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In vivo structure profiling reveals human tRNA structurome and interactions in response to stress

ABSTRACT: In vivo structure profiling reveals human tRNA structurome and interactions in response to stress

PROVIDER: PRJNA1094587 | ENA |

REPOSITORIES: ENA

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In vivo structure profiling reveals human tRNA structurome and interactions in response to stress

Project description:Transfer RNAs (tRNAs) are the most abundant RNA family in copy numbers in a cell. It not only folds into defined structures, but also has complex interaction networks in cells involving aminoacyl-tRNA synthetases, translation factors, and ribosomes. The human tRNAome is comprised of chromosomal-encoded tRNAs with a large sequence diversity, and mitochondrial-encoded tRNAs that have A/U-rich sequences and many with non-canonical tertiary interactions. How tRNA folding and interaction in a eukaryotic cell respond to stress is poorly understood. Here, we develop DM-DMS-MaPseq, which utilizes in vivo dimethyl-sulfate (DMS) chemical probing and mutational profiling (MaP) coupled with demethylase (DM) treatment in transcriptome-wide tRNA sequencing to profile tRNA structures and their cellular interactions for human chromosomal and mitochondrial-encoded tRNAs. We found that tRNAs maintain stable structures in vivo, but the in vivo DMS profiles are vastly different from in vitro, which can be explained by their interactions with cellular proteins and the ribosome. We also identify tRNA structure and interaction changes upon arsenite treatment, an oxidative stress that induces translational reprogramming, that are consistent with enhancing reductions of translation. Our results reveal variations of tRNA structurome and dynamic interactome that have functional consequences in translational regulation.

2025-03-29 | GSE262888 | GEO

Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

Project description:We employed Structure-seq2 method to probe RNA structure genome-wide in Arabidopsis shoot and root tissue separately and investigate the effect of salt stress on the RNA structurome in vivo.

2020-01-29 | GSE124866 | GEO

Rice RNA secondary structurome under heat stress

Project description:We used the Structure-seq2 protocol and applied it to 14-day-old rice (Oryza sativa) shoot tissue for genome-wide RNA structure probing to investigate the effect of heat stress on the RNA structurome.

2018-11-12 | GSE100714 | GEO

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

Project description:Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown in the presence and absence of amino acids. We show that the change in global RNA structurome is inversely proportional to the change in abundance upon amino acid starvation and that this trend is pronounced in the stringent response and codY regulons. We also use this data to characterize known and novel RNA switches.

2020-07-24 | GSE148936 | GEO

In vivo nuclear RNA structurome reveals the RNA-structure regulation of mRNA processing in plants

Project description:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites such as splice sites and polyadenylation sites when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. Here, we performed in vivo SHAPE chemical profiling on Arabidopsis nuclear RNAs and generated the in vivo nuclear RNA structure landscape. We found that nuclear mRNAs fold differently from cytosolic mRNAs. Notably, we discovered a two-nucleotide single-stranded RNA structure feature upstream of 5’ splice site that regulates splicing and is responsible for the selection of alternative 5’ splice sites. Moreover, we found branch point single-strandedness is associated with 3’ splice site recognition. We also identified an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. Our work demonstrates an RNA structure regulatory mechanism for mRNA processing.

2020-12-10 | GSE135711 | GEO

Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.

Project description:tRNA genes are believed to form clusters in three-dimensional space in smaller eukaryotes (yeasts). In the course of investigating a cluster of tRNA genes for insulator activity in humans, we addressed whether these tRNA genes clustered with other tRNA genes. We used an anchor point to generate 4C material from a tRNA cluster located on chromosome 17 (hg18 7.962400 MB). We identify interactions occurring within the 300kb region of this point, but only extending in one direction and suggesting these interactions occur between this tRNA cluster and other tRNA gene clusters from this locus. We did not observed any specific interactions outside of this region or on other chromsomes, perhaps due to an low number of mappable reads from our samples. Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.

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tRNA structure-seq in peptide-rich droplets

Project description:tRNA structure-seq in peptide-rich droplets

| PRJNA937237 | ENA

tRNA structure-seq in peptide-rich droplets

Project description:Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology, and has been proposed as a prebiotically-plausible way to accumulate RNA. Compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Transfer RNAs are essential for protein synthesis and predate the last universal common ancestor (LUCA) of all organisms, making them relevant to both extant and ancient biology. Since tRNAs are the most heavily modified RNAs known, with modifications crucial to RNA structure, function, and gene regulation, we also compared unmodified and naturally-modified tRNAs. We elucidate the effects of Mg2+ concentration, polyion charge ratio, and polyion length on tRNA structures. The approach herein, which can be applied to study other RNAs in diverse condensates, reveals that RNA can achieve native tertiary structure in a robust fashion in membraneless compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that modifications could have played a critical role in metabolic processes at the origin of life.

2023-09-27 | GSE225730 | GEO

Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.

2011-10-10 | GSE31105 | GEO

Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

Project description:Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

| PRJNA514040 | ENA