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Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape
Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap—a method that uncovers subce...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172111/ https://www.ncbi.nlm.nih.gov/pubmed/37038000 http://dx.doi.org/10.1038/s41592-023-01829-8 |
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author | Ren, Jingyi Zhou, Haowen Zeng, Hu Wang, Connie Kangni Huang, Jiahao Qiu, Xiaojie Sui, Xin Li, Qiang Wu, Xunwei Lin, Zuwan Lo, Jennifer A. Maher, Kamal He, Yichun Tang, Xin Lam, Judson Chen, Hongyu Li, Brian Fisher, David E. Liu, Jia Wang, Xiao |
author_facet | Ren, Jingyi Zhou, Haowen Zeng, Hu Wang, Connie Kangni Huang, Jiahao Qiu, Xiaojie Sui, Xin Li, Qiang Wu, Xunwei Lin, Zuwan Lo, Jennifer A. Maher, Kamal He, Yichun Tang, Xin Lam, Judson Chen, Hongyu Li, Brian Fisher, David E. Liu, Jia Wang, Xiao |
author_sort | Ren, Jingyi |
collection | PubMed |
description | Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap—a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed ‘kinetic gene clusters’ whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles. |
format | Online Article Text |
id | pubmed-10172111 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-101721112023-05-12 Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape Ren, Jingyi Zhou, Haowen Zeng, Hu Wang, Connie Kangni Huang, Jiahao Qiu, Xiaojie Sui, Xin Li, Qiang Wu, Xunwei Lin, Zuwan Lo, Jennifer A. Maher, Kamal He, Yichun Tang, Xin Lam, Judson Chen, Hongyu Li, Brian Fisher, David E. Liu, Jia Wang, Xiao Nat Methods Article Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap—a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed ‘kinetic gene clusters’ whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles. Nature Publishing Group US 2023-04-10 2023 /pmc/articles/PMC10172111/ /pubmed/37038000 http://dx.doi.org/10.1038/s41592-023-01829-8 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, Jingyi Zhou, Haowen Zeng, Hu Wang, Connie Kangni Huang, Jiahao Qiu, Xiaojie Sui, Xin Li, Qiang Wu, Xunwei Lin, Zuwan Lo, Jennifer A. Maher, Kamal He, Yichun Tang, Xin Lam, Judson Chen, Hongyu Li, Brian Fisher, David E. Liu, Jia Wang, Xiao Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title | Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title_full | Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title_fullStr | Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title_full_unstemmed | Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title_short | Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape |
title_sort | spatiotemporally resolved transcriptomics reveals the subcellular rna kinetic landscape |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172111/ https://www.ncbi.nlm.nih.gov/pubmed/37038000 http://dx.doi.org/10.1038/s41592-023-01829-8 |
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