Matching tRNA modifications in humans to their known and predicted enzymes

Crécy‐Lagard, Valérie de; Boccaletto, Pietro; Mangleburg, Carl Grant; Sharma, Puneet; Lowe, Todd M.; Leidel, Sebastian A.; Bujnicki, Janusz

doi:10.1093/nar/gkz011

Cited by 121 publications

(110 citation statements)

References 229 publications

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“…tRNAs are by far the most post-transcriptionally modified gene class (Boccaletto et al 2018). Research is just now starting to tease apart the many roles these modifications play Phizicky and Alfonzo 2010;Pereira et al 2018;de Crecy-Lagard et al 2019). Not all modifications are detectable through sequencing, but it has been estimated that RT-based methods can identify approximately 25% of tRNA modifications in humans (Clark et al 2016), and the modifications that can be detected by sequencing are known to have critical roles in tRNA folding, rigidity and stability (Pan 2018).…”

Section: The Landscape Of Base Modifications In Plant Trnasmentioning

confidence: 99%

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Warren

Salinas‐Giegé

Hummel

et al. 2019

Preprint

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Differences in tRNA expression have been implicated in a remarkable number of biological processes.There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of highthroughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be "hot spots" for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.

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Section: The Landscape Of Base Modifications In Plant Trnasmentioning

confidence: 99%

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Warren

Salinas‐Giegé

Hummel

et al. 2019

Preprint

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“…tRNA modifications involved in translation frame maintenance are reduced in activated T -cells. tRNA molecules are extremely rich with post-transcriptional RNA modifications, of which some can govern the stability, translation efficiency, decoding rate and fidelity 7,10,25,26 . Modifications can be detected using tRNA-seq as they can often cause failure in the reverse transcription reaction 9 .…”

Section: Induction Of a Proliferation Trna Signature Is Followed By Rmentioning

confidence: 99%

Dynamic changes in tRNA modifications and abundance during T-cell activation

Rak

Polonsky

Eizenberg

et al. 2020

Preprint

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The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of Tcells during their vigorous proliferation and differentiation upon triggering of the T cell antigen receptor. We observe a global signature of switch in demand for codon at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation of the T cells, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, Wybutosine and ms 2 t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode "slippery codons", that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a Wybutosine writer showed increased ribosomal frameshifting, as detected with a reporter that consists of a critical frameshifting site taken from the HIV gag-pol slippery codon motif. These results may explain HIV's specificity to proliferating T-Cells since it requires ribosomal frameshift exactly on this codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.The tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation-T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which relex when cells reduces their proliferation rate. We also found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication.

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“…Related information for each of these proteins (modification type, target RNA, localization) was extracted from Uniprot, as well as from relevant literature [42]. Additional tRNA writer proteins were gathered from a recent study matching tRNA modifications to their writers [84]. Readers, erasers and non-catalytic subunit proteins were obtained from annotated Uniprot genes as well as from published literature [85].…”

Section: Compilation Of Human Rna Modification-related Proteins (Rmps)mentioning

confidence: 99%

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

Begik

Lucas

Liu

et al. 2019

Preprint

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ABSTRACTBackgroundRNA modifications play central roles in cellular fate and differentiation. These features have placed the epitranscriptome in the forefront of developmental biology and cancer research. However, the machinery responsible for placing, removing and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification–related proteins (RMPs) may be dysregulated in each cancer type.ResultsHere we have performed a comprehensive annotation and evolutionary analysis of human RMPs as well as an integrative analysis of their expression patterns across 32 tissues, 10 species and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. Moreover, through the analysis of paired tumor-normal human samples we uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO, are not significantly up-regulated in most cancer types, once the sample is properly scaled and normalized to the full dataset, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers.ConclusionsOur analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues, and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviours that are orchestrated by RNA modifications.

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Matching tRNA modifications in humans to their known and predicted enzymes

Cited by 121 publications

References 229 publications

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Dynamic changes in tRNA modifications and abundance during T-cell activation

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

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