Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution.

IF 15.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Nature Communications Pub Date : 2025-10-06 DOI:10.1038/s41467-025-63918-w

Cheng-Wei Ju,Han Li,Bochen Jiang,Xuanhao Zhu,Liang Cui,Zhanghui Han,Junxi Zou,Yunzheng Liu,Shenghai Shen,Hardik Shah,Chang Ye,Yuhao Zhong,Ruiqi Ge,Peng Xia,Yiyi Ji,Shun Liu,Fan Yang,Bei Liu,Yuzhi Xu,Jiangbo Wei,Li-Sheng Zhang,Chuan He

{"title":"Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution.","authors":"Cheng-Wei Ju,Han Li,Bochen Jiang,Xuanhao Zhu,Liang Cui,Zhanghui Han,Junxi Zou,Yunzheng Liu,Shenghai Shen,Hardik Shah,Chang Ye,Yuhao Zhong,Ruiqi Ge,Peng Xia,Yiyi Ji,Shun Liu,Fan Yang,Bei Liu,Yuzhi Xu,Jiangbo Wei,Li-Sheng Zhang,Chuan He","doi":"10.1038/s41467-025-63918-w","DOIUrl":null,"url":null,"abstract":"Dihydrouridine (D) is an abundant RNA modification, yet its roles in mammals remain poorly understood due to limited detection methods. We even do not have a comprehensive profile of D site location and modification stoichiometry in tRNA. Here, we introduce Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI), a highly sensitive, quantitative approach for mapping D at single-base resolution. Using CRACI, we generate the transcriptome-wide maps of D in both cytoplasmic and mitochondrial tRNAs from mammals and plants. We uncover D sites in mitochondrial tRNAs and identify DUS2L as the 'writer' protein responsible for human mitochondrial tRNAs. Furthermore, we demonstrate that most D modifications have a limited impact on tRNA stability, except for D20a, which also exhibits cis-regulation of adjacent D20 sites. Application of CRACI to human mRNA reveals that D modifications are present but rare and occur at very low stoichiometry. CRACI thus provides a powerful platform for investigating D biology across species.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"81 1","pages":"8863"},"PeriodicalIF":15.7000,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nature Communications","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41467-025-63918-w","RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}

引用次数: 0

Abstract

Dihydrouridine (D) is an abundant RNA modification, yet its roles in mammals remain poorly understood due to limited detection methods. We even do not have a comprehensive profile of D site location and modification stoichiometry in tRNA. Here, we introduce Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI), a highly sensitive, quantitative approach for mapping D at single-base resolution. Using CRACI, we generate the transcriptome-wide maps of D in both cytoplasmic and mitochondrial tRNAs from mammals and plants. We uncover D sites in mitochondrial tRNAs and identify DUS2L as the 'writer' protein responsible for human mitochondrial tRNAs. Furthermore, we demonstrate that most D modifications have a limited impact on tRNA stability, except for D20a, which also exhibits cis-regulation of adjacent D20 sites. Application of CRACI to human mRNA reveals that D modifications are present but rare and occur at very low stoichiometry. CRACI thus provides a powerful platform for investigating D biology across species.

查看原文本刊更多论文

定量CRACI在碱基分辨率上揭示了RNA二氢吡啶的转录组分布。

二氢吡啶(D)是一种丰富的RNA修饰，但由于检测方法有限，对其在哺乳动物中的作用知之甚少。我们甚至没有对tRNA中D位点的位置和修饰化学计量学的全面描述。在这里，我们介绍了化学还原辅助胞嘧啶结合测序（CRACI），这是一种在单碱基分辨率下定位D的高灵敏度定量方法。利用CRACI，我们在哺乳动物和植物的细胞质和线粒体trna中生成了D的转录组图谱。我们发现了线粒体tRNAs中的D位点，并鉴定出DUS2L是负责人类线粒体tRNAs的“作者”蛋白。此外，我们证明了大多数D修饰对tRNA稳定性的影响有限，除了D20a，它也对邻近的D20位点进行顺式调节。CRACI对人mRNA的应用表明，D修饰是存在的，但很少发生，并且发生在非常低的化学计量。因此，CRACI为跨物种研究D生物学提供了一个强大的平台。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

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.