Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA<sup>Met</sup>(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Vitali, Patrice; Kiss, Tamás

doi:10.1101/gad.326363.119

Cited by 88 publications

(88 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…By analyzing different mutants from distinct pathways we will be able to increase our knowledge on tRFs biogenesis pathway and the interactions between these different mechanisms. For example, it has been recently shown that snoRNAs association with fibrillarin can cause tRNA-CAT 2'-O-methylation at position 34 in mammalian cells, similarly to CG7009 (Vitali and Kiss, 2019). Conversely, tRNA methylation could have an impact on snoRNAs biogenesis as observed in this study.…”

Section: Discussionsupporting

confidence: 65%

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

Mollà-Herman¹,

Angelova²,

Carré³

et al. 2019

Preprint

View full text Add to dashboard Cite

tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline to study tRFs populations and shed light onto tRNA fragments biogenesis. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant Drosophila ovaries affecting two different highly conserved steps of tRNA biogenesis: 5'pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2'-O-methylation (CG7009 and CG5220). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology. MATERIALS AND METHODS Fly stocksFly stocks are described in (Molla-Herman et al., 2015;M. Angelova, 2019). RNA extraction from ovariesRNA was extracted from Drosophila ovaries following standard methods detailed in (Molla-Herman et al., 2015;M. Angelova, 2019). Small RNA sequencingRNA samples of 3-5 µg were used for High-throughput sequencing using Illumina HiSeq, 10% single-reads lane 1×50 bp. (Fasteris). 15-29 nt RNAs sequences excluding rRNA (riboZero) were sequenced. All the analyses were performed with Galaxy tools https://mississippi.snv.jussieu.fr. Data set deposition is described in (Molla-Herman et al., 2015;M. Angelova, 2019). European Nucleotide Archive (ENA) of the EMBL-EBI (http://www.ebi.ac.uk/ena), accession numbers: PRJEB10569 (Rpp30 mutants), PRJEB35301 and PRJEB35713 (Nm mutants). Clipping and concatenationRaw data were used for clipping the adaptors [Clip adapter (Galaxy-Version 2.3.0, owner: artbio)] and FASTQ quality control was performed (FastQC Read Quality reports (Galaxy-Version 0.72)). Since replicates were homogeneous in quality and analysis (replicates for CG7009* heterozygous and homozygous, triplicates for CG7009*-CG5220* double mutants) we merged them [Concatenate multiple datasets tailto-head (Galaxy-Version 1.4.1, owner: artbio) to have single fasta files. CG7009*/Def9487 was used to obtain normalization numbers but is not shown in the figures. Data normalization using DeSeq miRNA countsData were normalized with bank Size Factors (SF) obtained by using [DESeq geometrical normalization (Galaxy-Version 1.0.1, owner: artbio)] with miRNA counts obtained using [miRcounts (Galaxy-Version 1.3.2)], allowing 0 mismatch (MM). Then, 1/SF values were used in Galaxy small RNA maps (Sup. Fig. 5). Data normalization with DeSeq using ...

show abstract

Section: Discussionsupporting

confidence: 65%

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

Mollà-Herman¹,

Angelova²,

Carré³

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Transfer RNA fragmentation is a conserved response to various stress conditions with functions ranging from protein synthesis, to apoptosis and the modulation of small non-coding RNA pathways (64)(65)(66)(67) . The influence of internal Nm modifications on tRNA stability has only been described very recently (9) . In support of the notion that Nm in tRNAs modulates their stability, we found that Nm 34 is protective against tRNA fragmentation in the ACL.…”

Section: Nm Limits Endonucleolytic Cleavage Of Trna Phementioning

confidence: 99%

“…Interestingly, it was proposed that tRNA fragments could affect small RNA silencing pathways through binding to Dicer and Argonaute proteins thereby reducing their activity (59) . In addition, during the preparation of this manuscript, a study showed that Nm 34 protected tRNA Met(CAT) from endonucleolytic cleavage by stress-induced angiogenin in human cell (9) .…”

Section: Nm Limits Endonucleolytic Cleavage Of Trna Phementioning

confidence: 99%

“…In contrast, most of the Nm deposition occurring in eukaryotic tRNAs are mediated by stand-alone proteins without the need for guidance by small RNAs. However, recently it was reported that one snoRNA and one scaRNA can guide Nm deposition to tRNA Met in mammalian cells (9) . Importantly, Nm deposition was also reported at 3'-terminal nucleotides in small non-coding RNAs (sncRNAs) such as microRNAs (miRNAs) and small-interfering RNAs (siRNAs) in plants (10)(11)(12) , in Argonaute-2 (Ago2) loaded siRNAs and miRNAs in flies and in PIWI-interacting RNAs (piRNAs) in animals (13)(14)(15) .…”

Section: Introductionmentioning

confidence: 99%

“…Nm can affect RNAs in multiple ways as it increases hydrophobicity, protects RNAs from nuclease degradation (9,15,18) , stabilizes helical structures or modulates interactions with proteins or other RNAs (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) . 2 The majority of all tRNA modifications are deposited at the wobble position N 34 in the anticodon loop (ACL), and at the anticodon-adjacent position N 37 .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

tRNA 2’-O-methylation modulates small RNA silencing and life span in Drosophila

Angelova

Dimitrova

Silva

et al. 2019

Preprint

View full text Add to dashboard Cite

2'-O-methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two novel Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1, respectively. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNA Phe , tRNA Trp and tRNA Leu , while subsequently, CG5220 methylates position C32 in the same tRNAs and targets also additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as life span reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalysing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

show abstract

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Yang

Sun

Zhao

et al. 2023

Clinical and Translational Dis

View full text Add to dashboard Cite

Transfer RNA‐derived small RNAs (tsRNAs) are fragments that originate from mature or precursor tRNAs and are a subclass of sRNAs. With the development of high‐throughput sequencing techniques, the real feature of tsRNAs has gradually been revealed. tsRNAs are functional fragments of distinct lengths produced by the cleavage of mature or precursor tRNAs by different ribonuclease enzymes. tsRNAs exert extensive functions, including gene silencing, translational regulation, and reverse transcriptional regulation, affecting cell viability and differentiation and participating in pathological processes of various diseases, including central nervous system (CNS) diseases. Emerging sequencing evidence indicates that tsRNAs are expressed differently in various CNS diseases, preliminary suggesting that tsRNAs are involved in the occurrence and progression of neurodegenerative diseases, stroke, glioma, epilepsy, and other CNS diseases. In addition, significant differences expression of extracellular tsRNAs in circulating or cerebrospinal fluid between patients and normal individuals have demonstrated the diagnostic and prognostic value of tsRNAs as biomarkers for liquid biopsy. In this review, we provide a detailed summary of the biogenesis, function, and chemical modification of tsRNAs, focusing on the current status and prospects of research on tsRNAs in neurodegenerative diseases, stroke, glioma, epilepsy, and others.

show abstract

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Cited by 88 publications

References 36 publications

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

tRNA 2’-O-methylation modulates small RNA silencing and life span in Drosophila

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Contact Info

Product

Resources

About

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNAMet(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Cited by 88 publications

References 36 publications

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

tRNA 2’-O-methylation modulates small RNA silencing and life span in Drosophila

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Contact Info

Product

Resources

About

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP