Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome
Pseudouridine (ψ) is a C-linked uracil modification originally discovered in tRNA. MS analysis and CeU-Seq, a method that permits chemical tagging, pulldown and sequencing of ψ residues, reveal that these modifications are more abundant in the mammalian transcriptome than previously thought. Pseudou...
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| Published in | Nature chemical biology Vol. 11; no. 8; pp. 592 - 597 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.08.2015
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Pseudouridine (ψ) is a C-linked uracil modification originally discovered in tRNA. MS analysis and CeU-Seq, a method that permits chemical tagging, pulldown and sequencing of ψ residues, reveal that these modifications are more abundant in the mammalian transcriptome than previously thought.
Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that Ψ is much more prevalent (Ψ/U ratio ∼0.2–0.6%) in mammalian mRNA than previously believed. We developed N
3
-CMC–enriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 Ψ sites within 1,929 human transcripts, of which four (in ribosomal RNA and
EEF1A1
mRNA) are biochemically verified. We show that hPUS1, a known Ψ synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeU-Seq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of Ψ-mediated epigenetic regulation. |
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| AbstractList | Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that Ψ is much more prevalent (Ψ/U ratio ∼0.2-0.6%) in mammalian mRNA than previously believed. We developed N3-CMC-enriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 Ψ sites within 1,929 human transcripts, of which four (in ribosomal RNA and EEF1A1 mRNA) are biochemically verified. We show that hPUS1, a known Ψ synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeU-Seq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of Ψ-mediated epigenetic regulation.Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that Ψ is much more prevalent (Ψ/U ratio ∼0.2-0.6%) in mammalian mRNA than previously believed. We developed N3-CMC-enriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 Ψ sites within 1,929 human transcripts, of which four (in ribosomal RNA and EEF1A1 mRNA) are biochemically verified. We show that hPUS1, a known Ψ synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeU-Seq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of Ψ-mediated epigenetic regulation. Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that Ψ is much more prevalent (Ψ/U ratio ∼0.2-0.6%) in mammalian mRNA than previously believed. We developed N3-CMC-enriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 Ψ sites within 1,929 human transcripts, of which four (in ribosomal RNA and EEF1A1 mRNA) are biochemically verified. We show that hPUS1, a known Ψ synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeU-Seq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of Ψ-mediated epigenetic regulation. Pseudouridine (ψ) is a C-linked uracil modification originally discovered in tRNA. MS analysis and CeU-Seq, a method that permits chemical tagging, pulldown and sequencing of ψ residues, reveal that these modifications are more abundant in the mammalian transcriptome than previously thought. Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that Ψ is much more prevalent (Ψ/U ratio ∼0.2–0.6%) in mammalian mRNA than previously believed. We developed N 3 -CMC–enriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 Ψ sites within 1,929 human transcripts, of which four (in ribosomal RNA and EEF1A1 mRNA) are biochemically verified. We show that hPUS1, a known Ψ synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeU-Seq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of Ψ-mediated epigenetic regulation. Pseudouridine () is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we performed quantitative MS analysis and show that is much more prevalent (/U ratio ~0.20.6%) in mammalian mRNA than previously believed. We developed N3-CMCenriched pseudouridine sequencing (CeU-Seq), a selective chemical labeling and pulldown method, to identify 2,084 sites within 1,929 human transcripts, of which four (in ribosomal RNA and EEF1A1 mRNA) are biochemically verified. We show that hPUS1, a known synthase, acts on human mRNA; under stress, CeU-Seq demonstrates inducible and stress-specific mRNA pseudouridylation. Applying CeUSeq to the mouse transcriptome revealed conserved and tissue-specific pseudouridylation. Collectively, our approaches allow comprehensive analysis of transcriptome-wide pseudouridylation and provide tools for functional studies of -mediated epigenetic regulation. |
| Author | Sun, Fangfang Li, Xiaoyu Bai, Jinyi Yi, Chengqi Zhu, Ping Ma, Shiqing Song, Jinghui |
| Author_xml | – sequence: 1 givenname: Xiaoyu surname: Li fullname: Li, Xiaoyu organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University – sequence: 2 givenname: Ping surname: Zhu fullname: Zhu, Ping organization: Biodynamic Optical Imaging Center, School of Life Sciences, Peking University – sequence: 3 givenname: Shiqing surname: Ma fullname: Ma, Shiqing organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Academy for Advanced Interdisciplinary Studies, Peking University – sequence: 4 givenname: Jinghui surname: Song fullname: Song, Jinghui organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University – sequence: 5 givenname: Jinyi surname: Bai fullname: Bai, Jinyi organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Academy for Advanced Interdisciplinary Studies, Peking University – sequence: 6 givenname: Fangfang surname: Sun fullname: Sun, Fangfang organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University – sequence: 7 givenname: Chengqi surname: Yi fullname: Yi, Chengqi email: chengqi.yi@pku.edu.cn organization: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Department of Chemical Biology, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26075521$$D View this record in MEDLINE/PubMed |
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| Snippet | Pseudouridine (ψ) is a C-linked uracil modification originally discovered in tRNA. MS analysis and CeU-Seq, a method that permits chemical tagging, pulldown... Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here,... Pseudouridine () is the most abundant post-transcriptional RNA modification, yet little is known about its prevalence, mechanism and function in mRNA. Here, we... |
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| SubjectTerms | 101/58 13/1 13/100 13/109 13/89 38/22 38/23 38/77 38/90 38/91 42/70 45/29 631/1647/296 631/337/1645/2570 631/553 631/92/500 82/80 Analysis Animals Biochemical Engineering Biochemistry Bioorganic Chemistry Cell Biology Chemistry Chemistry/Food Science Epigenesis, Genetic Humans Hydro-Lyases - chemistry Hydro-Lyases - genetics Hydro-Lyases - metabolism Mammals Mice Organ Specificity Peptide Elongation Factor 1 - chemistry Peptide Elongation Factor 1 - genetics Peptide Elongation Factor 1 - metabolism Pseudouridine - chemistry Pseudouridine - genetics Pseudouridine - metabolism Ribonucleic acid RNA RNA Processing, Post-Transcriptional RNA, Messenger - chemistry RNA, Messenger - genetics RNA, Messenger - metabolism RNA, Ribosomal - chemistry RNA, Ribosomal - genetics RNA, Ribosomal - metabolism Staining and Labeling - methods Stress, Physiological Studies Transcriptome |
| Title | Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome |
| URI | https://link.springer.com/article/10.1038/nchembio.1836 https://www.ncbi.nlm.nih.gov/pubmed/26075521 https://www.proquest.com/docview/1766267447 https://www.proquest.com/docview/1698390770 |
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