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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (soybean)

ABSTRACT: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (soybean)

PROVIDER: PRJNA1091613 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28440139.fastq.gz	Fastqsanger.gz
	SRR28440140.fastq.gz	Fastqsanger.gz
	SRR28440141.fastq.gz	Fastqsanger.gz
	SRR28440142.fastq.gz	Fastqsanger.gz
	SRR28440143.fastq.gz	Fastqsanger.gz

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (Arabidopsis)

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (maize)

Project description:Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (maize)

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (soybean)

Project description:Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ has been hindered by the lack of robust methods to profile Ψ and comprehensive Ψ maps. In this study, we utilize BID-seq, a newly developed Ψ sequencing method, to generate transcriptome-wide Ψ maps at single-base resolution across various plant species and tissues

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis total RNA [BID-seq]

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (maize)

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (Arabidopsis)

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Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (rice)

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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.

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The molecular basis of tRNA selectivity by human pseudouridine synthase 3 (PUS3)

Project description: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. Structure-guided and patient-derived mutations validate our structural findings in complementary biochemical assays. Furthermore, we deleted PUS1 and PUS3 in HEK293 cells and used Pseudo-seq to detect Ψ sites in the transcriptome. Although PUS1-dependent sites were detectable in tRNA and mRNA, we did not find any evidence for PUS3 modifying other RNA classes than tRNA. In summary, our work provides the molecular basis for PUS3-mediated tRNA modification in humans and aids in understanding how impairments in its activity lead to intellectual disabilities through defects in tRNA modifications.

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