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Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination

ABSTRACT: Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination

PROVIDER: PRJNA962927 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24348302_1.fastq.gz	Fastqsanger.gz
	SRR24348303_1.fastq.gz	Fastqsanger.gz
	SRR24348304_1.fastq.gz	Fastqsanger.gz
	SRR24348305_1.fastq.gz	Fastqsanger.gz
	SRR24348306_1.fastq.gz	Fastqsanger.gz

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Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination

Project description:Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination

| PRJEB72637 | ENA

Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination

Project description:N6-methyladenosine (m6A) and pseudouridine (Ψ) are the two most abundant modifications in mammalian mRNA, but the coordination of their biological functions remains poorly understood. We develop a machine learning-based nanopore direct RNA sequencing method (NanoSPA) that simultaneously analyzes m6A and Ψ in the human transcriptome. Applying NanoSPA to polysome profiling, we reveal opposing transcriptomic co-occurrence of m6A and Ψ and synergistic, hierarchical effects of m6A and Ψ on the polysome.

2024-01-06 | GSE230936 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

Project description:Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

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Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

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Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [Polysome-Seq]

Project description: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. 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 pseudouridine in tumorigenesis. Our findings unveil a critical function of pseudouridine in directing translational control in stem cells with promisingly broad implications for human disease.

2018-04-09 | GSE101485 | GEO

Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis

Project description:Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis

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Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Kidney]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 kidney tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77819 | biostudies-arrayexpress

Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Liver]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 liver tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77820 | biostudies-arrayexpress

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