Databases, Genetic; Disease Models, Animal; Disease Susceptibility; Gene Expression; Gene Expression Profiling; Heterografts; Humans; Immunohistochemistry; Kaplan-Meier Estimate; Mice; Pancreatic Neoplasms; Prognosis; ROC Curve; tRNA Methyltransferases
PubMed: 33418496
DOI: 10.1016/j.ebiom.2020.103195 -
RNA Biology 2015tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms.... (Review)
Review
tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed.
Topics: Animals; Humans; Methylation; RNA, Transfer; Substrate Specificity; tRNA Methyltransferases
PubMed: 25626150
DOI: 10.1080/15476286.2015.1008358 -
International Journal of Molecular... Nov 2018Transfer RNAs (tRNAs) are key players of protein synthesis, as they decode the genetic information organized in mRNA codons, translating them into the code of 20 amino... (Review)
Review
Transfer RNAs (tRNAs) are key players of protein synthesis, as they decode the genetic information organized in mRNA codons, translating them into the code of 20 amino acids. To be fully active, tRNAs undergo extensive post-transcriptional modifications, catalyzed by different tRNA-modifying enzymes. Lack of these modifications increases the level of missense errors and affects codon decoding rate, contributing to protein aggregation with deleterious consequences to the cell. Recent works show that tRNA hypomodification and tRNA-modifying-enzyme deregulation occur in several diseases where proteostasis is affected, namely, neurodegenerative and metabolic diseases. In this review, we discuss the recent findings that correlate aberrant tRNA modification with proteostasis imbalances, in particular in neurological and metabolic disorders, and highlight the association between tRNAs, their modifying enzymes, translational decoding, and disease onset.
Topics: Animals; DNA (Cytosine-5-)-Methyltransferases; Humans; Metabolic Diseases; Nervous System Diseases; Nucleic Acid Conformation; Protein Aggregates; Protein Biosynthesis; Proteostasis; RNA Processing, Post-Transcriptional; RNA, Transfer; Ubiquitins; tRNA Methyltransferases
PubMed: 30477220
DOI: 10.3390/ijms19123738 -
International Journal of Molecular... Dec 2018More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m⁷G) modification is found widely in... (Review)
Review
More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m⁷G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m⁷G modification occurs at position 46 in the variable region and is a product of tRNA (m⁷G46) methyltransferase. The m⁷G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. A reaction mechanism for eubacterial tRNA m⁷G methyltransferase has been proposed based on the results of biochemical, bioinformatic, and structural studies. However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. The physiological functions of m⁷G46 in tRNA have started to be determined over the past decade. For example, tRNA m⁷G46 or tRNA (m⁷G46) methyltransferase controls the amount of other tRNA modifications in thermophilic bacteria, contributes to the pathogenic infectivity, and is also associated with several diseases. In this review, information of tRNA m⁷G modifications and tRNA m⁷G methyltransferases is summarized and the differences in reaction mechanism between tRNA m⁷G methyltransferase and rRNA or mRNA m⁷G methylation enzyme are discussed.
Topics: Animals; Bacteria; Bacterial Proteins; Guanosine; Humans; RNA Processing, Post-Transcriptional; RNA, Bacterial; RNA, Transfer; tRNA Methyltransferases
PubMed: 30562954
DOI: 10.3390/ijms19124080 -
Current Opinion in Structural Biology Apr 2019All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops... (Review)
Review
All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops represent major modification hotspots. The attachment of small chemical groups at the heart of the ribosomal decoding machinery can directly affect translational rates, reading frame maintenance, co-translational folding dynamics and overall proteome stability. The variety of tRNA modification patterns is driven by the activity of specialized tRNA modifiers and large modification complexes. Notably, the absence or dysfunction of these cellular machines is correlated with several human pathophysiologies. In this review, we aim to highlight the most recent scientific progress and summarize currently available structural information of the most prominent eukaryotic tRNA modifiers.
Topics: Anticodon; Eukaryotic Cells; Humans; Intramolecular Transferases; Methylation; RNA, Transfer; Ribosomes; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; tRNA Methyltransferases
PubMed: 31102979
DOI: 10.1016/j.sbi.2019.03.014 -
Nucleic Acids Research Sep 20235-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian...
5-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian enzyme for m5U formation at tRNA position 54. However, its RNA binding specificity and functional role in the cell are not well understood. Here we dissected structural and sequence requirements for binding and methylation of its RNA targets. Specificity of tRNA modification by hTRMT2A is achieved by a combination of modest binding preference and presence of a uridine in position 54 of tRNAs. Mutational analysis together with cross-linking experiments identified a large hTRMT2A-tRNA binding surface. Furthermore, complementing hTRMT2A interactome studies revealed that hTRMT2A interacts with proteins involved in RNA biogenesis. Finally, we addressed the question of the importance of hTRMT2A function by showing that its knockdown reduces translation fidelity. These findings extend the role of hTRMT2A beyond tRNA modification towards a role in translation.
Topics: Animals; Humans; Mammals; Methylation; RNA; RNA, Transfer; tRNA Methyltransferases
PubMed: 37395448
DOI: 10.1093/nar/gkad565 -
Future Medicinal Chemistry Apr 2019Transfer RNAs (tRNAs) undergo extensive chemical modification within cells through the activity of tRNA methyltransferase enzymes (TRMs). Although tRNA modifications are... (Review)
Review
Transfer RNAs (tRNAs) undergo extensive chemical modification within cells through the activity of tRNA methyltransferase enzymes (TRMs). Although tRNA modifications are dynamic, how they impact cell behavior after stress and during tumorigenesis is not well understood. This review discusses how tRNA modifications influence the translation of codon-biased transcripts involved in responses to oxidative stress. We further discuss emerging mechanistic details about how aberrant TRM activity in cancer cells can direct programs of codon-biased translation that drive cancer cell phenotypes. The studies reviewed here predict future preventative therapies aimed at augmenting TRM activity in individuals at risk for cancer due to exposure. They further predict that attenuating TRM-dependent translation in cancer cells may limit disease progression while leaving noncancerous cells unharmed.
Topics: Animals; Codon; Gene Expression Regulation, Neoplastic; Humans; Methylation; Neoplasms; Oxidative Stress; RNA, Transfer; tRNA Methyltransferases
PubMed: 30744422
DOI: 10.4155/fmc-2018-0404