Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in soybean

ABSTRACT: Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ has been hindered by the lack of robust methods to profile Ψ and comprehensive Ψ maps. In this study, we utilize BID-seq, a newly developed Ψ sequencing method, to generate transcriptome-wide Ψ maps at single-base resolution across various plant species and tissues

ORGANISM(S): Glycine max

PROVIDER: GSE262373 | GEO | 2025/01/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in rice

Project description:Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ has been hindered by the lack of robust methods to profile Ψ and comprehensive Ψ maps. In this study, we utilize BID-seq, a newly developed Ψ sequencing method, to generate transcriptome-wide Ψ maps at single-base resolution across various plant species and tissues

2025-01-15 | GSE262374 | GEO

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis

2025-01-15 | GSE262375 | GEO

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in maize

2025-01-15 | GSE262376 | GEO

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis total RNA [BID-seq]

2025-01-15 | GSE277198 | GEO

BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution

Project description:Pseudouridine (Ψ) is an abundant RNA modification that is present in and impacts the functions of diverse non-coding RNA species, including rRNA, tRNA, snRNA, etc. Pseudouridine also exists in mammalian mRNA and likely exhibits functional roles; however, functional investigations of pseudouridine in mammalian mRNA have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed Bisulfite-Induced Deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol to generate highly reproducible results, displaying nearly zero background deletions at unmodified uridines after bisulfite treatment and uncovering 8,407 Ψ sites starting from as little as 10 ng mouse embryonic stem cell (mESC) polyA+ RNA, with the steps that are fast in both library preparation and data analysis. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS), and data analysis. The library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe (https://github.com/y9c/pseudoU-BIDseq), a user-friendly data analysis pipeline for BID-seq, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from NGS data.

2023-08-07 | GSE238245 | GEO

Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution

Project description:Functional characterization of pseudouridine (Ψ) in mammalian messenger RNA (mRNA) has been hampered by the lack of a quantitative method that maps pseudouridine in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq) that utilizes a bisulfite-mediated reaction to stoichiometrically convert pseudouridine into deletion upon reverse transcription. BID-seq enabled detection of abundant pseudouridine sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncovered consensus sequences for pseudouridine in mammalian mRNA and assigned different ‘writer’ proteins to individual pseudouridine deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detected presence of Ψ within stop codons of mammalian mRNA, and confirmed the role of Ψ in promoting stop codon read-through in vivo. This new method for sensitive and comprehensive detection of Ψ sets the stage for future investigations of the roles of Ψ in diverse biological processes.

2022-09-05 | GSE179798 | GEO

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in soybean

Project description:Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in soybean

| PRJNA1091613 | ENA

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis total RNA [BID-seq]

Project description:Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis total RNA [BID-seq]

| PRJNA1161168 | ENA

Site specific pseudouridine (Psi) on Leishmania rRNA regulates translation of subset of proteins

Project description:Leishmania are unicellular parasites that cycle between the insect and mammalian host and is the causative agent of Leishmaniasis. Previous studies from our lab suggested that individual rRNA modification such as pseudouridine (Psi) and 2-O-methylation are developmentally regulated during the complex life cycle of these parasites. Ablation of a single snoRNA guiding Psi in the inter-subunit bridge, helix69 of the ribosome affects its affinity to translate specific mRNA. Mutational analysis in the pseudouridylation pocket of this snoRNA supports the notion that the guided modification and not the chaperone activity, is essential for the observed phenotype. Structural studies using CryoEM suggested that a single Psi modification can affect the rRNA structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.

2024-05-09 | PXD034116 | Pride

Quantitative profiling of pseudouridylation landscape in the human transcriptome

Project description:Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, transcriptome-wide measurement of individual Ψ sites remains unaddressed. Here, we develop “PRAISE”, via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional RNA/DNA bisulfite treatment, our approach is based on quaternary base mapping and identifies 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1. In addition, we identified known and novel Ψ sites in mitochondrial mRNA, which are catalyzed by a mitochondria-localized isoform of PUS1. Collectively, we provide a reliable, sensitive and convenient method to quantify transcriptome-wide Ψ; we envision this approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.

2023-02-06 | GSE212210 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data