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TRNA-overlapping long non-coding RNAs repress codon-biased genes in trans

ABSTRACT: tRNA-overlapping long non-coding RNAs repress codon-biased genes in trans

PROVIDER: PRJNA1143053 | ENA |

REPOSITORIES: ENA

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tRNA-overlapping long non-coding RNAs repress codon-biased genes in trans

Project description:The functions of most long non-coding RNAs (lncRNAs) are not known. Here, we define a group of ‘tRNA-Overlapping LncRNA’ (tROL) genes that are upregulated during in vitro cartilage development. Deletions of tROLs result in changes in the expression of codon-biased genes, where downregulated genes are enriched in codons corresponding to tRNAs overlapping disrupted tROLs. However, tROL lncRNA expression is controlled independently of the overlapping tRNA loci. Remarkably, tROL loci are located in gene-dense regions and interact extensively in trans between chromosomes, and tROL deletions result in the upregulation of significantly overlapping subsets of genes in the vicinity of tROL loci. Taken together, the results suggest that tROL loci coalesce and are dependent on each other’s transcription to repress surrounding genes in trans. Our investigation thus sheds light on a unique role for tROLs as a regulatory bridge between the non-coding and coding genomes.

2025-08-22 | GSE273784 | GEO

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming

Project description:Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming

| PRJNA955266 | ENA

A snoRNA–tRNA modification network governs codon-biased cellular states

Project description:A snoRNA–tRNA modification network governs codon-biased cellular states

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A snoRNA–tRNA modification network governs codon-biased cellular states [RMseq]

Project description:A snoRNA–tRNA modification network governs codon-biased cellular states [RMseq]

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A snoRNA–tRNA modification network governs codon-biased cellular states

Project description:The dynamic balance between tRNA supply and codon usage demand is a fundamental principle in the cellular translation economy. However, the regulation and functional consequences of this balance remain unclear. Here, we use PARIS2 interactome capture, structure modeling, conservation analysis, RNA–protein interaction analysis, and modification mapping to reveal the targets of hundreds of snoRNAs, many of which were previously considered orphans. We identify a snoRNA–tRNA interaction network that is required for global tRNA modifications, including 2′-O-methylation and others. Loss of Fibrillarin, the snoRNA-guided 2′-O-methyltransferase, induces global upregulation of tRNA fragments, a large group of regulatory RNAs. In particular, the snoRNAs D97/D133 guide the 2′-O-methylation of multiple tRNAs, especially for the amino acid methionine (Met), a protein-intrinsic antioxidant. Loss of D97/D133 snoRNAs in human HEK293 cells reduced target tRNA levels and induced codon adaptation of the transcriptome and translatome. Both D97/D133 single and double knockouts in HEK293 cells suppress Met-enriched proliferation-related gene expression programs, including, translation, splicing, and mitochondrial energy metabolism, and promote Met-depleted programs related to development, differentiation, and morphogenesis. In a mouse embryonic stem cell model of development, knockdown and knockout of D97/D133 promote differentiation to mesoderm and endoderm fates, such as cardiomyocytes, without compromising pluripotency, consistent with the enhanced development-related gene expression programs in human cells. This work solves a decade-old mystery about orphan snoRNAs and reveals a function of snoRNAs in controlling the codon-biased dichotomous cellular states of proliferation and development.

2023-09-21 | GSE234689 | GEO

A snoRNA–tRNA modification network governs codon-biased cellular states [RNAseq & Riboseq]

Project description:A snoRNA–tRNA modification network governs codon-biased cellular states [RNAseq & Riboseq]

| PRJNA982760 | ENA

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (Ribosome profiling)

Project description:Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (Ribosome profiling)

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Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (RNA-Seq)

Project description:Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (RNA-Seq)

| PRJNA955269 | ENA

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (tRNA-Seq)

Project description:Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (tRNA-Seq)

| PRJNA1026841 | ENA

A snoRNA–tRNA modification network governs codon-biased cellular states [PARIS2-seq]

Project description:A snoRNA–tRNA modification network governs codon-biased cellular states [PARIS2-seq]

| PRJNA982110 | ENA

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