GEO DataSets

(Submitter supplied) Pseudouridine (Ψ), the isomer of uridine, is ubiquitous in most RNA families, including tRNA, rRNA and mRNA. Pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs, but whether it can modify other RNA types, including mRNA, remains elusive. Here, we determine the single particle cryo-EM structure of apo and tRNA-bound human PUS3, showing how it forms a symmetric homodimer that recognizes the characteristic L-shape of tRNA across two distinct interaction interfaces. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

36 Samples

Download data: TXT

(Submitter supplied) Pseudouridine (ψ) is the most common non-canonical ribonucleoside present on mammalian non-coding RNAs (ncRNAs), where is contributes ~10% of the total uridine level. However, ψ constitutes only ~0.3% of the uridines present on mRNAs and its effect on mRNA function remains unclear. Ψ residues have however been shown to inhibit the detection of exogenous RNA transcripts by host innate immune factors, thus raising the possibility that viruses might have subverted the addition of ψ residues to mRNAs by host pseudouridine synthase (PUS) enzymes as a way to inhibit antiviral responses in infected cells. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

19 Samples

Download data: BED

(Submitter supplied) Pseudouridine (Ψ) is the most abundant RNA modification, yet little is known about its content, dynamics and function in mRNA and ncRNA. Here, we perform quantitative MS analysis and develop CAP-seq for transcriptome-wide Ψ profiling. The unexpected high Ψ content (Ψ/U ratio: ~ 0.2% to 0.6%) indicates that pseudouridylation in mammalian mRNA is much more prevalent and comprehensive than previously believed. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL11154 GPL17021 GPL16791

34 Samples

Download data: TXT

(Submitter supplied) Using a technique based on the ability of CMC to specifically label pseudouridines and to stop reverse transcriptase, we provide a transcriptome-wide map of pseudouridylation in S. cerevisiae under log phase and heat shock conditions

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL9377

16 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Candida albicans; Homo sapiens; Saccharomyces cerevisiae; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

86 Samples

Download data: TXT

(Submitter supplied) We report the development of Pseudo-Seq, a sequencing based technique for identification of pseuoduridine (Ψ) modifications within RNA. We performed Pseudo-Seq on S. cerevisiae and HeLa cells and find the first evidence for pseusouridylation of endogenous mRNAs.

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL13821

109 Samples

Download data: TXT, WIG

(Submitter supplied) 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.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL11154

38 Samples

Download data: BW

(Submitter supplied) Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Dro­­­­sophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL22106

22 Samples

Download data: TXT

(Submitter supplied) We performed pseudouridine profiling (Pseudo-seq) on 11 biological replicates of chromatin-associated RNA. We performed mRNA-seq of PUS1 knockout, PUS7 knockdown, RPUSD4 knockdown and wildtype HepG2 cells. We used an in vitro pool based strategy to assign pre-mRNA targets to individual human pseudouridine synthases (PUS) .

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

60 Samples

Download data: CSV, FASTA, TXT

(Submitter supplied) Pseudouridylation (pseudouridine) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of pseudouridine remains poorly understood. Here, we show that a pseudouridine-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the pseudouridine ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15520 GPL18573

18 Samples

Download data: TXT

(Submitter supplied) Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

10 Samples

Download data: TXT

(Submitter supplied) Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT