Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unveiling the Clinical Significance of RNA Pseudouridylation in Colorectal Cancer

ABSTRACT: Colorectal cancer is a common malignant tumor worldwide, and its morbidity and mortality are increasing year by year. RNA pseudouracil modified synthetase is closely related to the development of colorectal cancer, but the whole transcriptomic level of pseudouridine（ψ） in colorectal cancer has not been fully explored. This study examined the extent of RNA ψ modification in 21 pairs of colorectal cancer tissues and adjacent normal tissues, as well as 10 blood samples from patients, utilizing RNA ψ modification sequencing technology. These findings underscore the significance of RNA ψ modification events in colorectal cancer and offer insights into its application for clinical detection and treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE272345 | GEO | 2025/07/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Bacterial mRNA pseudouridylation by RluA [pseudoseq]

Project description:Pseudouridine (Ψ) is an ubiquitous RNA modification, present in the tRNAs and rRNAs of species across all domains of life. Conserved pseudouridine synthases modify the mRNAs of diverse eukaryotes, but the modification has yet to be identified in bacterial mRNAs. Here, we report the discovery of pseudouridines in mRNA from E. coli. By testing the mRNA modification capacity of all 11 known pseudouridine synthases, we identify RluA as the predominant mRNA-modifying enzyme, modifying the majority of high-confidence sites.

2024-08-10 | GSE243800 | GEO

Bacterial mRNA pseudouridylation by RluA [Rend-seq]

2024-08-10 | GSE243807 | GEO

Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridylation of mRNA

Project description:Pseudouridine is the most abundant modification occurring on RNA, yet with the exception of a few well-studied RNA molecules little is known about the modified positions and their function(s). Here, we develop Ψ-seq, a method for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with synthetic spike-ins and de novo identification of the vast majority of previously reported pseudouridylated positions. Ψ-seq permits discovery of hundreds of novel pseudouridine modifications in human and yeast mRNAs and snoRNAs. Knockdown and knockout of pseudouridine synthases uncovers the cognate PUSs mediating pseudouridine catalysis at these individual novel sites and their target sequence features. In both human and yeast pseudouridine formation on mRNA depends on both site-specific PUSs – often guided by a specific sequence motif - and snoRNA-guided PUSs. Importantly, upon heat shock in yeast, Pus7-mediated pseudouridylation is induced at >200 sites in diverse mRNAs. Pus7 deletion in yeast leads to decreased recovery from heat shock and decreased RNA levels at otherwise pseudouridylated messages, suggesting a role for pseudouridine in enhancing transcript stability. Pseudouridine stoichiometries in rRNA are highly conserved from yeast to mammals, but are reduced in cells derived from dyskeratosis congenita patients, where the pseudouridine synthase DKC1 is mutated, compared to age matched controls. Our results establish pseudouridine as a ubiquitous and dynamic modification in mRNA, and provide a sensitive, quantitative and transcriptome-wide methodology to address its underlying mechanisms and function.

2014-09-11 | GSE60047 | GEO

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

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 | GSE262373 | GEO

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

2025-01-15 | GSE262376 | GEO

Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (Arabidopsis)

2025-01-15 | GSE262375 | GEO

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

2025-01-15 | GSE262374 | GEO

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

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

edu-Ψ-seq Reveals snoRNA-guided mRNA Pseudouridylation that Regulates Protein Synthesis

Project description:Purpose:Pseudouridine (Ψ) is the most abundant RNA epigenetic modification and plays vital roles in various biological processes. However, its biogenesis and functions in mRNAs remain elusive. Method:Here, we developed an approach for enriching Ψ sites with deep sequencing (edu-Ψ-seq), which utilizes both exoribonuclease and restriction endonuclease activity to eliminate other nucleosides or reads without Ψ modifications. Results:Using edu-Ψ-seq approach in the dyskerin pseudouridine synthase 1 (DKC1) knockdown cells, we identified that more than 100 pseudouridines could be catalyzed by DKC1 in human mRNAs and non-coding RNAs (ncRNAs). Surprisingly, we discovered, for the first time, 10 pseudouridines in mRNAs might be guided by 11 small nucleolar ncRNAs (snoRNAs). Interestingly, we found that SNORA10 could guide DKC1 protein to induce the pseudouridylation of RPL15 mRNA. Importantly, loss of SNORA10 impaired the protein synthesis of RPL15 and inhibited cell proliferation. Conclusion:Overall, our study not only developed a powerful method for detecting Ψ sites but also uncovered another layer of gene expression regulation that involves crosstalk among snoRNAs, mRNA pseudouridylation and protein synthesis.

2024-10-18 | GSE190820 | 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