CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution.

IF 14.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Nature Communications Pub Date : 2025-07-20 DOI:10.1038/s41467-025-61697-y

Yuanbo Liu,Dean Li,Xueting Wang,Kongyan Niu,Jun Bai,Lefeng Qu,Nan Liu

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引用次数: 0

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.

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CompasSeq：在转录物分辨率下对代谢物上限RNA的全表转录组百分比评估。

含有核苷酸的代谢物，如NAD，可以在转录过程中作为非规范起始核苷酸（NCIN），产生NCIN-capped rna （NCIN- rna）。目前的分析策略仅限于检测特定的代谢物帽，并且缺乏一种全表转录组范围的方法来量化NCIN-和m7g -帽型之间的比例。在这里，我们开发了CompasSeq分析平台，它集成了实验和计算框架，能够在转录本分辨率上对ncin - rna进行全面和定量的评估。CompasSeq利用精心设计的酶促反应来选择性地捕获ncin - rna。通过引入适当的尖刺，CompasSeq可以分析NCIN帽的化学计量学。我们进一步设计了一种正交方法，定量核糖核酸酶还原试验，以验证新鉴定的ncin - rna及其封顶比。使用CompasSeq，我们量化了以前未探索的小鼠肝脏NCIN封顶百分比，并说明了它们与年龄相关的动态。此外，我们发现在影响年龄相关通路的基因中，RNA表达和NCIN封顶之间存在二分法。我们的研究为深入分析ncin - rna提供了实验和计算解决方案，为ncin - rna的功能研究铺平了道路。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature Communications Biological Science Disciplines-

CiteScore

24.90

自引率

2.40%

发文量

6928

审稿时长

3.7 months

期刊介绍： Nature Communications, an open-access journal, publishes high-quality research spanning all areas of the natural sciences. Papers featured in the journal showcase significant advances relevant to specialists in each respective field. With a 2-year impact factor of 16.6 (2022) and a median time of 8 days from submission to the first editorial decision, Nature Communications is committed to rapid dissemination of research findings. As a multidisciplinary journal, it welcomes contributions from biological, health, physical, chemical, Earth, social, mathematical, applied, and engineering sciences, aiming to highlight important breakthroughs within each domain.