Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.

IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Nature Methods Pub Date : 2024-10-28 DOI:10.1038/s41592-024-02457-6
Ashley F Tsue, Evan E Kania, Diana Q Lei, Rose Fields, Christopher D McGann, Daphnée M Marciniak, Elliot A Hershberg, Xinxian Deng, Maryanne Kihiu, Shao-En Ong, Christine M Disteche, Sita Kugel, Brian J Beliveau, Devin K Schweppe, David M Shechner
{"title":"Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.","authors":"Ashley F Tsue, Evan E Kania, Diana Q Lei, Rose Fields, Christopher D McGann, Daphnée M Marciniak, Elliot A Hershberg, Xinxian Deng, Maryanne Kihiu, Shao-En Ong, Christine M Disteche, Sita Kugel, Brian J Beliveau, Devin K Schweppe, David M Shechner","doi":"10.1038/s41592-024-02457-6","DOIUrl":null,"url":null,"abstract":"<p><p>RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":null,"pages":null},"PeriodicalIF":36.1000,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nature Methods","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1038/s41592-024-02457-6","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

Abstract

RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
通过寡核苷酸介导的近端-交互组图谱对 RNA 微环境进行多组表征。
RNA 分子形成复杂的分子相互作用网络,对其功能和细胞结构至关重要。但这些相互作用网络很难进行原位探测。在这里,我们介绍了寡核苷酸介导的邻近相互作用组 MAPping(O-MAP),这是一种在 RNA 的原生环境中阐明其附近生物分子的方法。O-MAP 使用类似于 RNA 荧光原位杂交的寡核苷酸探针,在原位向目标 RNA 运送邻近生物素化酶,从而通过链霉亲和素下拉富集附近的分子。这种方法能诱导异常精确的生物素化,易于优化并可移植到新的靶标或样本类型。以非编码 RNA 47S、7SK 和 Xist 为模型,我们开发了 O-MAP 工作流程,用于发现 RNA 近端蛋白、转录本和基因组位点,从而对这些 RNA 的亚细胞区和新的调控相互作用进行多组表征。O-MAP 不需要基因操作,只使用现成的部件,所需的细胞数量比现有方法少很多,因此大多数实验室都能使用。
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 去求助
来源期刊
Nature Methods
Nature Methods 生物-生化研究方法
CiteScore
58.70
自引率
1.70%
发文量
326
审稿时长
1 months
期刊介绍: Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.
期刊最新文献
Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Uncovering cell cycle speed modulations with statistical inference. Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics. Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1