Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.

Autor: Dai Q; Department of Chemistry, The University of Chicago, Chicago, IL, USA. daiqing@uchicago.edu.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. daiqing@uchicago.edu., Zhang LS; Department of Chemistry, The University of Chicago, Chicago, IL, USA. lszhang@uchicago.edu.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. lszhang@uchicago.edu., Sun HL; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Pajdzik K; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Yang L; First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China., Ye C; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Ju CW; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA., Liu S; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Wang Y; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Zheng Z; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Zhang L; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Harada BT; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Dou X; Department of Chemistry, The University of Chicago, Chicago, IL, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA., Irkliyenko I; Department of Chemistry, The University of Chicago, Chicago, IL, USA., Feng X; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.; Department of Human Genetics, The University of Chicago, Chicago, IL, USA., Zhang W; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA., Pan T; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA., He C; Department of Chemistry, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2023 Mar; Vol. 41 (3), pp. 344-354. Date of Electronic Publication: 2022 Oct 27.
DOI: 10.1038/s41587-022-01505-w
Abstrakt: Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different 'writer' proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.
(© 2022. The Author(s).)
Databáze: MEDLINE
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