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Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [RNA-Seq]

ABSTRACT: Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. The absence of the modification onto the nda2 mRNA strongly impacts meiosis by inducing a metaphase delay or by completely preventing the formation of spindles during meiosis I and meiosis II, eventually resulting in low gamete viability. Collectively these data show that the codon specific reduction of uridine within mRNA is required for proper meiotic chromosome segregation and gamete viability.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE145683 | GEO | 2021/10/26

REPOSITORIES: GEO

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Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [Rho-Seq]

Project description:Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. The absence of the modification onto the nda2 mRNA strongly impacts meiosis by inducing a metaphase delay or by completely preventing the formation of spindles during meiosis I and meiosis II, eventually resulting in low gamete viability. Collectively these data show that the codon specific reduction of uridine within mRNA is required for proper meiotic chromosome segregation and gamete viability.

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Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation [Ribo/RNA-seq]

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RNA-mediated activity-based protein profiling reveals dihydrouridine modification on human mRNA

Project description:Epitranscriptomic RNA modifications can regulate RNA activity, however there remains a major gap in our understanding of the scope of mRNA chemistry present in biological systems. Here, we develop RNA-mediated activity-based protein profiling (RNABPP), a chemoproteomic strategy relying upon metabolic RNA labeling with the mechanism-based inhibitor 5-fluorocytidine, mRNA interactome capture, and quantitative proteomics, to investigate pyrimidine-modifying enzymes in human cells. In addition to profiling 5-methylcytidine (m5C) methyltransferase activity on mRNA, metabolic deamination of 5-fluorocytidine to 5-fluorouridine allowed us to show that 5-methyluridine (m5U) is present on human mRNA and demonstrate that its formation is primarily mediated by the tRNA-modifying enzyme TRMT2A. Further, our approach uncovered DUS3L, the mammalian homolog of the yeast tRNA-dihydrouridine synthase DUS3, as a novel 5-fluoropyrimidine-reactive protein. We investigate the mechanism of protein-RNA crosslinking, which involves the conserved catalytic Cys residue, and use genetic knockdown combined with quantitative LC-MS/MS analysis to establish that DUS3L installs dihydrouridine (DHU) on human mRNA and small RNA. Finally, we find that DUS3L is important for cell proliferation and protein translation. Taken together, our work provides a general approach for profiling RNA modifying enzyme activity in vivo, and reveals the existence of new pathways for the epitranscriptomic regulation of mRNA behavior in human cells.

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Transcriptome-wide mapping of dihydrouridine sites with D-seq

Project description:We report the development of D-Seq, a sequencing based technique for identification of dihydrouridine (D) modifications within RNA. We performed D-Seq on S. cerevisiae and find the first evidence for dihydrouridylation of endogenous mRNAs.

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Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [Rho-Seq]

Project description:Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [Rho-Seq]

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