Precursors of tRNAs are stabilized by methylguanosine cap structures

Ohira, Takayuki; Suzuki, Tsutomu

doi:10.1038/nchembio.2117

Cited by 58 publications

(53 citation statements)

References 52 publications

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“…To substantiate the results, RNA-x was digested with RNase T 1 and subjected to capillary LC-nano ESI-MS analysis (16,25). The series of RNA fragments were definitively assigned to the entire sequence of cytoplasmic tRNA His with post-transcriptional modifications (23) (Figure 1D, Supplementary Figure S1A–C).…”

Section: Resultsmentioning

confidence: 99%

Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA

et al. 2017

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Human RNA methyltransferase BCDIN3D is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. Here, we show that cytoplasmic tRNAHis is the primary target of BCDIN3D in human cells. Recombinant human BCDIN3D, expressed in Escherichia coli, monomethylates the 5΄-monophosphate of cytoplasmic tRNAHis efficiently in vitro. In BCDN3D-knockout cells, established by CRISPR/Cas9 editing, the methyl moiety at the 5΄-monophosphate of cytoplasmic tRNAHis is lost, and the exogenous expression of BCDIN3D in the knockout cells restores the modification in cytoplasmic tRNAHis. BCIDN3D recognizes the 5΄-guanosine nucleoside at position −1 (G−1) and the eight-nucleotide acceptor helix with the G−1–A73 mis-pair at the top of the acceptor stem of cytoplasmic tRNAHis, which are exceptional structural features among cytoplasmic tRNA species. While the monomethylation of the 5΄-monophosphate of cytoplasmic tRNAHis affects neither the overall aminoacylation process in vitro nor the steady-state level of cytoplasmic tRNAHisin vivo, it protects the cytoplasmic tRNAHis transcript from degradation in vitro. Thus, BCDIN3D acts as a cytoplasmic tRNAHis-specific 5΄-methylphosphate capping enzyme. The present results also suggest the possible involvement of the monomethylation of the 5΄-monophosphate of cytoplasmic tRNAHis and/or cytoplasmic tRNAHis itself in the tumorigenesis of breast cancer cells.

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Section: Resultsmentioning

confidence: 99%

Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA

et al. 2017

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“…RNA fragments are ionized by ESI as negative ions derived from phosphate groups. Hence, ionization efficiencies of RNA fragments bearing the same sequences, but different modifications, do not significantly differ in general, because ESI ionization relies mainly on numbers of phosphate groups, rather than the type of base modifications (23). The relative amounts of these fragments can be calculated by their detection intensities.…”

Section: Discussionmentioning

confidence: 99%

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications

Kawarada

Suzuki

Ohira

et al. 2017

Nucleic Acids Research

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ALKBH1 is a 2-oxoglutarate- and Fe2+-dependent dioxygenase responsible for multiple cellular functions. Here, we show that ALKBH1 is involved in biogenesis of 5-hydroxymethyl-2΄-O-methylcytidine (hm5Cm) and 5-formyl-2΄-O-methylcytidine (f5Cm) at the first position (position 34) of anticodon in cytoplasmic tRNALeu, as well as f5C at the same position in mitochondrial tRNAMet. Because f5C34 of mitochondrial tRNAMet is essential for translation of AUA, a non-universal codon in mammalian mitochondria, ALKBH1-knockout cells exhibited a strong reduction in mitochondrial translation and reduced respiratory complex activities, indicating that f5C34 formation mediated by ALKBH1 is required for efficient mitochondrial functions. We reconstituted formation of f5C34 on mitochondrial tRNAMetin vitro, and found that ALKBH1 first hydroxylated m5C34 to form hm5C34, and then oxidized hm5C34 to form f5C34. Moreover, we found that the frequency of 1-methyladenosine (m1A) in two mitochondrial tRNAs increased in ALKBH1-knockout cells, indicating that ALKBH1 also has demethylation activity toward m1A in mt-tRNAs. Based on these results, we conclude that nuclear and mitochondrial ALKBH1 play distinct roles in tRNA modification.

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“…In eukaryotic cells, tRNAs are transcribed by RNA polymerase III, with transcription terminating after a stretch of four or more Ts located 10-60 nt downstream of the 3′ end of the tRNA mature sequence (5,6). Pre-tRNAs and mature tRNAs undergo extensive modifications before and after exportation to the cytoplasm (7) resulting in the production of three types of tRNA-derived ncRNAs: tRNA-derived small RNAs (tsRNAs) (4), tRNA halves (tiRNAs) (8), and tRNA-derived fragments (tRFs or tDRs) (9,10). tsRNAs are generated in the nucleus as a consequence of the pre-tRNA 3′ end cleavage (4), whereas tiRNAs are generated from mature tRNAs by cytoplasmic angiogenin activated in response to stress (6,11).…”

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tsRNA signatures in cancer

Balatti

Nigita

Veneziano

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

217

262

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Small, noncoding RNAs are short untranslated RNA molecules, some of which have been associated with cancer development. Recently we showed that a class of small RNAs generated during the maturation process of tRNAs (tRNA-derived small RNAs, hereafter "tsRNAs") is dysregulated in cancer. Specifically, we uncovered tsRNA signatures in chronic lymphocytic leukemia and lung cancer and demonstrated that the ts-4521/3676 cluster (now called "ts-101" and "ts-53," respectively), ts-46, and ts-47 are down-regulated in these malignancies. Furthermore, we showed that tsRNAs are similar to Piwi-interacting RNAs (piRNAs) and demonstrated that ts-101 and ts-53 can associate with PiwiL2, a protein involved in the silencing of transposons. In this study, we extended our investigation on tsRNA signatures to samples collected from patients with colon, breast, or ovarian cancer and cell lines harboring specific oncogenic mutations and representing different stages of cancer progression. We detected tsRNA signatures in all patient samples and determined that tsRNA expression is altered upon oncogene activation and during cancer staging. In addition, we generated a knockedout cell model for ts-101 and ts-46 in HEK-293 cells and found significant differences in gene-expression patterns, with activation of genes involved in cell survival and down-regulation of genes involved in apoptosis and chromatin structure. Finally, we overexpressed ts-46 and ts-47 in two lung cancer cell lines and performed a clonogenic assay to examine their role in cell proliferation. We observed a strong inhibition of colony formation in cells overexpressing these tsRNAs compared with untreated cells, confirming that tsRNAs affect cell growth and survival.tsRNA | tRF | tDR | ncRNA | tRNA fragments

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Precursors of tRNAs are stabilized by methylguanosine cap structures

Cited by 58 publications

References 52 publications

Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA

Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications

tsRNA signatures in cancer

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