Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing
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ABSTRACT:
PROVIDER: PRJNA509379 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16967339_1.fastq.gz | Fastqsanger.gz | |||
| SRR16967339_2.fastq.gz | Fastqsanger.gz | |||
| SRR16967340_1.fastq.gz | Fastqsanger.gz | |||
| SRR16967340_2.fastq.gz | Fastqsanger.gz | |||
| SRR16967341_1.fastq.gz | Fastqsanger.gz |
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Project description: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) .
2022-02-15 | GSE123613 | GEO
Project description:Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.
| S-EPMC8859966 | biostudies-literature
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 | GSE243807 | GEO
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
Project description:We developed a novel technique, called pseudouridine site identification sequencing (PSI-seq), for the transcriptome-wide mapping of pseudouridylation sites with single-base resolution from cellular RNAs based on the induced termination of reverse transcription specifically at pseudouridines following CMCT treatment. PSI-seq analysis of RNA samples from S. cerevisiae correctly detected all of the 43 known pseudouridines in yeast 18S and 25S ribosomal RNA with high specificity. Moreover, application of PSI-seq to the yeast transcriptome revealed the presence of site-specific pseudouridylation within dozens of mRNAs, including RPL11a, TEF1, and other genes implicated in translation. To identify the mechanisms responsible for mRNA pseudouridylation, we genetically deleted candidate pseudouridine synthase (Pus) enzymes and reconstituted their activities in vitro. These experiments demonstrated that the Pus1 enzyme was necessary and sufficient for pseudouridylation of RPL11a mRNA, whereas Pus4 modified TEF1 mRNA, and Pus6 pseudouridylated KAR2 mRNA. Finally, we determined that modification of RPL11a at Ψ -68 was observed in RNA from the related yeast S. mikitae, and Ψ -239 in TEF1 mRNA was maintained in S. mikitae as well as S. pombe, indicating that these pseudouridylations are ancient, evolutionarily conserved RNA modifications. This work establishes that site-specific pseudouridylation of eukaryotic mRNAs is a genetically programmed RNA modification that naturally occurs in multiple yeast transcripts via distinct mechanisms, suggesting that mRNA pseudouridylation may provide an important novel regulatory function. The approach and strategies that we report here should be generally applicable to the discovery of pseudouridylation, or other RNA modifications, in diverse biological contexts.
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Project description:Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage. However, the molecular mechanism behind it remains not fully understood. In this study, we evaluated the expression of 5 pseudouridine (Ψ) synthases between young and aged HSCs, and observed that three of them are increased during aging. Functional evaluation assay reveals that enforced PUS10 and PUS7 recapitulate the phenotype aged HSCs. The increase of PUS10 in aged HSCs is due to aging-declined CRL4DCAF1-mediated ubiquitination degradation signaling. Mechanistically, the destructive role of enforced PUS10 on HSCs is not achieved by its Ψ synthases activity, but through miR139, dysfunction of which impairs the reconstitution capacity of HSCs. Consistently, we observed no difference of tRNA pseudouridylation profile between young and aged HSPCs, while enforced PUS10 alters the microRNA profile in HSCs. Targeted dysfunction of Pus10 results in compromises the self-renewal capacity of HSC.
2023-05-13 | GSE213419 | GEO
Project description:Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage. However, the molecular mechanism behind it remains not fully understood. In this study, we evaluated the expression of 5 pseudouridine (Ψ) synthases between young and aged HSCs, and observed that three of them are increased during aging. Functional evaluation assay reveals that enforced PUS10 and PUS7 recapitulate the phenotype aged HSCs. The increase of PUS10 in aged HSCs is due to aging-declined CRL4DCAF1-mediated ubiquitination degradation signaling. Mechanistically, the destructive role of enforced PUS10 on HSCs is not achieved by its Ψ synthases activity, but through miR139, dysfunction of which impairs the reconstitution capacity of HSCs. Consistently, we observed no difference of tRNA pseudouridylation profile between young and aged HSPCs, while enforced PUS10 alters the microRNA profile in HSCs. Targeted dysfunction of Pus10 results in compromises the self-renewal capacity of HSC.
2023-05-13 | GSE213421 | GEO
Project description:Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage. However, the molecular mechanism behind it remains not fully understood. In this study, we evaluated the expression of 5 pseudouridine (Ψ) synthases between young and aged HSCs, and observed that three of them are increased during aging. Functional evaluation assay reveals that enforced PUS10 and PUS7 recapitulate the phenotype aged HSCs. The increase of PUS10 in aged HSCs is due to aging-declined CRL4DCAF1-mediated ubiquitination degradation signaling. Mechanistically, the destructive role of enforced PUS10 on HSCs is not achieved by its Ψ synthases activity, but through miR139, dysfunction of which impairs the reconstitution capacity of HSCs. Consistently, we observed no difference of tRNA pseudouridylation profile between young and aged HSPCs, while enforced PUS10 alters the microRNA profile in HSCs. Targeted dysfunction of Pus10 results in compromises the self-renewal capacity of HSC.
2023-05-13 | GSE213420 | GEO
Project description:Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.
2023-08-07 | GSE230228 | GEO
Project description:Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.
2023-08-07 | GSE222751 | GEO