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| Status |
Public on Apr 20, 2021 |
| Title |
Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification [Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Transfer RNA (tRNA) molecules contain a variety of post-transcriptional modifications which are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation, to gene expression control and cellular stress response. Recent evidence show that tsRNAs are also modified, however the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. This modification is catalyzed by the tRNA methyltransferase TRMT2A, but its biological role remains largely unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification, resulting in angiogenin (ANG) dependent tsRNA formation. More specifically, m5U54 hypomodification is followed by ANG overexpression and tRNA cleavage near the anticodon, resulting in accumulation of 5’tRNA-derived stress-induced RNAs (5’tiRNAs), in particular 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tsRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tsRNA formation in mammalian cells. These results establish a link between tRNA demethylation and tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
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| Overall design |
Human tRF and tiRNAs were sequenced from HeLa cells transfected with a siCTRL (control condition) and HeLa cells transfected with siTRMT2A samples (tested condition). Three biological replicates were tested for each condition. For standard small RNA sequencing, the Illumina NextSeq instrument was used.Prior sequencing, between 1-2 ug of total RNA were purified from each sample. Integrity, quality and quantity of each RNA sample was checked using agarose gel electrophoresis and NanodropTM instrument. Since tRNA derived fragments (tRF & tiRNA) are heavily decorated by RNA modifications that interfere with small RNA-seq library construction, total RNA samples were pre treated with the following: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’adaptor ligation, 5’-OH (hydroxyl group) phosphorylationto 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Sequencing libraries were size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries were qualified and absolutely quantified using Agilent BioAnalyzer 2100. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type was 50bp singleread. Cytoplasmic tRNA sequences were downloaded from GtRNAdb. Mitochondrial tRNA sequences were predicted with tRNAscan-SE software. To generate the mature tRNA libraries, we removed the predicted intronic sequences (if present) and added an additional 3’-terminal “CCA” to each tRNA. To generate the precursor tRNA libraries, we included 40 nucleotides of flanking genomic sequence on either side of the original tRNA sequence.
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| Contributor(s) |
Pereira M, Soares AR |
| Citation(s) |
33799331 |
| Submission date |
Jan 07, 2021 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Ana Soares |
| E-mail(s) |
ana.r.soares@ua.pt
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| Organization name |
University of Aveiro
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| Street address |
Campus de Santiago
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| City |
Aveiro |
| ZIP/Postal code |
3810 |
| Country |
Portugal |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE164406 |
Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification |
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| Relations |
| BioProject |
PRJNA690556 |
| SRA |
SRP300795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164405_DOWN_siTRMT2A_vs_siCtrl.xlsx |
17.4 Kb |
(ftp)(http) |
XLSX |
| GSE164405_Expression.xlsx |
145.5 Kb |
(ftp)(http) |
XLSX |
| GSE164405_UP_siTRMT2A_vs_siCtrl.xlsx |
37.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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