CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution
Abstract Nucleotide-containing metabolites, e.g., NAD, can serve as noncanonical initiating nucleotides (NCIN) during transcription, yielding NCIN-capped RNAs (NCIN-RNAs). Current profiling strategies are limited to detecting specific metabolite caps and lack an epitranscriptome-wide approach for qu...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61697-y |
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| _version_ | 1849234510807302144 |
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| author | Yuanbo Liu Dean Li Xueting Wang Kongyan Niu Jun Bai Lefeng Qu Nan Liu |
| author_facet | Yuanbo Liu Dean Li Xueting Wang Kongyan Niu Jun Bai Lefeng Qu Nan Liu |
| author_sort | Yuanbo Liu |
| collection | DOAJ |
| description | Abstract Nucleotide-containing metabolites, e.g., NAD, can serve as noncanonical initiating nucleotides (NCIN) during transcription, yielding NCIN-capped RNAs (NCIN-RNAs). Current profiling strategies are limited to detecting specific metabolite caps and lack an epitranscriptome-wide approach for quantifying the ratio between NCIN- and m7G-capped forms. Here, we develop the CompasSeq analytical platform, which integrates experimental and computational frameworks, enabling comprehensive and quantitative assessment of NCIN-RNAs at the transcript resolution. CompasSeq utilizes carefully devised enzymatic reactions to selectively capture NCIN-RNAs. By introducing proper spike-ins, CompasSeq can analyze the stoichiometry of NCIN caps. We further design an orthogonal method, the quantitative exoribonuclease reduction assay, to validate newly identified NCIN-RNAs and their capping ratios. Using CompasSeq, we quantify previously unexplored NCIN capping percentages from mouse liver and illustrate their age-associated dynamics. Moreover, we uncover a dichotomy between RNA expression and NCIN capping in genes impinging on age-related pathways. Our study presents both experimental and computational solutions for in-depth analysis of NCIN-RNAs, paving the road for functional investigations into NCIN-RNAs. |
| format | Article |
| id | doaj-art-ff7e0ece7d014f9bbdd3bdbc71357843 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-ff7e0ece7d014f9bbdd3bdbc713578432025-08-20T04:03:07ZengNature PortfolioNature Communications2041-17232025-07-0116111710.1038/s41467-025-61697-yCompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolutionYuanbo Liu0Dean Li1Xueting Wang2Kongyan Niu3Jun Bai4Lefeng Qu5Nan Liu6Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesDepartment of Vascular and Endovascular Surgery, The Second Affiliated Hospital of Naval Medical UniversityDepartment of Vascular and Endovascular Surgery, The Second Affiliated Hospital of Naval Medical UniversityInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesAbstract Nucleotide-containing metabolites, e.g., NAD, can serve as noncanonical initiating nucleotides (NCIN) during transcription, yielding NCIN-capped RNAs (NCIN-RNAs). Current profiling strategies are limited to detecting specific metabolite caps and lack an epitranscriptome-wide approach for quantifying the ratio between NCIN- and m7G-capped forms. Here, we develop the CompasSeq analytical platform, which integrates experimental and computational frameworks, enabling comprehensive and quantitative assessment of NCIN-RNAs at the transcript resolution. CompasSeq utilizes carefully devised enzymatic reactions to selectively capture NCIN-RNAs. By introducing proper spike-ins, CompasSeq can analyze the stoichiometry of NCIN caps. We further design an orthogonal method, the quantitative exoribonuclease reduction assay, to validate newly identified NCIN-RNAs and their capping ratios. Using CompasSeq, we quantify previously unexplored NCIN capping percentages from mouse liver and illustrate their age-associated dynamics. Moreover, we uncover a dichotomy between RNA expression and NCIN capping in genes impinging on age-related pathways. Our study presents both experimental and computational solutions for in-depth analysis of NCIN-RNAs, paving the road for functional investigations into NCIN-RNAs.https://doi.org/10.1038/s41467-025-61697-y |
| spellingShingle | Yuanbo Liu Dean Li Xueting Wang Kongyan Niu Jun Bai Lefeng Qu Nan Liu CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution Nature Communications |
| title | CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution |
| title_full | CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution |
| title_fullStr | CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution |
| title_full_unstemmed | CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution |
| title_short | CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution |
| title_sort | compasseq epitranscriptome wide percentage assessment of metabolite capped rna at the transcript resolution |
| url | https://doi.org/10.1038/s41467-025-61697-y |
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