Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA

ABSTRACT: Pseudouridine is considered as the most abundant modified nucleotides in RNA, playing an indispensable role in various life processes. The identification of pseudouridine sites provides the basis for the study of their function. Here, we proposed a new method for the identification of pseudouridine sites with a higher signal-to-noise ratio, combining CMC-specific labeling of pseudouridine sites and exonuclease-assisted strategy. We called this method exonuclease-assisted identification of pseudouridine sites (EAIPS).

ORGANISM(S): synthetic construct

PROVIDER: GSE229317 | GEO | 2024/11/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA

Project description:Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA

| PRJNA954003 | ENA

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA957458 | ENA

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA1108725 | ENA

A radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection

Project description:Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification. Various methods have been developed to achieve locus-specific Ψ detection; however, the existing methods often involve radiolabeling of RNA, require advanced experimental skills and can be time-consuming. Herein we report a radiolabeling-free，qPCR-based method to detect locus-specific Ψs in rRNA and mRNA. This method is based on Ψ chemical adduct (Ψ-CMC) induced mutation/deletion during reverse transcription (RT), leading to qPCR products of different melting temperatures. Utilizing high-throughput sequencing, we demonstrate that such misincorporation is a general feature of Ψ-CMC adduct during our improved RT conditions. We validated this method on known Ψ sites in rRNA and showed that the melting curves correlate with the modification level. Moreover, we successfully detected Ψs in mRNA and lncRNA of different abundance, and identified Ψ synthase that targets mRNA. Our facile method takes only 1.5 days to complete, and with slight adjustment it can be applied to detect other epitranscriptomic marks in the transcriptome.

2017-10-03 | GSE102476 | GEO

Pseudouridine profiling reveals widespread regulated mRNA pseudouridylation in yeast and human cells

Project description:We report the development of Pseudo-Seq, a sequencing based technique for identification of pseuoduridine (Î¨) modifications within RNA. We performed Pseudo-Seq on S. cerevisiae and HeLa cells and find the first evidence for pseusouridylation of endogenous mRNAs. RNA was treated with CMC to modify Î¨ residues, which cause RT stops. The sites of CMC-dependent RT stops were used to identify sites of pseudouridyation.

2014-09-05 | E-GEOD-58200 | biostudies-arrayexpress

Promoted Read-through and Mutation Against Pseudouridine-CMC By An Evolved Reverse Transcriptase

Project description:Pseudouridine (Y) is an abundant chemical modification that plays critical roles in cellular RNA metabolism and functions, and in RNA therapeutic applications. Transcriptome-wide mapping technologies present major advantages in discovering the functional contexts and crucial effector proteins of Y. Current mapping strategies for Ys are limited in identifying Ys at base-resolution within consecutive uridine sequence contexts where Y occurs frequently. Here we report “Mut-Y-seq” that utilities a recently evolved reverse transcriptase (“RT-1306”) coupled with the selective labeling of Y by the CMC treatment to identify Ys in mRNAs and non-coding RNAs from human cells. We showed that RT-1306 showed significantly promoted read-through and mutation signatures against the CMC-Y adduct; the mutation signatures generated by RT-1306 can discern the position of Y in consecutive uridine sequence contexts. We quantitatively characterized the Y-identification efficiencies by Mut-Y-seq under variable chemical treatment conditions by the receiver operating characteristic curve analysis and revealed the presence of potential false positive discoveries generated by side-reactions on unmodified uridines. Finally, the intersection of sites identified by orthogonal chemical treatments (i.e. CMC and bisulfite) produced a high-confidence list of Y sites in mRNAs and non-ribosomal long non-coding RNAs from HEK-293T cells. This report presents datasets for biological functional studies of endogenous Y sites, and sheds light on the combination of the reverse transcriptase engineering and selective chemical reactions for further expanding the toolkit for studying RNA chemical modifications.

2024-08-08 | GSE269406 | GEO

Bisulfite Incorporation Hindered Ligation-based Method for Locus-Specific Detection and Quantification of Pseudouridine

Project description:We applied BIHIND-seq to 15 sites of Hela 18S rRNA to probe Pseudouridine modification at the target sites and checked how pseudouridine level changed after DKC1 knockdown.

2024-11-01 | GSE269170 | GEO

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

Project description:Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of Ψ at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a Ψ-to-C transition. Compared to previous methods, BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS successfully detected all known Ψ sites in human rRNA and spliceosomal snRNAs and generated the first quantitative Ψ map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites and N1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant Ψ114 site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of Ψ in future studies.

2024-07-31 | GSE241849 | GEO

Detergents assisted glycoprotein capture

Project description:A detergents assisted glycoprotein capture method was developed to increase the coverage of N-glycoproteome of various samples.Application of this approach in the larger scale N-glycoproteomics analysis of the HEK 293 cell membrane led to the identification of 2253 unique N-glycosites from 953 proteins. Application of this approach to human serum resulted in the identification of 850 N-glycosylation sites without any immuno-depletion and fractionation.

2016-12-23 | PXD003485 | Pride

Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

Project description:To interrogate single-base resolution 6mA sites in the genome-wide, we develop DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an optimized sequencing method taking advantage of restriction enzyme DpnI, which exclusively cleaves methylated adenine sites. We find DpnI also recognizes other sequence motifs besides the canonical GATC restriction sites, largely expanding the application range of this method. DA-6mA-seq requires less starting material and lower sequencing depth than previous methods, but achieves higher sensitivity, providing a good strategy to identify 6mA in large genome with a low abundance of 6mA. We rebuild the 6mA maps of Chlamydomonas by DA-6mA-seq and then apply this method to another two eukaryotic organisms, Plasmodium and Penicillium. Further analysis reveals most 6mA sites are symmetric at various sequence contexts, suggesting 6mA may function as a new heritable epigenetic mark in eukaryotes. A new sequencing method is developed to detect 6mA in eukaryotes

2016-04-12 | E-GEOD-74430 | biostudies-arrayexpress

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