دورية أكاديمية
أعرض في EDS

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

التفاصيل البيبلوغرافية
العنوان: Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.
المؤلفون: Engel KL; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Lo HG; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Goering R; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Li Y; Department of Chemistry, Hong Kong University., Spitale RC; Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.; Department of Chemistry, University of California Irvine, Irvine, CA, USA., Taliaferro JM; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
المصدر: Nucleic acids research [Nucleic Acids Res] 2022 Feb 28; Vol. 50 (4), pp. e24.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: RNA*/chemistry , Transcriptome*, Active Transport, Cell Nucleus ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Sequence Analysis, RNA
مستخلص: Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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معلومات مُعتمدة: DP2 GM119164 United States GM NIGMS NIH HHS; R35 GM133385 United States GM NIGMS NIH HHS; T32 GM008730 United States GM NIGMS NIH HHS; T32 GM136444 United States GM NIGMS NIH HHS
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20211207 Date Completed: 20220415 Latest Revision: 20221112
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8887463
DOI: 10.1093/nar/gkab1185
PMID: 34875090
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkab1185