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

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

PROVIDER: PRJNA749032 | ENA |

REPOSITORIES: ENA

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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.

2021-11-18 | GSE180654 | GEO

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

2021-11-18 | GSE180655 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Project description:Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

| PRJNA749031 | ENA

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

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

| PRJNA749033 | ENA

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling.

Project description: Not available

| S-EPMC8646010 | biostudies-literature

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-11-18 | GSE180656 | GEO

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.

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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.

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