Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10038430_1.fastq.gz | Fastqsanger.gz | |||
| ERR10038430_2.fastq.gz | Fastqsanger.gz | |||
| ERR10033482.fastq.gz | Fastqsanger.gz | |||
| ERR10890701_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Acronicta psi genome assembly, ilAcrPsix1, alternate haplotype
| PRJEB55459 | ENA
Project description: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. Here, we describe and validate a novel antibody-based ψ mapping technique called photo-crosslinking assisted ψ sequencing (PA-ψ-seq) and then use it to map ψ residues on not only multiple cellular RNAs but also the mRNAs and genomic RNA encoded by HIV-1. We also describe several 293T-derived cell lines in which human PUS enzymes previously reported to add ψ residues to mRNAs, specifically PUS1, PUS7 and TRUB1/PUS4, were individually inactivated by gene editing. Surprisingly, while this allowed us to assign several sites of ψ addition on cellular mRNAs to each of these three PUS enzymes, the ψ sites present on HIV-1 transcripts remained unaffected. However, loss of PUS1 function did significantly reduce HIV-1 gene expression by a presumably indirect mechanism.
2021-09-01 | GSE172136 | GEO
Project description:Prions are infectious proteins that can adopt a structural conformation different from that of the normal protein. This change of conformation is then propagated among other molecules of the same protein. Prions are associated with neurodegenerative diseases in mammals, but are also found in fungi (in the yeast Saccharomyces cerevisiae and the filamentous fungus Podospora anserina), in which they control heritable traits. They are widespread in wild yeast strains, suggesting a biologically important role. [PSI+] is one of the most widely studied yeast prions. It corresponds to an aggregated conformation of the translational release factor, eRF3, which suppresses nonsense codons. [PSI+] modifies cellular fitness, inducing various phenotypes, depending on the genetic background. However, the genes displaying [PSI+]-controlled expression remain largely unknown. We used the recently described ribosome profiling approach to identify genes displaying changes in expression in the presence of [PSI+]. This made it possible to determine the positions of all active ribosomes within the genome, in both [PSI+] and [PSI-] isogenic strains. Comparisons of the translatomes and transcriptomes of the two strains revealed that the primary effect of [PSI+] was to repress genes involved in the stress response. Thus, we provide the first description of the global translational effect of [PSI+] and a new genetic explanation of the phenotypic differences between [PSI-] and [PSI+] strains under stress conditions.
2014-07-18 | GSE41590 | GEO
Project description: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. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translational regulation leading to high protein biosynthesis and abnormal germ layer specification. Dysregulation of PUS7 and tRFs in myeloid malignancies associates with altered translation rates, suggesting a role of Ψ in tumorigenesis. Our findings unveil a critical function of Ψ in directing translational control in stem cells with promisingly broad implications for human disease.
2018-04-22 | GSE101004 | GEO
Project description: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. In concordance, CAP-seq identified 2,084 Ψ sites within 1,929 human transcripts. We prove four previously unknown Ψ sites in rRNA and EEF1A1 mRNA. Genetic and biochemical analysis uncover PUS1 as a major human mRNA Ψ synthase. In response to stimuli, Ψ level and sites are dynamically modulated in stimulus-specific manners. Comparisons between human and mouse pseudouridylation reveal conserved and unique sites across tissue and species. We observe stop codon pseudouridylation and readthrough events simultaneously for HSPB1 mRNA, indicating a role in nonsense suppression. Together, these approaches allow in-depth analysis of transcriptome-wide pseudouridylation events and our comprehensive study provides a resource for functional studies of Ψ-mediated epigenetic regulation. Here we report a transcriptome-wide profiling method that utilizes a chemically synthesized N3-CMC, which pre-enriches the Ψ-containing RNAs and blocks the reverse transcription.Mapping the Ψ sites in human transcriptome was performed using HEK293T and PUS1 dependent Ψ sites were identified by comparing PUS1 knock out cells with wildtype cells. Stress inducible or suppressed Ψ sites were identified by comparing stress treated cells with untreated cells. And mouse brain and liver were used to map Ψ sites in mouse transcriptome.
2015-06-05 | E-GEOD-63655 | biostudies-arrayexpress