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Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Herein, we apply a proximi...

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Autores principales: Ren, Ziqi, Tang, Wei, Peng, Luxin, Zou, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651888/
https://www.ncbi.nlm.nih.gov/pubmed/37968266
http://dx.doi.org/10.1038/s41467-023-43194-2
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author Ren, Ziqi
Tang, Wei
Peng, Luxin
Zou, Peng
author_facet Ren, Ziqi
Tang, Wei
Peng, Luxin
Zou, Peng
author_sort Ren, Ziqi
collection PubMed
description Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Herein, we apply a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of SG-proximal transcriptome in live mammalian cells. CAP-seq captures 457 and 822 RNAs in arsenite- and sorbitol-induced SGs in HEK293T cells, respectively, revealing that SG enrichment is positively correlated with RNA length and AU content, but negatively correlated with translation efficiency. The high spatial specificity of CAP-seq dataset is validated by single-molecule FISH imaging. We further apply CAP-seq to map dynamic changes in SG-proximal transcriptome along the time course of granule assembly and disassembly processes. Our data portray a model of AU-rich and translationally repressed SG nanostructure that are memorized long after the removal of stress.
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spelling pubmed-106518882023-11-15 Profiling stress-triggered RNA condensation with photocatalytic proximity labeling Ren, Ziqi Tang, Wei Peng, Luxin Zou, Peng Nat Commun Article Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Herein, we apply a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of SG-proximal transcriptome in live mammalian cells. CAP-seq captures 457 and 822 RNAs in arsenite- and sorbitol-induced SGs in HEK293T cells, respectively, revealing that SG enrichment is positively correlated with RNA length and AU content, but negatively correlated with translation efficiency. The high spatial specificity of CAP-seq dataset is validated by single-molecule FISH imaging. We further apply CAP-seq to map dynamic changes in SG-proximal transcriptome along the time course of granule assembly and disassembly processes. Our data portray a model of AU-rich and translationally repressed SG nanostructure that are memorized long after the removal of stress. Nature Publishing Group UK 2023-11-15 /pmc/articles/PMC10651888/ /pubmed/37968266 http://dx.doi.org/10.1038/s41467-023-43194-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ren, Ziqi
Tang, Wei
Peng, Luxin
Zou, Peng
Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title_full Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title_fullStr Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title_full_unstemmed Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title_short Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
title_sort profiling stress-triggered rna condensation with photocatalytic proximity labeling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651888/
https://www.ncbi.nlm.nih.gov/pubmed/37968266
http://dx.doi.org/10.1038/s41467-023-43194-2
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