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Elucidating the human tRNA transcriptome dependent upon the TRMT1 and TRMT1L paralogs for modification, stability, and function

ABSTRACT: Elucidating the human tRNA transcriptome dependent upon the TRMT1 and TRMT1L paralogs for modification, stability, and function

PROVIDER: PRJNA1098624 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28610326.fastq.gz	Fastqsanger.gz
	SRR28610327.fastq.gz	Fastqsanger.gz
	SRR28610328.fastq.gz	Fastqsanger.gz
	SRR28610329.fastq.gz	Fastqsanger.gz
	SRR28610330.fastq.gz	Fastqsanger.gz

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Similar Datasets

Elucidating the human tRNA transcriptome dependent upon the TRMT1 and TRMT1L paralogs for modification, stability, and function

Project description:The tRNA methyltransferase 1 (TRMT1) enzyme catalyzes the formation of dimethylguanosine (m2,2G) in tRNAs. Loss-of-function mutations in TRMT1 lead to intellectual disability disorders in humans. In addition to TRMT1, vertebrates encode a tRNA methyltransferase 1-like (TRMT1L) paralog. Here, we use a comprehensive tRNA sequencing approach to decipher the landscape of tRNAs that are modified by human TRMT1 and TRMT1L. We find that TRMT1 modifies a single position in more than half of all cytoplasmic tRNAs and a subset of mitochondrial tRNAs. Notably, TRMT1 and TRMT1L catalyze m2,2G formation at distinct positions in tyrosine tRNAs that are each required for the efficient installation of additional modifications. Moreover, we identify a role for m2,2G modification in the stability of tyrosine and serine tRNAs that is abrogated in human patient cells homozygous for pathogenic TRMT1 variants. Human cells deficient in TRMT1 and/or TRMT1L exhibit reduced translation of specific codons, indicating that m2,2G modifications are necessary for maintaining functional levels of certain tRNAs. These findings uncover key roles for the m2,2G modification, and pinpoint tRNAs that are dysregulated in neurodevelopmental disorders caused by tRNA modification deficiency.

2024-08-09 | GSE263642 | GEO

TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [Nano-tRNAseq]

Project description:Mapping of the epitranscriptome has revealed the chemical diversity of RNA modifications and their functional importance in regulating gene expression. Transfer RNAs (tRNAs) are one of the most modified cellular RNAs, containing on average 10-13 modifications per molecule. These modifications have been shown to be critical for several aspects of tRNA functions, such as decoding, folding, and stability. Here we report that the human RNA methyltransferase TRMT1L associates with components of the Rix1 ribosome biogenesis complex and co-sediments with pre-60S ribosomes. Using eCLIP-Seq, we show that TRMT1L binds to a subset of tRNAs and to the 28S rRNA. Additionally, we demonstrate that TRMT1L is responsible for catalyzing N2, N2-dimethylguanosine (m22G) solely at position 27 of tRNA-Tyr-GUA by Nano-tRNAseq and RNA LC-MS. Surprisingly, TRMT1L depletion also impaired the deposition of acp3U and dihydrouridine on tRNA-Tyr-GUA, Cys-GCA, and Ala-CGC. TRMT1L knockout cells have a marked decrease in tRNA-Tyr-GUA levels, coinciding with a reduction in global translation rates and hypersensitivity of oxidative stress. Our results establish TRMT1L as the elusive methyltransferase catalyzing the m22G27 modification on tRNA Tyr, resolving a long-standing gap of knowledge and highlighting its potential role in a tRNA modification circuit crucial for translation regulation and stress response.

2024-05-08 | GSE266588 | GEO

TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [eCLIP-seq]

2024-05-08 | GSE266587 | GEO

small RNA sequencing analysis of TRMT1L KO vs WT brain

Project description:TRMT1L is a paralog of the tRNA m22G-methyltransferase TRMT1 and, similarly to TRMT1, it is involved in cognitive functioning. To functionally dissect the biological role of TRMT1L, here we have employed a combined strategy of LC-MS/MS and next-generation sequencing of both long and short RNAs, to compare the levels and locations of m2,2G in brain tissues from TRMT1L knock-out mice, relative to wild-type.

2021-02-08 | GSE152429 | GEO

long RNA sequencing analysis of TRMT1L KO vs WT brain

2021-02-08 | GSE156858 | GEO

Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs.

Project description:The tRNA methyltransferase 1 (TRMT1) enzyme catalyzes the N2,N2-dimethylguanosine (m2,2G) modification in tRNAs. Intriguingly, vertebrates encode an additional tRNA methyltransferase 1-like (TRMT1L) paralog. Here, we use a comprehensive tRNA sequencing approach to decipher targets of human TRMT1 and TRMT1L. We find that TRMT1 methylates all known tRNAs containing guanosine at position 26, while TRMT1L represents the elusive enzyme catalyzing m2,2G at position 27 in tyrosine tRNAs. Surprisingly, TRMT1L is also necessary for maintaining 3-(3-amino-3-carboxypropyl)uridine (acp3U) modifications in a subset of tRNAs through a process that can be uncoupled from methyltransferase activity. We also demonstrate that tyrosine and serine tRNAs are dependent upon m2,2G modifications for their stability and function in translation. Notably, human patient cells with disease-associated TRMT1 variants exhibit reduced levels of tyrosine and serine tRNAs. These findings uncover unexpected roles for TRMT1 paralogs, decipher functions for m2,2G modifications, and pinpoint tRNAs dysregulated in human disorders caused by tRNA modification deficiency.

| S-EPMC11831618 | biostudies-literature

Impact of tRNA-Glu(UUC) and tRNA-Arg(CCG) on mRNA stability

Project description:Stable expression of tRNA-Glu(UUC) and tRNA-Arg(CCG) followed by whole-genome transcript stability measurements using a-amanitin mediated inhibition of RNA Pol II.

2016-06-07 | GSE77349 | GEO

The thiolation modification of tRNA is essential for plant immunity

Project description:Plants have evolved sophisticated mechanisms to regulate gene expression to activate immune responses against pathogen infections. However, how the translation system contributes to plant immunity is largely unknown. The evolutionarily conserved thiolation modification of tRNA ensures efficient decoding during translation. Here we show that tRNA thiolation is required for plant immunity in Arabidopsis. The Arabidopsis cgb mutant is hyper-susceptible to the pathogen Pseudomonas syringae. CGB encodes ROL5, a homolog of yeast NCS6 required for tRNA thiolation. ROL5 physically interacts with CTU2, a homolog of yeast NCS2. Mutations in either ROL5 or CTU2 result in loss of tRNA thiolation. Further analyses reveal that tRNA thiolation is required for both transcriptional reprogramming and translational reprogramming during immune responses. The translation efficiency of immune-related proteins reduces when tRNA thiolation is absent. Our study not only uncovers a new biological function of tRNA thiolation but also reveals a new mechanism for plant immunity.

2022-08-31 | GSE183087 | GEO

TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [Nano-tRNAseq]

Project description:TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [Nano-tRNAseq]

| PRJNA1107681 | ENA

TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [eCLIP-seq]

Project description:TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [eCLIP-seq]

| PRJNA1107680 | ENA

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